HEADER PROTEIN FIBRIL 02-MAR-18 6CLF TITLE 1.15 A MICROED STRUCTURE OF GSNQNNF AT 1.9 E- / A^2 COMPND MOL_ID: 1; COMPND 2 MOLECULE: GSNQNNF; COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 SYNTHETIC: YES; SOURCE 3 ORGANISM_SCIENTIFIC: SYNTHETIC CONSTRUCT; SOURCE 4 ORGANISM_TAXID: 32630 KEYWDS AMYLOID FIBRIL, PRION, ZINC BINDING, PROTEIN FIBRIL EXPDTA ELECTRON CRYSTALLOGRAPHY AUTHOR J.HATTNE,D.SHI,C.GLYNN,C.-T.ZEE,M.GALLAGHER-JONES,M.W.MARTYNOWYCZ, AUTHOR 2 J.A.RODRIGUEZ,T.GONEN REVDAT 2 13-MAR-24 6CLF 1 LINK REVDAT 1 16-MAY-18 6CLF 0 JRNL AUTH J.HATTNE,D.SHI,C.GLYNN,C.T.ZEE,M.GALLAGHER-JONES, JRNL AUTH 2 M.W.MARTYNOWYCZ,J.A.RODRIGUEZ,T.GONEN JRNL TITL ANALYSIS OF GLOBAL AND SITE-SPECIFIC RADIATION DAMAGE IN JRNL TITL 2 CRYO-EM. JRNL REF STRUCTURE V. 26 759 2018 JRNL REFN ISSN 1878-4186 JRNL PMID 29706530 JRNL DOI 10.1016/J.STR.2018.03.021 REMARK 2 REMARK 2 RESOLUTION. 1.15 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.8.0194 REMARK 3 AUTHORS : MURSHUDOV,SKUBAK,LEBEDEV,PANNU,STEINER, REMARK 3 : NICHOLLS,WINN,LONG,VAGIN REMARK 3 REMARK 3 REFINEMENT TARGET : NULL REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.15 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 13.98 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 81.3 REMARK 3 NUMBER OF REFLECTIONS : 1208 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 CROSS-VALIDATION METHOD : THROUGHOUT REMARK 3 FREE R VALUE TEST SET SELECTION : RANDOM REMARK 3 R VALUE (WORKING + TEST SET) : 0.268 REMARK 3 R VALUE (WORKING SET) : 0.266 REMARK 3 FREE R VALUE : 0.293 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 9.200 REMARK 3 FREE R VALUE TEST SET COUNT : 122 REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : 20 REMARK 3 BIN RESOLUTION RANGE HIGH (A) : 1.15 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.18 REMARK 3 REFLECTION IN BIN (WORKING SET) : 106 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 84.17 REMARK 3 BIN R VALUE (WORKING SET) : 0.1890 REMARK 3 BIN FREE R VALUE SET COUNT : 11 REMARK 3 BIN FREE R VALUE : 0.3280 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 55 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 5 REMARK 3 SOLVENT ATOMS : 3 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 5.61 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -1.01000 REMARK 3 B22 (A**2) : -0.16000 REMARK 3 B33 (A**2) : 1.07000 REMARK 3 B12 (A**2) : -0.04000 REMARK 3 B13 (A**2) : -0.15000 REMARK 3 B23 (A**2) : -0.32000 REMARK 3 REMARK 3 ESTIMATED OVERALL COORDINATE ERROR. REMARK 3 ESU BASED ON R VALUE (A): 0.087 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.085 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.057 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 1.123 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.917 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.881 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 58 ; 0.023 ; 0.020 REMARK 3 BOND LENGTHS OTHERS (A): 39 ; 0.043 ; 0.020 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 76 ; 2.160 ; 1.886 REMARK 3 BOND ANGLES OTHERS (DEGREES): 92 ; 1.092 ; 3.000 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 6 ; 6.323 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 5 ;58.295 ;28.000 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 7 ;12.015 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): NULL ; NULL ; NULL REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 6 ; 0.124 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 73 ; 0.008 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): 11 ; 0.001 ; 0.020 REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED CONTACTS OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION OTHERS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) OTHERS (A): NULL ; NULL ; NULL REMARK 3 POTENTIAL METAL-ION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 POTENTIAL METAL-ION OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY VDW REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY VDW OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY METAL-ION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY METAL-ION OTHERS (A): NULL ; NULL ; NULL REMARK 3 REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. COUNT RMS WEIGHT REMARK 3 MAIN-CHAIN BOND REFINED ATOMS (A**2): 28 ; 0.406 ; 0.568 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): 26 ; 0.400 ; 0.539 REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 30 ; 0.713 ; 0.815 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): 31 ; 0.704 ; 0.815 REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 30 ; 0.306 ; 0.565 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): 31 ; 0.302 ; 0.589 REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE OTHER ATOMS (A**2): 43 ; 0.496 ; 0.854 REMARK 3 LONG RANGE B REFINED ATOMS (A**2): 42 ; 1.001 ; 5.529 REMARK 3 LONG RANGE B OTHER ATOMS (A**2): 43 ; 0.991 ; 5.566 REMARK 3 REMARK 3 ANISOTROPIC THERMAL FACTOR RESTRAINTS. COUNT RMS WEIGHT REMARK 3 RIGID-BOND RESTRAINTS (A**2): NULL ; NULL ; NULL REMARK 3 SPHERICITY; FREE ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SPHERICITY; BONDED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 REMARK 3 NCS RESTRAINTS STATISTICS REMARK 3 NUMBER OF DIFFERENT NCS GROUPS : NULL REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : NULL REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : NULL REMARK 3 PARAMETERS FOR MASK CALCULATION REMARK 3 VDW PROBE RADIUS : 1.20 REMARK 3 ION PROBE RADIUS : 0.80 REMARK 3 SHRINKAGE RADIUS : 0.80 REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: HYDROGENS HAVE BEEN ADDED IN THE RIDING REMARK 3 POSITIONS REMARK 4 REMARK 4 6CLF COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 02-MAR-18. REMARK 100 THE DEPOSITION ID IS D_1000232866. REMARK 240 REMARK 240 EXPERIMENTAL DETAILS REMARK 240 RECONSTRUCTION METHOD : CRYSTALLOGRAPHY REMARK 240 SAMPLE TYPE : 3D ARRAY REMARK 240 SPECIMEN TYPE : NULL REMARK 240 DATA ACQUISITION REMARK 240 DATE OF DATA COLLECTION : 29-JUL-17 REMARK 240 TEMPERATURE (KELVIN) : NULL REMARK 240 PH : NULL REMARK 240 NUMBER OF CRYSTALS USED : NULL REMARK 240 MICROSCOPE MODEL : FEI TECNAI F20 REMARK 240 DETECTOR TYPE : TVIPS TEMCAM-F416 (4K X 4K) REMARK 240 ACCELERATION VOLTAGE (KV) : 200 REMARK 240 NUMBER OF UNIQUE REFLECTIONS : NULL REMARK 240 RESOLUTION RANGE HIGH (A) : NULL REMARK 240 RESOLUTION RANGE LOW (A) : NULL REMARK 240 DATA SCALING SOFTWARE : XSCALE REMARK 240 COMPLETENESS FOR RANGE (%) : NULL REMARK 240 DATA REDUNDANCY : NULL REMARK 240 IN THE HIGHEST RESOLUTION SHELL REMARK 240 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) :NULL REMARK 240 HIGHEST RESOLUTION SHELL, RANGE LOW (A) :NULL REMARK 240 COMPLETENESS FOR SHELL (%) : NULL REMARK 240 DATA REDUNDANCY IN SHELL : NULL REMARK 240 R MERGE FOR SHELL (I) : NULL REMARK 240 METHOD USED TO DETERMINE THE STRUCTURE: NULL REMARK 240 SOFTWARE USED : NULL REMARK 240 STARTING MODEL : NULL REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 REMARK 290 WHERE NNN -> OPERATOR NUMBER REMARK 290 MMM -> TRANSLATION VECTOR REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY TRANSFORMATIONS REMARK 290 THE FOLLOWING TRANSFORMATIONS OPERATE ON THE ATOM/HETATM REMARK 290 RECORDS IN THIS ENTRY TO PRODUCE CRYSTALLOGRAPHICALLY REMARK 290 RELATED MOLECULES. REMARK 290 SMTRY1 1 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 1 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 1 0.000000 0.000000 1.000000 0.00000 REMARK 290 REMARK 290 REMARK: NULL REMARK 300 REMARK 300 BIOMOLECULE: 1 REMARK 300 SEE REMARK 350 FOR THE AUTHOR PROVIDED AND/OR PROGRAM REMARK 300 GENERATED ASSEMBLY INFORMATION FOR THE STRUCTURE IN REMARK 300 THIS ENTRY. THE REMARK MAY ALSO PROVIDE INFORMATION ON REMARK 300 BURIED SURFACE AREA. REMARK 350 REMARK 350 COORDINATES FOR A COMPLETE MULTIMER REPRESENTING THE KNOWN REMARK 350 BIOLOGICALLY SIGNIFICANT OLIGOMERIZATION STATE OF THE REMARK 350 MOLECULE CAN BE GENERATED BY APPLYING BIOMT TRANSFORMATIONS REMARK 350 GIVEN BELOW. BOTH NON-CRYSTALLOGRAPHIC AND REMARK 350 CRYSTALLOGRAPHIC OPERATIONS ARE GIVEN. REMARK 350 REMARK 350 BIOMOLECULE: 1 REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: MONOMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 APPLY THE FOLLOWING TO CHAINS: A REMARK 350 BIOMT1 1 1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 1 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT3 1 0.000000 0.000000 1.000000 0.00000 REMARK 620 REMARK 620 METAL COORDINATION REMARK 620 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 620 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE): REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN A 102 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 GLY A 1 N REMARK 620 2 GLY A 1 O 79.5 REMARK 620 3 PHE A 7 O 114.9 42.0 REMARK 620 4 PHE A 7 OXT 116.8 46.6 5.5 REMARK 620 5 ACT A 101 O 146.6 93.0 75.9 77.1 REMARK 620 6 ACT A 101 OXT 147.4 97.2 79.1 80.1 4.1 REMARK 620 N 1 2 3 4 5 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue ACT A 101 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue ZN A 102 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: EMD-7498 RELATED DB: EMDB REMARK 900 1.15 A MICROED STRUCTURE OF GSNQNNF AT 1.9 E- / A^2 DBREF 6CLF A 1 7 PDB 6CLF 6CLF 1 7 SEQRES 1 A 7 GLY SER ASN GLN ASN ASN PHE HET ACT A 101 4 HET ZN A 102 1 HETNAM ACT ACETATE ION HETNAM ZN ZINC ION FORMUL 2 ACT C2 H3 O2 1- FORMUL 3 ZN ZN 2+ FORMUL 4 HOH *3(H2 O) LINK N GLY A 1 ZN ZN A 102 1555 1555 2.37 LINK O GLY A 1 ZN ZN A 102 1555 1555 1.92 LINK O PHE A 7 ZN ZN A 102 1555 1644 2.67 LINK OXT PHE A 7 ZN ZN A 102 1555 1644 1.92 LINK O ACT A 101 ZN ZN A 102 1555 1555 2.12 LINK OXT ACT A 101 ZN ZN A 102 1555 1455 2.04 SITE 1 AC1 3 GLY A 1 ASN A 3 ZN A 102 SITE 1 AC2 2 GLY A 1 ACT A 101 CRYST1 4.840 14.140 17.710 85.02 85.93 82.70 P 1 1 ORIGX1 1.000000 0.000000 0.000000 0.00000 ORIGX2 0.000000 1.000000 0.000000 0.00000 ORIGX3 0.000000 0.000000 1.000000 0.00000 SCALE1 0.206612 -0.026453 -0.012656 0.00000 SCALE2 0.000000 0.071299 -0.005625 0.00000 SCALE3 0.000000 0.000000 0.056784 0.00000 ATOM 1 N GLY A 1 3.540 30.358 19.908 1.00 8.41 N ATOM 2 CA GLY A 1 3.910 30.280 18.458 1.00 8.40 C ATOM 3 C GLY A 1 2.949 29.373 17.699 1.00 7.80 C ATOM 4 O GLY A 1 2.332 28.476 18.292 1.00 8.73 O ATOM 5 N SER A 2 2.824 29.610 16.391 1.00 7.26 N ATOM 6 CA SER A 2 2.042 28.733 15.455 1.00 6.70 C ATOM 7 C SER A 2 2.758 27.452 14.847 1.00 6.40 C ATOM 8 O SER A 2 3.981 27.412 14.629 1.00 6.31 O ATOM 9 CB SER A 2 1.473 29.599 14.313 1.00 6.40 C ATOM 10 OG SER A 2 0.544 30.571 14.769 1.00 6.73 O ATOM 11 N ASN A 3 1.976 26.398 14.522 1.00 5.62 N ATOM 12 CA ASN A 3 2.560 25.085 14.161 1.00 5.63 C ATOM 13 C ASN A 3 1.970 24.458 12.858 1.00 4.96 C ATOM 14 O ASN A 3 0.780 24.451 12.716 1.00 4.68 O ATOM 15 CB ASN A 3 2.289 24.121 15.327 1.00 6.36 C ATOM 16 CG ASN A 3 2.914 24.585 16.652 1.00 6.77 C ATOM 17 OD1 ASN A 3 2.294 25.172 17.522 1.00 6.31 O ATOM 18 ND2 ASN A 3 4.149 24.248 16.811 1.00 7.58 N ATOM 19 N GLN A 4 2.770 23.904 11.924 1.00 4.32 N ATOM 20 CA GLN A 4 2.283 23.250 10.714 1.00 3.90 C ATOM 21 C GLN A 4 3.017 21.918 10.432 1.00 3.85 C ATOM 22 O GLN A 4 4.271 21.949 10.425 1.00 3.75 O ATOM 23 CB GLN A 4 2.438 24.192 9.503 1.00 3.89 C ATOM 24 CG GLN A 4 1.651 23.809 8.246 1.00 3.84 C ATOM 25 CD GLN A 4 2.240 24.446 6.967 1.00 3.94 C ATOM 26 OE1 GLN A 4 3.448 24.297 6.645 1.00 4.22 O ATOM 27 NE2 GLN A 4 1.381 25.139 6.207 1.00 3.98 N ATOM 28 N ASN A 5 2.244 20.791 10.243 1.00 4.10 N ATOM 29 CA ASN A 5 2.766 19.442 9.975 1.00 4.27 C ATOM 30 C ASN A 5 2.329 19.137 8.546 1.00 4.40 C ATOM 31 O ASN A 5 1.138 19.084 8.253 1.00 4.09 O ATOM 32 CB ASN A 5 2.155 18.395 10.903 1.00 4.67 C ATOM 33 CG ASN A 5 2.627 18.452 12.361 1.00 4.78 C ATOM 34 OD1 ASN A 5 3.806 18.219 12.670 1.00 5.09 O ATOM 35 ND2 ASN A 5 1.687 18.646 13.292 1.00 5.09 N ATOM 36 N ASN A 6 3.302 18.963 7.660 1.00 4.42 N ATOM 37 CA ASN A 6 3.061 18.477 6.294 1.00 4.55 C ATOM 38 C ASN A 6 3.540 16.984 6.144 1.00 4.69 C ATOM 39 O ASN A 6 4.684 16.720 5.853 1.00 4.49 O ATOM 40 CB ASN A 6 3.730 19.461 5.274 1.00 4.38 C ATOM 41 CG ASN A 6 3.381 20.943 5.551 1.00 4.32 C ATOM 42 OD1 ASN A 6 2.219 21.369 5.578 1.00 4.53 O ATOM 43 ND2 ASN A 6 4.425 21.722 5.776 1.00 4.11 N ATOM 44 N PHE A 7 2.633 16.028 6.356 1.00 4.85 N ATOM 45 CA PHE A 7 2.954 14.613 6.221 1.00 5.28 C ATOM 46 C PHE A 7 3.092 14.245 4.720 1.00 5.57 C ATOM 47 O PHE A 7 2.633 14.920 3.748 1.00 6.17 O ATOM 48 CB PHE A 7 1.895 13.738 6.917 1.00 5.36 C ATOM 49 CG PHE A 7 1.836 13.899 8.377 1.00 5.35 C ATOM 50 CD1 PHE A 7 2.658 13.135 9.130 1.00 5.12 C ATOM 51 CD2 PHE A 7 1.035 14.864 9.000 1.00 5.27 C ATOM 52 CE1 PHE A 7 2.694 13.269 10.491 1.00 5.16 C ATOM 53 CE2 PHE A 7 1.022 14.956 10.401 1.00 5.43 C ATOM 54 CZ PHE A 7 1.905 14.168 11.148 1.00 5.27 C ATOM 55 OXT PHE A 7 3.749 13.226 4.470 1.00 5.78 O TER 56 PHE A 7 HETATM 57 C ACT A 101 -0.372 26.519 20.428 1.00 12.81 C HETATM 58 O ACT A 101 0.338 27.507 20.211 1.00 12.70 O HETATM 59 OXT ACT A 101 -1.614 26.613 20.525 1.00 13.14 O HETATM 60 CH3 ACT A 101 0.276 25.174 20.586 1.00 13.21 C HETATM 61 ZN ZN A 102 2.268 28.385 20.205 1.00 8.18 ZN HETATM 62 O HOH A 201 4.283 32.691 20.870 1.00 12.07 O HETATM 63 O HOH A 202 4.512 21.868 18.264 1.00 9.04 O HETATM 64 O HOH A 203 1.218 20.147 2.285 1.00 10.03 O CONECT 1 61 CONECT 4 61 CONECT 57 58 59 60 CONECT 58 57 61 CONECT 59 57 CONECT 60 57 CONECT 61 1 4 58 MASTER 224 0 2 0 0 0 2 6 63 1 7 1 END