HEADER PROTEIN FIBRIL 02-MAR-18 6CLG TITLE 1.35 A MICROED STRUCTURE OF GSNQNNF AT 2.4 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 6CLG 1 LINK REVDAT 1 16-MAY-18 6CLG 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. 1.35 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) : 1.35 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 13.75 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 77.2 REMARK 3 NUMBER OF REFLECTIONS : 712 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) : 0.224 REMARK 3 R VALUE (WORKING SET) : 0.219 REMARK 3 FREE R VALUE : 0.269 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 9.200 REMARK 3 FREE R VALUE TEST SET COUNT : 72 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) : 1.35 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.39 REMARK 3 REFLECTION IN BIN (WORKING SET) : 58 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 73.26 REMARK 3 BIN R VALUE (WORKING SET) : 0.3310 REMARK 3 BIN FREE R VALUE SET COUNT : 5 REMARK 3 BIN FREE R VALUE : 0.3860 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) : 5.48 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -1.27000 REMARK 3 B22 (A**2) : -0.33000 REMARK 3 B33 (A**2) : 1.50000 REMARK 3 B12 (A**2) : 0.03000 REMARK 3 B13 (A**2) : -0.29000 REMARK 3 B23 (A**2) : -0.59000 REMARK 3 REMARK 3 ESTIMATED OVERALL COORDINATE ERROR. REMARK 3 ESU BASED ON R VALUE (A): 0.124 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.121 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.081 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 2.163 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.924 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.892 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 58 ; 0.019 ; 0.020 REMARK 3 BOND LENGTHS OTHERS (A): 39 ; 0.000 ; 0.020 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 76 ; 1.317 ; 1.886 REMARK 3 BOND ANGLES OTHERS (DEGREES): 92 ; 0.912 ; 3.000 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 6 ; 4.869 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 5 ;55.058 ;28.000 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 7 ; 9.309 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): NULL ; NULL ; NULL REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 6 ; 0.064 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 73 ; 0.009 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): 11 ; 0.000 ; 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 ; 0.292 ; 0.522 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): 26 ; 0.280 ; 0.457 REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 32 ; 0.536 ; 0.679 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): 33 ; 0.530 ; 0.676 REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 30 ; 0.375 ; 0.524 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): 31 ; 0.372 ; 0.583 REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE OTHER ATOMS (A**2): 44 ; 0.334 ; 0.865 REMARK 3 LONG RANGE B REFINED ATOMS (A**2): 47 ; 1.636 ; 4.676 REMARK 3 LONG RANGE B OTHER ATOMS (A**2): 48 ; 1.619 ; 5.284 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 6CLG 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_1000232859. 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 : 01-AUG-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 74.4 REMARK 620 3 PHE A 7 OXT 118.4 53.2 REMARK 620 4 ACT A 101 OXT 140.1 97.5 82.3 REMARK 620 5 ACT A 101 O 141.4 92.1 76.4 6.3 REMARK 620 6 ACT A 101 OXT 140.1 97.5 82.3 0.0 6.3 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-7499 RELATED DB: EMDB REMARK 900 1.35 A MICROED STRUCTURE OF GSNQNNF AT 2.4 E- / A^2 DBREF 6CLG A 1 7 PDB 6CLG 6CLG 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 2.51 LINK O GLY A 1 ZN ZN A 102 1555 1555 1.92 LINK OXT PHE A 7 ZN ZN A 102 1555 1644 1.93 LINK OXT ACT A 101 ZN ZN A 102 1555 1555 2.49 LINK O ACT A 101 ZN ZN A 102 1555 1455 1.76 LINK OXT ACT A 101 ZN ZN A 102 1555 1455 2.64 SITE 1 AC1 2 GLY A 1 ZN A 102 SITE 1 AC2 2 GLY A 1 ACT A 101 CRYST1 4.850 13.930 17.720 86.30 84.50 81.12 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 0.206186 -0.032199 -0.018248 0.00000 SCALE2 0.000000 0.072658 -0.003680 0.00000 SCALE3 0.000000 0.000000 0.056767 0.00000 ATOM 1 N GLY A 1 4.809 29.181 19.854 1.00 7.32 N ATOM 2 CA GLY A 1 5.110 29.181 18.383 1.00 7.14 C ATOM 3 C GLY A 1 4.124 28.314 17.625 1.00 7.15 C ATOM 4 O GLY A 1 3.521 27.416 18.227 1.00 7.62 O ATOM 5 N SER A 2 3.985 28.526 16.309 1.00 6.56 N ATOM 6 CA SER A 2 3.070 27.696 15.453 1.00 5.94 C ATOM 7 C SER A 2 3.783 26.478 14.879 1.00 5.42 C ATOM 8 O SER A 2 5.009 26.486 14.727 1.00 5.53 O ATOM 9 CB SER A 2 2.451 28.561 14.330 1.00 5.96 C ATOM 10 OG SER A 2 1.639 29.554 14.894 1.00 6.02 O ATOM 11 N ASN A 3 3.039 25.416 14.591 1.00 4.81 N ATOM 12 CA ASN A 3 3.642 24.202 14.120 1.00 4.48 C ATOM 13 C ASN A 3 2.994 23.748 12.850 1.00 4.17 C ATOM 14 O ASN A 3 1.801 23.904 12.690 1.00 4.26 O ATOM 15 CB ASN A 3 3.477 23.119 15.124 1.00 4.54 C ATOM 16 CG ASN A 3 4.008 23.480 16.467 1.00 4.67 C ATOM 17 OD1 ASN A 3 3.343 24.162 17.234 1.00 4.70 O ATOM 18 ND2 ASN A 3 5.197 23.012 16.779 1.00 4.73 N ATOM 19 N GLN A 4 3.752 23.169 11.935 1.00 3.95 N ATOM 20 CA GLN A 4 3.181 22.570 10.757 1.00 3.80 C ATOM 21 C GLN A 4 3.868 21.234 10.454 1.00 3.72 C ATOM 22 O GLN A 4 5.092 21.148 10.387 1.00 3.54 O ATOM 23 CB GLN A 4 3.222 23.499 9.561 1.00 3.84 C ATOM 24 CG GLN A 4 2.518 23.030 8.302 1.00 3.92 C ATOM 25 CD GLN A 4 2.979 23.750 7.051 1.00 4.03 C ATOM 26 OE1 GLN A 4 4.165 23.678 6.686 1.00 4.12 O ATOM 27 NE2 GLN A 4 2.086 24.475 6.410 1.00 3.94 N ATOM 28 N ASN A 5 3.049 20.204 10.319 1.00 3.67 N ATOM 29 CA ASN A 5 3.513 18.855 9.927 1.00 3.62 C ATOM 30 C ASN A 5 3.099 18.627 8.530 1.00 3.54 C ATOM 31 O ASN A 5 1.927 18.759 8.173 1.00 3.63 O ATOM 32 CB ASN A 5 2.933 17.792 10.844 1.00 3.68 C ATOM 33 CG ASN A 5 3.518 17.852 12.235 1.00 3.80 C ATOM 34 OD1 ASN A 5 4.748 17.886 12.395 1.00 4.13 O ATOM 35 ND2 ASN A 5 2.667 17.950 13.241 1.00 3.93 N ATOM 36 N ASN A 6 4.058 18.379 7.686 1.00 3.44 N ATOM 37 CA ASN A 6 3.770 17.993 6.337 1.00 3.39 C ATOM 38 C ASN A 6 4.157 16.544 6.185 1.00 3.44 C ATOM 39 O ASN A 6 5.282 16.222 5.935 1.00 3.57 O ATOM 40 CB ASN A 6 4.524 18.919 5.371 1.00 3.34 C ATOM 41 CG ASN A 6 4.140 20.411 5.547 1.00 3.31 C ATOM 42 OD1 ASN A 6 2.958 20.767 5.746 1.00 3.25 O ATOM 43 ND2 ASN A 6 5.153 21.268 5.510 1.00 3.22 N ATOM 44 N PHE A 7 3.230 15.656 6.416 1.00 3.60 N ATOM 45 CA PHE A 7 3.551 14.228 6.272 1.00 3.68 C ATOM 46 C PHE A 7 3.610 13.851 4.785 1.00 3.95 C ATOM 47 O PHE A 7 2.941 14.471 3.954 1.00 4.30 O ATOM 48 CB PHE A 7 2.511 13.404 6.933 1.00 3.57 C ATOM 49 CG PHE A 7 2.467 13.534 8.426 1.00 3.49 C ATOM 50 CD1 PHE A 7 3.256 12.753 9.226 1.00 3.38 C ATOM 51 CD2 PHE A 7 1.568 14.413 9.031 1.00 3.45 C ATOM 52 CE1 PHE A 7 3.159 12.831 10.607 1.00 3.31 C ATOM 53 CE2 PHE A 7 1.465 14.476 10.417 1.00 3.38 C ATOM 54 CZ PHE A 7 2.260 13.683 11.190 1.00 3.46 C ATOM 55 OXT PHE A 7 4.242 12.903 4.328 1.00 4.15 O TER 56 PHE A 7 HETATM 57 C ACT A 101 0.384 25.295 20.407 1.00 22.83 C HETATM 58 O ACT A 101 -0.772 25.377 19.949 1.00 24.59 O HETATM 59 OXT ACT A 101 1.177 26.230 20.282 1.00 23.23 O HETATM 60 CH3 ACT A 101 0.829 24.034 21.089 1.00 23.72 C HETATM 61 ZN ZN A 102 3.522 27.037 20.111 1.00 11.39 ZN HETATM 62 O HOH A 201 2.907 16.425 2.379 1.00 13.26 O HETATM 63 O HOH A 202 5.651 21.256 18.607 1.00 4.97 O HETATM 64 O HOH A 203 1.965 20.256 2.474 1.00 15.56 O CONECT 1 61 CONECT 4 61 CONECT 57 58 59 60 CONECT 58 57 CONECT 59 57 61 CONECT 60 57 CONECT 61 1 4 59 MASTER 224 0 2 0 0 0 2 6 63 1 7 1 END