HEADER PROTEIN FIBRIL 02-MAR-18 6CLR TITLE 1.31 A MICROED STRUCTURE OF GSNQNNF AT 3.1 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 6CLR 1 REMARK REVDAT 1 16-MAY-18 6CLR 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. 1.31 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) : 1.31 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 13.77 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 79.5 REMARK 3 NUMBER OF REFLECTIONS : 815 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) : 0.245 REMARK 3 R VALUE (WORKING SET) : 0.241 REMARK 3 FREE R VALUE : 0.288 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 8.700 REMARK 3 FREE R VALUE TEST SET COUNT : 78 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) : 1.31 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.34 REMARK 3 REFLECTION IN BIN (WORKING SET) : 64 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 84.81 REMARK 3 BIN R VALUE (WORKING SET) : 0.4180 REMARK 3 BIN FREE R VALUE SET COUNT : 3 REMARK 3 BIN FREE R VALUE : 0.5640 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) : 7.58 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -1.41000 REMARK 3 B22 (A**2) : -0.30000 REMARK 3 B33 (A**2) : 1.56000 REMARK 3 B12 (A**2) : -0.14000 REMARK 3 B13 (A**2) : -0.17000 REMARK 3 B23 (A**2) : -0.89000 REMARK 3 REMARK 3 ESTIMATED OVERALL COORDINATE ERROR. REMARK 3 ESU BASED ON R VALUE (A): 0.117 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.117 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.112 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 3.025 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.936 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.889 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 58 ; 0.016 ; 0.020 REMARK 3 BOND LENGTHS OTHERS (A): 39 ; 0.045 ; 0.020 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 76 ; 1.655 ; 1.886 REMARK 3 BOND ANGLES OTHERS (DEGREES): 92 ; 0.975 ; 3.000 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 6 ; 5.608 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 5 ;54.015 ;28.000 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 7 ; 8.731 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): NULL ; NULL ; NULL REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 6 ; 0.054 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 73 ; 0.006 ; 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 ; 0.657 ; 0.712 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): 26 ; 0.406 ; 0.623 REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 31 ; 0.904 ; 0.945 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): 32 ; 0.911 ; 0.950 REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 30 ; 0.641 ; 0.745 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): 31 ; 0.631 ; 0.817 REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE OTHER ATOMS (A**2): 44 ; 0.953 ; 1.206 REMARK 3 LONG RANGE B REFINED ATOMS (A**2): 50 ; 2.821 ; 7.107 REMARK 3 LONG RANGE B OTHER ATOMS (A**2): 51 ; 2.815 ; 7.764 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 6CLR 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_1000232832. 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 TOTAL BURIED SURFACE AREA: 100 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 1200 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -14.0 KCAL/MOL 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 77.1 REMARK 620 3 PHE A 7 OXT 118.1 50.9 REMARK 620 4 ACT A 101 O 145.4 89.8 73.2 REMARK 620 5 ACT A 101 OXT 138.4 116.5 97.8 28.3 REMARK 620 N 1 2 3 4 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 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-7510 RELATED DB: EMDB REMARK 900 1.31 A MICROED STRUCTURE OF GSNQNNF AT 3.1 E- / A^2 DBREF 6CLR A 1 7 PDB 6CLR 6CLR 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 2.41 LINK O GLY A 1 ZN ZN A 102 1555 1555 1.94 LINK OXT PHE A 7 ZN ZN A 102 1555 1644 2.29 LINK O ACT A 101 ZN ZN A 102 1555 1455 1.95 LINK OXT ACT A 101 ZN ZN A 102 1555 1455 2.46 SITE 1 AC1 1 GLY A 1 CRYST1 4.880 13.920 17.980 86.97 84.73 81.83 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 0.204918 -0.029420 -0.017729 0.00000 SCALE2 0.000000 0.072576 -0.002929 0.00000 SCALE3 0.000000 0.000000 0.055899 0.00000 ATOM 1 N GLY A 1 4.447 28.947 20.092 1.00 8.92 N ATOM 2 CA GLY A 1 4.597 29.089 18.615 1.00 8.66 C ATOM 3 C GLY A 1 3.694 28.182 17.838 1.00 8.60 C ATOM 4 O GLY A 1 3.125 27.246 18.410 1.00 9.11 O ATOM 5 N SER A 2 3.569 28.421 16.540 1.00 8.43 N ATOM 6 CA SER A 2 2.665 27.643 15.696 1.00 8.12 C ATOM 7 C SER A 2 3.387 26.452 15.105 1.00 7.51 C ATOM 8 O SER A 2 4.630 26.468 14.989 1.00 7.51 O ATOM 9 CB SER A 2 2.036 28.505 14.629 1.00 8.56 C ATOM 10 OG SER A 2 1.151 29.460 15.195 1.00 8.90 O ATOM 11 N ASN A 3 2.644 25.406 14.759 1.00 6.83 N ATOM 12 CA ASN A 3 3.240 24.136 14.361 1.00 6.30 C ATOM 13 C ASN A 3 2.588 23.666 13.051 1.00 5.43 C ATOM 14 O ASN A 3 1.430 23.842 12.880 1.00 5.38 O ATOM 15 CB ASN A 3 3.071 23.054 15.424 1.00 6.92 C ATOM 16 CG ASN A 3 3.629 23.413 16.790 1.00 7.49 C ATOM 17 OD1 ASN A 3 3.034 24.177 17.561 1.00 8.24 O ATOM 18 ND2 ASN A 3 4.771 22.839 17.117 1.00 8.12 N ATOM 19 N GLN A 4 3.343 23.122 12.111 1.00 4.97 N ATOM 20 CA GLN A 4 2.802 22.523 10.903 1.00 4.70 C ATOM 21 C GLN A 4 3.547 21.190 10.695 1.00 4.58 C ATOM 22 O GLN A 4 4.797 21.102 10.769 1.00 3.79 O ATOM 23 CB GLN A 4 2.912 23.395 9.678 1.00 4.66 C ATOM 24 CG GLN A 4 2.388 22.872 8.345 1.00 4.78 C ATOM 25 CD GLN A 4 2.789 23.733 7.137 1.00 4.92 C ATOM 26 OE1 GLN A 4 3.946 23.794 6.793 1.00 5.10 O ATOM 27 NE2 GLN A 4 1.827 24.405 6.503 1.00 4.82 N ATOM 28 N ASN A 5 2.740 20.167 10.430 1.00 4.72 N ATOM 29 CA ASN A 5 3.224 18.825 10.067 1.00 4.79 C ATOM 30 C ASN A 5 2.860 18.547 8.652 1.00 4.78 C ATOM 31 O ASN A 5 1.707 18.566 8.294 1.00 4.89 O ATOM 32 CB ASN A 5 2.621 17.728 10.922 1.00 4.99 C ATOM 33 CG ASN A 5 3.217 17.647 12.289 1.00 5.31 C ATOM 34 OD1 ASN A 5 4.437 17.613 12.449 1.00 6.27 O ATOM 35 ND2 ASN A 5 2.381 17.542 13.277 1.00 5.94 N ATOM 36 N ASN A 6 3.836 18.299 7.835 1.00 4.97 N ATOM 37 CA ASN A 6 3.576 17.940 6.457 1.00 5.28 C ATOM 38 C ASN A 6 3.957 16.474 6.324 1.00 5.73 C ATOM 39 O ASN A 6 5.075 16.131 6.000 1.00 5.69 O ATOM 40 CB ASN A 6 4.351 18.847 5.489 1.00 5.23 C ATOM 41 CG ASN A 6 3.934 20.319 5.588 1.00 5.11 C ATOM 42 OD1 ASN A 6 2.751 20.660 5.602 1.00 4.73 O ATOM 43 ND2 ASN A 6 4.923 21.176 5.620 1.00 5.12 N ATOM 44 N PHE A 7 3.022 15.614 6.630 1.00 6.46 N ATOM 45 CA PHE A 7 3.276 14.204 6.482 1.00 6.82 C ATOM 46 C PHE A 7 3.319 13.901 4.990 1.00 7.96 C ATOM 47 O PHE A 7 3.078 14.790 4.174 1.00 9.40 O ATOM 48 CB PHE A 7 2.204 13.403 7.156 1.00 6.42 C ATOM 49 CG PHE A 7 2.216 13.498 8.647 1.00 5.82 C ATOM 50 CD1 PHE A 7 3.032 12.667 9.388 1.00 5.36 C ATOM 51 CD2 PHE A 7 1.338 14.366 9.307 1.00 5.49 C ATOM 52 CE1 PHE A 7 3.036 12.725 10.765 1.00 5.21 C ATOM 53 CE2 PHE A 7 1.342 14.443 10.704 1.00 5.25 C ATOM 54 CZ PHE A 7 2.207 13.612 11.411 1.00 5.49 C ATOM 55 OXT PHE A 7 3.574 12.746 4.560 1.00 8.99 O TER 56 PHE A 7 HETATM 57 C ACT A 101 -0.320 25.003 21.006 1.00 29.15 C HETATM 58 O ACT A 101 -1.120 25.127 20.041 1.00 26.66 O HETATM 59 OXT ACT A 101 -0.174 25.881 21.893 1.00 27.05 O HETATM 60 CH3 ACT A 101 0.490 23.736 21.094 1.00 29.69 C HETATM 61 ZN ZN A 102 3.130 26.948 20.328 1.00 16.26 ZN HETATM 62 O HOH A 201 5.371 21.542 19.104 1.00 20.90 O HETATM 63 O HOH A 202 2.465 16.784 2.739 1.00 16.14 O HETATM 64 O HOH A 203 5.624 20.407 3.107 1.00 17.14 O CONECT 1 61 CONECT 4 61 CONECT 57 58 59 60 CONECT 58 57 CONECT 59 57 CONECT 60 57 CONECT 61 1 4 MASTER 222 0 2 0 0 0 1 6 63 1 7 1 END