HEADER PROTEIN FIBRIL 02-MAR-18 6CLQ TITLE 1.21 A MICROED STRUCTURE OF GSNQNNF AT 2.8 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 6CLQ 1 REMARK REVDAT 1 16-MAY-18 6CLQ 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. 1.21 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) : 1.21 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 13.79 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 79.3 REMARK 3 NUMBER OF REFLECTIONS : 1005 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) : 0.238 REMARK 3 R VALUE (WORKING SET) : 0.236 REMARK 3 FREE R VALUE : 0.262 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 9.000 REMARK 3 FREE R VALUE TEST SET COUNT : 100 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) : 1.21 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.24 REMARK 3 REFLECTION IN BIN (WORKING SET) : 66 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 77.89 REMARK 3 BIN R VALUE (WORKING SET) : 0.3830 REMARK 3 BIN FREE R VALUE SET COUNT : 8 REMARK 3 BIN FREE R VALUE : 0.3000 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) : 7.56 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -1.27000 REMARK 3 B22 (A**2) : -0.40000 REMARK 3 B33 (A**2) : 1.55000 REMARK 3 B12 (A**2) : 0.04000 REMARK 3 B13 (A**2) : -0.34000 REMARK 3 B23 (A**2) : -0.90000 REMARK 3 REMARK 3 ESTIMATED OVERALL COORDINATE ERROR. REMARK 3 ESU BASED ON R VALUE (A): 0.092 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.088 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.091 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 2.464 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.940 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.911 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 58 ; 0.015 ; 0.020 REMARK 3 BOND LENGTHS OTHERS (A): 39 ; 0.054 ; 0.020 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 76 ; 1.625 ; 1.886 REMARK 3 BOND ANGLES OTHERS (DEGREES): 92 ; 1.203 ; 3.000 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 6 ; 5.733 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 5 ;52.051 ;28.000 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 7 ; 9.332 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): NULL ; NULL ; NULL REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 6 ; 0.079 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 73 ; 0.008 ; 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 ; 0.626 ; 0.718 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): 26 ; 0.384 ; 0.647 REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 31 ; 0.822 ; 0.961 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): 32 ; 0.827 ; 0.963 REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 30 ; 0.702 ; 0.755 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): 31 ; 0.700 ; 0.819 REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE OTHER ATOMS (A**2): 44 ; 1.147 ; 1.134 REMARK 3 LONG RANGE B REFINED ATOMS (A**2): 49 ; 1.751 ; 7.149 REMARK 3 LONG RANGE B OTHER ATOMS (A**2): 50 ; 1.735 ; 7.752 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 6CLQ 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_1000232836. 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 : NULL 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 78.3 REMARK 620 3 PHE A 7 OXT 113.1 47.8 REMARK 620 4 ACT A 101 O 148.4 87.1 74.3 REMARK 620 5 ACT A 101 OXT 143.5 110.2 96.6 24.7 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 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-7509 RELATED DB: EMDB REMARK 900 1.21 A MICROED STRUCTURE OF GSNQNNF AT 2.8 E- / A^2 DBREF 6CLQ A 1 7 PDB 6CLQ 6CLQ 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 2.31 LINK O GLY A 1 ZN ZN A 102 1555 1555 1.99 LINK OXT PHE A 7 ZN ZN A 102 1555 1644 1.99 LINK O ACT A 101 ZN ZN A 102 1555 1455 2.01 LINK OXT ACT A 101 ZN ZN A 102 1555 1455 2.47 SITE 1 AC1 2 ASN A 3 ZN A 102 SITE 1 AC2 2 GLY A 1 ACT A 101 CRYST1 4.870 13.960 17.830 86.38 85.33 81.65 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 0.205339 -0.030135 -0.015220 0.00000 SCALE2 0.000000 0.072401 -0.003778 0.00000 SCALE3 0.000000 0.000000 0.056349 0.00000 ATOM 1 N GLY A 1 4.293 29.142 19.970 1.00 9.10 N ATOM 2 CA GLY A 1 4.606 29.106 18.533 1.00 9.05 C ATOM 3 C GLY A 1 3.549 28.364 17.763 1.00 9.13 C ATOM 4 O GLY A 1 2.859 27.498 18.341 1.00 9.64 O ATOM 5 N SER A 2 3.451 28.626 16.461 1.00 8.87 N ATOM 6 CA SER A 2 2.557 27.848 15.610 1.00 8.42 C ATOM 7 C SER A 2 3.303 26.621 15.065 1.00 7.67 C ATOM 8 O SER A 2 4.531 26.632 15.002 1.00 7.67 O ATOM 9 CB SER A 2 1.931 28.734 14.537 1.00 8.65 C ATOM 10 OG SER A 2 1.222 29.808 15.138 1.00 8.61 O ATOM 11 N ASN A 3 2.582 25.562 14.730 1.00 7.15 N ATOM 12 CA ASN A 3 3.180 24.299 14.264 1.00 6.68 C ATOM 13 C ASN A 3 2.547 23.858 12.936 1.00 6.06 C ATOM 14 O ASN A 3 1.359 23.985 12.770 1.00 5.78 O ATOM 15 CB ASN A 3 3.000 23.193 15.297 1.00 7.39 C ATOM 16 CG ASN A 3 3.503 23.563 16.693 1.00 7.74 C ATOM 17 OD1 ASN A 3 2.880 24.348 17.430 1.00 8.28 O ATOM 18 ND2 ASN A 3 4.617 22.987 17.071 1.00 8.07 N ATOM 19 N GLN A 4 3.323 23.302 11.999 1.00 5.33 N ATOM 20 CA GLN A 4 2.796 22.667 10.817 1.00 5.15 C ATOM 21 C GLN A 4 3.521 21.326 10.589 1.00 4.96 C ATOM 22 O GLN A 4 4.762 21.246 10.651 1.00 4.31 O ATOM 23 CB GLN A 4 2.936 23.501 9.585 1.00 5.15 C ATOM 24 CG GLN A 4 2.250 23.034 8.322 1.00 5.09 C ATOM 25 CD GLN A 4 2.677 23.848 7.117 1.00 5.32 C ATOM 26 OE1 GLN A 4 3.870 23.943 6.825 1.00 5.26 O ATOM 27 NE2 GLN A 4 1.734 24.483 6.450 1.00 4.98 N ATOM 28 N ASN A 5 2.730 20.293 10.340 1.00 5.23 N ATOM 29 CA ASN A 5 3.182 18.941 9.983 1.00 5.43 C ATOM 30 C ASN A 5 2.770 18.630 8.555 1.00 5.24 C ATOM 31 O ASN A 5 1.591 18.699 8.195 1.00 5.43 O ATOM 32 CB ASN A 5 2.531 17.908 10.880 1.00 6.02 C ATOM 33 CG ASN A 5 3.157 17.844 12.243 1.00 6.51 C ATOM 34 OD1 ASN A 5 4.384 17.713 12.334 1.00 8.05 O ATOM 35 ND2 ASN A 5 2.376 17.961 13.298 1.00 7.08 N ATOM 36 N ASN A 6 3.728 18.403 7.706 1.00 5.06 N ATOM 37 CA ASN A 6 3.493 18.041 6.335 1.00 5.10 C ATOM 38 C ASN A 6 3.873 16.574 6.187 1.00 5.41 C ATOM 39 O ASN A 6 5.015 16.214 5.867 1.00 5.47 O ATOM 40 CB ASN A 6 4.288 18.906 5.373 1.00 4.98 C ATOM 41 CG ASN A 6 3.867 20.381 5.401 1.00 4.82 C ATOM 42 OD1 ASN A 6 2.697 20.712 5.372 1.00 4.70 O ATOM 43 ND2 ASN A 6 4.847 21.246 5.393 1.00 5.02 N ATOM 44 N PHE A 7 2.937 15.729 6.469 1.00 5.85 N ATOM 45 CA PHE A 7 3.228 14.335 6.317 1.00 6.35 C ATOM 46 C PHE A 7 3.351 13.981 4.844 1.00 7.30 C ATOM 47 O PHE A 7 2.755 14.628 3.956 1.00 8.40 O ATOM 48 CB PHE A 7 2.161 13.499 6.998 1.00 6.03 C ATOM 49 CG PHE A 7 2.156 13.601 8.496 1.00 5.81 C ATOM 50 CD1 PHE A 7 2.963 12.791 9.249 1.00 5.62 C ATOM 51 CD2 PHE A 7 1.294 14.476 9.160 1.00 5.78 C ATOM 52 CE1 PHE A 7 2.937 12.840 10.619 1.00 5.52 C ATOM 53 CE2 PHE A 7 1.270 14.530 10.541 1.00 5.54 C ATOM 54 CZ PHE A 7 2.126 13.710 11.266 1.00 5.84 C ATOM 55 OXT PHE A 7 3.969 12.966 4.492 1.00 8.87 O TER 56 PHE A 7 HETATM 57 C ACT A 101 -0.189 25.578 20.549 1.00 25.66 C HETATM 58 O ACT A 101 -1.320 25.415 20.057 1.00 27.54 O HETATM 59 OXT ACT A 101 0.039 26.388 21.466 1.00 23.42 O HETATM 60 CH3 ACT A 101 0.884 24.737 19.944 1.00 27.58 C HETATM 61 ZN ZN A 102 2.933 27.311 20.317 1.00 14.24 ZN HETATM 62 O HOH A 201 5.353 21.627 19.321 1.00 12.63 O HETATM 63 O HOH A 202 2.519 16.932 2.484 1.00 16.17 O HETATM 64 O HOH A 203 1.951 19.776 2.359 1.00 20.46 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 223 0 2 0 0 0 2 6 63 1 7 1 END