HEADER PROTEIN FIBRIL 02-MAR-18 6CLP TITLE 1.16 A MICROED STRUCTURE OF GSNQNNF AT 2.5 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 6CLP 1 REMARK REVDAT 1 16-MAY-18 6CLP 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. 1.16 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) : 1.16 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 13.79 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 76.0 REMARK 3 NUMBER OF REFLECTIONS : 1097 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) : 0.243 REMARK 3 R VALUE (WORKING SET) : 0.239 REMARK 3 FREE R VALUE : 0.277 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 9.300 REMARK 3 FREE R VALUE TEST SET COUNT : 113 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) : 1.16 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.19 REMARK 3 REFLECTION IN BIN (WORKING SET) : 85 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 74.80 REMARK 3 BIN R VALUE (WORKING SET) : 0.3020 REMARK 3 BIN FREE R VALUE SET COUNT : 10 REMARK 3 BIN FREE R VALUE : 0.4060 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) : 6.32 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -1.02000 REMARK 3 B22 (A**2) : -0.15000 REMARK 3 B33 (A**2) : 1.03000 REMARK 3 B12 (A**2) : -0.05000 REMARK 3 B13 (A**2) : -0.29000 REMARK 3 B23 (A**2) : -0.72000 REMARK 3 REMARK 3 ESTIMATED OVERALL COORDINATE ERROR. REMARK 3 ESU BASED ON R VALUE (A): 0.086 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.087 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.074 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 1.739 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.930 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.878 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 58 ; 0.017 ; 0.020 REMARK 3 BOND LENGTHS OTHERS (A): 39 ; 0.000 ; 0.020 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 76 ; 1.827 ; 1.886 REMARK 3 BOND ANGLES OTHERS (DEGREES): 92 ; 1.152 ; 3.000 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 6 ; 3.936 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 5 ;50.177 ;28.000 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 7 ; 9.569 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): NULL ; NULL ; NULL REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 6 ; 0.096 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 73 ; 0.011 ; 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 ; 0.648 ; 0.591 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): 26 ; 0.430 ; 0.526 REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 29 ; 1.027 ; 0.799 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): 30 ; 1.045 ; 0.807 REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 30 ; 0.619 ; 0.615 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): 31 ; 0.613 ; 0.659 REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE OTHER ATOMS (A**2): 44 ; 0.839 ; 0.988 REMARK 3 LONG RANGE B REFINED ATOMS (A**2): 47 ; 2.278 ; 5.998 REMARK 3 LONG RANGE B OTHER ATOMS (A**2): 48 ; 2.257 ; 6.480 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 6CLP 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_1000232837. 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 74.7 REMARK 620 3 PHE A 7 OXT 111.6 50.8 REMARK 620 4 ACT A 101 O 148.6 87.9 73.9 REMARK 620 5 ACT A 101 OXT 143.1 107.9 95.9 23.2 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-7508 RELATED DB: EMDB REMARK 900 1.16 A MICROED STRUCTURE OF GSNQNNF AT 2.5 E- / A^2 DBREF 6CLP A 1 7 PDB 6CLP 6CLP 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 2.34 LINK O GLY A 1 ZN ZN A 102 1555 1555 2.03 LINK OXT PHE A 7 ZN ZN A 102 1555 1644 1.86 LINK O ACT A 101 ZN ZN A 102 1555 1455 2.04 LINK OXT ACT A 101 ZN ZN A 102 1555 1455 2.47 SITE 1 AC1 1 ZN A 102 SITE 1 AC2 2 GLY A 1 ACT A 101 CRYST1 4.850 13.940 17.830 86.42 85.40 82.01 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 -0.028944 -0.015110 0.00000 SCALE2 0.000000 0.072439 -0.003768 0.00000 SCALE3 0.000000 0.000000 0.056343 0.00000 ATOM 1 N GLY A 1 4.127 29.104 19.954 1.00 8.87 N ATOM 2 CA GLY A 1 4.357 29.222 18.486 1.00 8.13 C ATOM 3 C GLY A 1 3.348 28.404 17.728 1.00 7.64 C ATOM 4 O GLY A 1 2.670 27.570 18.333 1.00 7.91 O ATOM 5 N SER A 2 3.301 28.590 16.412 1.00 6.89 N ATOM 6 CA SER A 2 2.400 27.801 15.575 1.00 6.47 C ATOM 7 C SER A 2 3.155 26.588 15.013 1.00 5.68 C ATOM 8 O SER A 2 4.404 26.577 14.967 1.00 5.63 O ATOM 9 CB SER A 2 1.757 28.667 14.504 1.00 6.66 C ATOM 10 OG SER A 2 0.957 29.665 15.081 1.00 7.04 O ATOM 11 N ASN A 3 2.405 25.558 14.659 1.00 5.11 N ATOM 12 CA ASN A 3 2.989 24.309 14.212 1.00 4.80 C ATOM 13 C ASN A 3 2.355 23.835 12.922 1.00 4.20 C ATOM 14 O ASN A 3 1.174 23.950 12.718 1.00 4.03 O ATOM 15 CB ASN A 3 2.876 23.188 15.245 1.00 5.36 C ATOM 16 CG ASN A 3 3.365 23.576 16.645 1.00 6.14 C ATOM 17 OD1 ASN A 3 2.758 24.427 17.315 1.00 6.43 O ATOM 18 ND2 ASN A 3 4.425 22.930 17.109 1.00 6.36 N ATOM 19 N GLN A 4 3.137 23.228 12.030 1.00 3.89 N ATOM 20 CA GLN A 4 2.623 22.646 10.820 1.00 3.77 C ATOM 21 C GLN A 4 3.349 21.313 10.611 1.00 3.72 C ATOM 22 O GLN A 4 4.585 21.265 10.566 1.00 3.27 O ATOM 23 CB GLN A 4 2.828 23.489 9.579 1.00 3.72 C ATOM 24 CG GLN A 4 2.131 23.039 8.279 1.00 3.71 C ATOM 25 CD GLN A 4 2.566 23.846 7.048 1.00 3.86 C ATOM 26 OE1 GLN A 4 3.759 23.902 6.734 1.00 3.67 O ATOM 27 NE2 GLN A 4 1.630 24.485 6.363 1.00 3.69 N ATOM 28 N ASN A 5 2.553 20.279 10.348 1.00 4.14 N ATOM 29 CA ASN A 5 3.032 18.908 10.064 1.00 4.46 C ATOM 30 C ASN A 5 2.628 18.596 8.624 1.00 4.41 C ATOM 31 O ASN A 5 1.425 18.589 8.310 1.00 4.68 O ATOM 32 CB ASN A 5 2.408 17.874 10.986 1.00 4.94 C ATOM 33 CG ASN A 5 3.013 17.822 12.359 1.00 5.31 C ATOM 34 OD1 ASN A 5 4.226 17.667 12.501 1.00 6.35 O ATOM 35 ND2 ASN A 5 2.206 17.908 13.378 1.00 6.06 N ATOM 36 N ASN A 6 3.591 18.426 7.732 1.00 4.31 N ATOM 37 CA ASN A 6 3.369 18.006 6.333 1.00 4.54 C ATOM 38 C ASN A 6 3.742 16.544 6.172 1.00 4.90 C ATOM 39 O ASN A 6 4.867 16.171 5.889 1.00 5.20 O ATOM 40 CB ASN A 6 4.124 18.914 5.321 1.00 4.45 C ATOM 41 CG ASN A 6 3.727 20.417 5.460 1.00 4.44 C ATOM 42 OD1 ASN A 6 2.535 20.746 5.570 1.00 4.46 O ATOM 43 ND2 ASN A 6 4.700 21.285 5.517 1.00 4.28 N ATOM 44 N PHE A 7 2.790 15.703 6.411 1.00 5.50 N ATOM 45 CA PHE A 7 3.107 14.297 6.270 1.00 6.18 C ATOM 46 C PHE A 7 3.308 13.942 4.777 1.00 7.61 C ATOM 47 O PHE A 7 2.784 14.613 3.877 1.00 9.14 O ATOM 48 CB PHE A 7 2.075 13.457 6.985 1.00 5.50 C ATOM 49 CG PHE A 7 2.085 13.593 8.514 1.00 5.31 C ATOM 50 CD1 PHE A 7 2.899 12.781 9.274 1.00 4.94 C ATOM 51 CD2 PHE A 7 1.199 14.464 9.203 1.00 5.14 C ATOM 52 CE1 PHE A 7 2.886 12.809 10.656 1.00 5.03 C ATOM 53 CE2 PHE A 7 1.190 14.488 10.597 1.00 5.07 C ATOM 54 CZ PHE A 7 2.042 13.637 11.321 1.00 5.44 C ATOM 55 OXT PHE A 7 3.947 12.933 4.384 1.00 9.67 O TER 56 PHE A 7 HETATM 57 C ACT A 101 -0.389 25.451 20.777 1.00 18.94 C HETATM 58 O ACT A 101 -1.388 25.392 20.018 1.00 20.15 O HETATM 59 OXT ACT A 101 0.073 26.516 21.211 1.00 20.54 O HETATM 60 CH3 ACT A 101 0.235 24.152 21.164 1.00 20.14 C HETATM 61 ZN ZN A 102 2.733 27.264 20.341 1.00 13.18 ZN HETATM 62 O HOH A 201 4.992 21.522 18.885 1.00 12.71 O HETATM 63 O HOH A 202 2.359 16.630 2.435 1.00 19.07 O HETATM 64 O HOH A 203 1.619 20.066 2.698 1.00 21.79 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