HEADER PROTEIN FIBRIL 02-MAR-18 6CLL TITLE 1.02 A MICROED STRUCTURE OF GSNQNNF AT 1.2 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 6CLL 1 LINK REVDAT 1 16-MAY-18 6CLL 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. 1.02 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) : 1.02 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 11.39 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 73.2 REMARK 3 NUMBER OF REFLECTIONS : 1526 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) : 0.249 REMARK 3 R VALUE (WORKING SET) : 0.246 REMARK 3 FREE R VALUE : 0.280 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 9.000 REMARK 3 FREE R VALUE TEST SET COUNT : 151 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) : 1.02 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.05 REMARK 3 REFLECTION IN BIN (WORKING SET) : 98 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 72.11 REMARK 3 BIN R VALUE (WORKING SET) : 0.3220 REMARK 3 BIN FREE R VALUE SET COUNT : 8 REMARK 3 BIN FREE R VALUE : 0.2160 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) : 5.22 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -0.88000 REMARK 3 B22 (A**2) : -0.23000 REMARK 3 B33 (A**2) : 0.98000 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : -0.20000 REMARK 3 B23 (A**2) : -0.37000 REMARK 3 REMARK 3 ESTIMATED OVERALL COORDINATE ERROR. REMARK 3 ESU BASED ON R VALUE (A): 0.064 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.066 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.049 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 0.939 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.911 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.882 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 ; 1.370 ; 1.886 REMARK 3 BOND ANGLES OTHERS (DEGREES): 92 ; 1.022 ; 3.000 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 6 ; 4.622 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 5 ;60.967 ;28.000 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 7 ; 8.715 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): NULL ; NULL ; NULL REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 6 ; 0.088 ; 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 ; 0.555 ; 0.478 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): 26 ; 0.492 ; 0.446 REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 29 ; 0.904 ; 0.680 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): 30 ; 0.910 ; 0.686 REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 30 ; 0.589 ; 0.529 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): 31 ; 0.579 ; 0.546 REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE OTHER ATOMS (A**2): 44 ; 0.884 ; 0.788 REMARK 3 LONG RANGE B REFINED ATOMS (A**2): 48 ; 2.521 ; 5.560 REMARK 3 LONG RANGE B OTHER ATOMS (A**2): 48 ; 2.500 ; 5.644 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 6CLL 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_1000232843. 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 : NULL 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 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 79.3 REMARK 620 3 PHE A 7 OXT 115.7 53.0 REMARK 620 4 ACT A 101 O 142.2 81.1 75.3 REMARK 620 5 ACT A 101 OXT 147.2 87.0 76.9 6.4 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-7504 RELATED DB: EMDB REMARK 900 1.02 A MICROED STRUCTURE OF GSNQNNF AT 1.2 E- / A^2 DBREF 6CLL A 1 7 PDB 6CLL 6CLL 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 2.22 LINK O GLY A 1 ZN ZN A 102 1555 1555 2.10 LINK OXT PHE A 7 ZN ZN A 102 1555 1644 1.86 LINK O ACT A 101 ZN ZN A 102 1555 1555 2.01 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 14.090 17.380 83.80 85.34 82.94 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 -0.025592 -0.014367 0.00000 SCALE2 0.000000 0.071515 -0.007117 0.00000 SCALE3 0.000000 0.000000 0.058013 0.00000 ATOM 1 N GLY A 1 3.502 30.424 19.412 1.00 6.57 N ATOM 2 CA GLY A 1 3.756 30.444 17.920 1.00 6.58 C ATOM 3 C GLY A 1 2.833 29.573 17.110 1.00 6.03 C ATOM 4 O GLY A 1 2.034 28.858 17.686 1.00 7.81 O ATOM 5 N SER A 2 2.913 29.650 15.795 1.00 5.62 N ATOM 6 CA SER A 2 2.067 28.815 14.960 1.00 5.31 C ATOM 7 C SER A 2 2.798 27.547 14.467 1.00 4.70 C ATOM 8 O SER A 2 4.036 27.508 14.402 1.00 4.52 O ATOM 9 CB SER A 2 1.498 29.665 13.831 1.00 5.49 C ATOM 10 OG SER A 2 0.617 30.628 14.381 1.00 5.99 O ATOM 11 N ASN A 3 2.017 26.495 14.112 1.00 4.46 N ATOM 12 CA ASN A 3 2.606 25.169 13.851 1.00 4.40 C ATOM 13 C ASN A 3 1.960 24.575 12.624 1.00 3.71 C ATOM 14 O ASN A 3 0.736 24.649 12.454 1.00 3.55 O ATOM 15 CB ASN A 3 2.455 24.232 15.045 1.00 5.36 C ATOM 16 CG ASN A 3 3.023 24.827 16.298 1.00 5.98 C ATOM 17 OD1 ASN A 3 2.296 25.435 17.105 1.00 6.47 O ATOM 18 ND2 ASN A 3 4.317 24.671 16.481 1.00 6.90 N ATOM 19 N GLN A 4 2.775 24.012 11.722 1.00 3.17 N ATOM 20 CA GLN A 4 2.266 23.365 10.557 1.00 3.16 C ATOM 21 C GLN A 4 2.988 22.021 10.339 1.00 3.22 C ATOM 22 O GLN A 4 4.232 21.930 10.377 1.00 3.10 O ATOM 23 CB GLN A 4 2.467 24.203 9.325 1.00 3.14 C ATOM 24 CG GLN A 4 1.736 23.749 8.077 1.00 3.23 C ATOM 25 CD GLN A 4 2.207 24.484 6.807 1.00 3.41 C ATOM 26 OE1 GLN A 4 3.400 24.476 6.465 1.00 3.71 O ATOM 27 NE2 GLN A 4 1.284 25.105 6.094 1.00 3.30 N ATOM 28 N ASN A 5 2.195 20.982 10.026 1.00 3.66 N ATOM 29 CA ASN A 5 2.707 19.621 9.784 1.00 4.10 C ATOM 30 C ASN A 5 2.320 19.241 8.390 1.00 3.86 C ATOM 31 O ASN A 5 1.114 19.234 8.051 1.00 4.23 O ATOM 32 CB ASN A 5 2.099 18.562 10.743 1.00 5.12 C ATOM 33 CG ASN A 5 2.622 18.697 12.157 1.00 5.79 C ATOM 34 OD1 ASN A 5 3.821 18.455 12.394 1.00 7.21 O ATOM 35 ND2 ASN A 5 1.760 19.132 13.109 1.00 7.48 N ATOM 36 N ASN A 6 3.292 18.998 7.523 1.00 3.72 N ATOM 37 CA ASN A 6 3.065 18.568 6.138 1.00 3.91 C ATOM 38 C ASN A 6 3.549 17.124 5.986 1.00 4.17 C ATOM 39 O ASN A 6 4.713 16.859 5.658 1.00 4.06 O ATOM 40 CB ASN A 6 3.809 19.498 5.159 1.00 3.93 C ATOM 41 CG ASN A 6 3.375 20.938 5.352 1.00 3.85 C ATOM 42 OD1 ASN A 6 2.185 21.234 5.330 1.00 4.02 O ATOM 43 ND2 ASN A 6 4.304 21.792 5.665 1.00 3.80 N ATOM 44 N PHE A 7 2.642 16.194 6.186 1.00 4.69 N ATOM 45 CA PHE A 7 2.982 14.775 6.042 1.00 5.21 C ATOM 46 C PHE A 7 3.165 14.394 4.587 1.00 6.32 C ATOM 47 O PHE A 7 2.756 15.072 3.650 1.00 7.25 O ATOM 48 CB PHE A 7 1.921 13.926 6.677 1.00 4.90 C ATOM 49 CG PHE A 7 1.868 14.063 8.124 1.00 4.97 C ATOM 50 CD1 PHE A 7 2.732 13.320 8.876 1.00 4.96 C ATOM 51 CD2 PHE A 7 1.013 14.999 8.771 1.00 5.26 C ATOM 52 CE1 PHE A 7 2.750 13.389 10.241 1.00 5.09 C ATOM 53 CE2 PHE A 7 1.026 15.094 10.183 1.00 5.30 C ATOM 54 CZ PHE A 7 1.902 14.247 10.926 1.00 5.60 C ATOM 55 OXT PHE A 7 3.750 13.330 4.308 1.00 6.92 O TER 56 PHE A 7 HETATM 57 C ACT A 101 -0.240 26.847 19.825 1.00 10.51 C HETATM 58 O ACT A 101 0.427 27.867 19.576 1.00 11.01 O HETATM 59 OXT ACT A 101 -1.494 26.851 19.783 1.00 10.95 O HETATM 60 CH3 ACT A 101 0.467 25.571 20.182 1.00 10.65 C HETATM 61 ZN ZN A 102 2.295 28.595 19.750 1.00 8.76 ZN HETATM 62 O HOH A 201 4.850 22.507 17.919 1.00 21.17 O HETATM 63 O HOH A 202 5.981 17.424 3.306 1.00 19.59 O HETATM 64 O HOH A 203 1.163 20.624 2.240 1.00 14.01 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 221 0 2 0 0 0 2 6 63 1 7 1 END