HEADER PROTEIN FIBRIL 06-NOV-13 4NIN TITLE DSVISLS SEGMENT 101-107 FROM HUMAN SUPEROXIDE DISMUTASE COMPND MOL_ID: 1; COMPND 2 MOLECULE: DSVISLS SEGMENT FROM SUPEROXIDE DISMUTASE [CU-ZN]; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: UNP RESIDUES 102-108; COMPND 5 SYNONYM: SUPEROXIDE DISMUTASE 1, HSOD1; COMPND 6 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 SYNTHETIC: YES; SOURCE 3 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 4 ORGANISM_COMMON: HUMAN; SOURCE 5 ORGANISM_TAXID: 9606 KEYWDS STERIC ZIPPER, CROSS-BETA SPINE, AMYLOID FIBER, PROTEIN FIBRIL EXPDTA X-RAY DIFFRACTION AUTHOR S.A.SIEVERS,M.R.SAWAYA,D.EISENBERG REVDAT 4 28-FEB-24 4NIN 1 REMARK LINK REVDAT 3 22-NOV-17 4NIN 1 REMARK REVDAT 2 22-JAN-14 4NIN 1 JRNL REVDAT 1 04-DEC-13 4NIN 0 JRNL AUTH M.I.IVANOVA,S.A.SIEVERS,E.L.GUENTHER,L.M.JOHNSON, JRNL AUTH 2 D.D.WINKLER,A.GALALELDEEN,M.R.SAWAYA,P.J.HART,D.S.EISENBERG JRNL TITL AGGREGATION-TRIGGERING SEGMENTS OF SOD1 FIBRIL FORMATION JRNL TITL 2 SUPPORT A COMMON PATHWAY FOR FAMILIAL AND SPORADIC ALS. JRNL REF PROC.NATL.ACAD.SCI.USA V. 111 197 2014 JRNL REFN ISSN 0027-8424 JRNL PMID 24344300 JRNL DOI 10.1073/PNAS.1320786110 REMARK 2 REMARK 2 RESOLUTION. 1.40 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.7.1_743 REMARK 3 AUTHORS : PAUL ADAMS,PAVEL AFONINE,VINCENT CHEN,IAN REMARK 3 : DAVIS,KRESHNA GOPAL,RALF GROSSE-KUNSTLEVE, REMARK 3 : LI-WEI HUNG,ROBERT IMMORMINO,TOM IOERGER, REMARK 3 : AIRLIE MCCOY,ERIK MCKEE,NIGEL MORIARTY, REMARK 3 : REETAL PAI,RANDY READ,JANE RICHARDSON, REMARK 3 : DAVID RICHARDSON,TOD ROMO,JIM SACCHETTINI, REMARK 3 : NICHOLAS SAUTER,JACOB SMITH,LAURENT REMARK 3 : STORONI,TOM TERWILLIGER,PETER ZWART REMARK 3 REMARK 3 REFINEMENT TARGET : ML REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.40 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 22.67 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.660 REMARK 3 COMPLETENESS FOR RANGE (%) : 74.1 REMARK 3 NUMBER OF REFLECTIONS : 705 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.191 REMARK 3 R VALUE (WORKING SET) : 0.187 REMARK 3 FREE R VALUE : 0.228 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 9.220 REMARK 3 FREE R VALUE TEST SET COUNT : 65 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT (IN BINS). REMARK 3 BIN RESOLUTION RANGE COMPL. NWORK NFREE RWORK RFREE REMARK 3 1 22.6715 - 1.4023 0.74 640 65 0.1872 0.2281 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : FLAT BULK SOLVENT MODEL REMARK 3 SOLVENT RADIUS : 1.10 REMARK 3 SHRINKAGE RADIUS : 0.83 REMARK 3 K_SOL : 0.44 REMARK 3 B_SOL : 58.79 REMARK 3 REMARK 3 ERROR ESTIMATES. REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : 0.000 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 34.160 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 11.41 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 19.28 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -4.91060 REMARK 3 B22 (A**2) : -5.65070 REMARK 3 B33 (A**2) : 10.56130 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : -2.58500 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 TWINNING INFORMATION. REMARK 3 FRACTION: NULL REMARK 3 OPERATOR: NULL REMARK 3 REMARK 3 DEVIATIONS FROM IDEAL VALUES. REMARK 3 RMSD COUNT REMARK 3 BOND : 0.006 49 REMARK 3 ANGLE : 0.923 66 REMARK 3 CHIRALITY : 0.061 10 REMARK 3 PLANARITY : 0.002 8 REMARK 3 DIHEDRAL : 10.205 17 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : NULL REMARK 3 REMARK 3 NCS DETAILS REMARK 3 NUMBER OF NCS GROUPS : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 4NIN COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 19-NOV-13. REMARK 100 THE DEPOSITION ID IS D_1000083250. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 22-JUL-11 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 6.0 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : APS REMARK 200 BEAMLINE : 24-ID-E REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.9792 REMARK 200 MONOCHROMATOR : CRYOGENICALLY-COOLED SINGLE REMARK 200 CRYSTAL SI(220) REMARK 200 OPTICS : MIRRORS REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 315 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : DENZO REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 717 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.400 REMARK 200 RESOLUTION RANGE LOW (A) : 100.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : -3.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 73.6 REMARK 200 DATA REDUNDANCY : 3.700 REMARK 200 R MERGE (I) : 0.18600 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 24.1000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.40 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.51 REMARK 200 COMPLETENESS FOR SHELL (%) : 28.4 REMARK 200 DATA REDUNDANCY IN SHELL : 1.50 REMARK 200 R MERGE FOR SHELL (I) : 0.16600 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : NULL REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: PHASER 2.1.4 REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 26.84 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 1.68 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.1 M MES PH 6.0, 20% PEG 6000, AND 5 REMARK 280 MM ZNCL2, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 298K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 1 21 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,Y+1/2,-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 SMTRY1 2 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 2 0.000000 1.000000 0.000000 22.66850 REMARK 290 SMTRY3 2 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 300 REMARK: BIOLOGICAL UNIT IS A PAIR OF BETA-SHEETS FORMED BY THE REMARK 300 SYMMETRY OPERATORS X,Y,Z AND X,Y,Z-1 WITH POSITIVE AND NEGATIVE REMARK 300 UNIT CELL TRANSLATIONS ALONG THE X AXIS. FOR EXAMPLE ONE SHEET IS REMARK 300 COMPOSED OF SYMMETRY OPERATORS X,Y,Z; X+1,Y,Z; X-1,Y,Z; X+2,Y,Z; X- REMARK 300 2,Y,Z: THE OPPOSING SHEET IS COMPOSED OF SYMMETRY OPERATORS X,Y,Z-1; REMARK 300 X+1,Y,Z-1; X-1,Y,Z-1; X+2,Y,Z-1; X-2,Y,Z-1, ETC. 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: DECAMERIC 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 350 BIOMT1 2 1.000000 0.000000 0.000000 4.80500 REMARK 350 BIOMT2 2 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT3 2 0.000000 0.000000 1.000000 0.00000 REMARK 350 BIOMT1 3 1.000000 0.000000 0.000000 9.61000 REMARK 350 BIOMT2 3 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT3 3 0.000000 0.000000 1.000000 0.00000 REMARK 350 BIOMT1 4 1.000000 0.000000 0.000000 -9.61000 REMARK 350 BIOMT2 4 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT3 4 0.000000 0.000000 1.000000 0.00000 REMARK 350 BIOMT1 5 1.000000 0.000000 0.000000 -4.80500 REMARK 350 BIOMT2 5 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT3 5 0.000000 0.000000 1.000000 0.00000 REMARK 350 BIOMT1 6 1.000000 0.000000 0.000000 2.06314 REMARK 350 BIOMT2 6 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT3 6 0.000000 0.000000 1.000000 -11.11006 REMARK 350 BIOMT1 7 1.000000 0.000000 0.000000 6.86814 REMARK 350 BIOMT2 7 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT3 7 0.000000 0.000000 1.000000 -11.11006 REMARK 350 BIOMT1 8 1.000000 0.000000 0.000000 11.67314 REMARK 350 BIOMT2 8 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT3 8 0.000000 0.000000 1.000000 -11.11006 REMARK 350 BIOMT1 9 1.000000 0.000000 0.000000 -7.54686 REMARK 350 BIOMT2 9 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT3 9 0.000000 0.000000 1.000000 -11.11006 REMARK 350 BIOMT1 10 1.000000 0.000000 0.000000 -2.74186 REMARK 350 BIOMT2 10 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT3 10 0.000000 0.000000 1.000000 -11.11006 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 101 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP A 1 OD1 REMARK 620 2 ASP A 1 N 89.0 REMARK 620 3 HOH A 201 O 85.9 163.4 REMARK 620 4 HOH A 202 O 80.3 76.7 86.9 REMARK 620 5 HOH A 203 O 103.2 102.6 93.9 176.5 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 101 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 4NIO RELATED DB: PDB REMARK 900 RELATED ID: 4NIP RELATED DB: PDB DBREF 4NIN A 1 7 UNP P00441 SODC_HUMAN 102 108 SEQRES 1 A 7 ASP SER VAL ILE SER LEU SER HET ZN A 101 1 HETNAM ZN ZINC ION FORMUL 2 ZN ZN 2+ FORMUL 3 HOH *4(H2 O) LINK OD1 ASP A 1 ZN ZN A 101 1555 1555 2.05 LINK N ASP A 1 ZN ZN A 101 1555 1555 2.25 LINK ZN ZN A 101 O HOH A 201 1555 1555 2.17 LINK ZN ZN A 101 O HOH A 202 1555 1555 2.06 LINK ZN ZN A 101 O HOH A 203 1555 1555 2.22 SITE 1 AC1 4 ASP A 1 HOH A 201 HOH A 202 HOH A 203 CRYST1 4.805 45.337 11.300 90.00 100.52 90.00 P 1 21 1 2 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 0.208117 0.000000 0.038632 0.00000 SCALE2 0.000000 0.022057 0.000000 0.00000 SCALE3 0.000000 0.000000 0.090007 0.00000 ATOM 1 N ASP A 1 -0.909 -2.105 10.037 1.00 22.52 N ATOM 2 CA ASP A 1 -0.241 -3.339 9.628 1.00 21.40 C ATOM 3 C ASP A 1 -0.954 -3.918 8.405 1.00 21.39 C ATOM 4 O ASP A 1 -2.162 -3.730 8.249 1.00 20.97 O ATOM 5 CB ASP A 1 -0.241 -4.360 10.776 1.00 20.70 C ATOM 6 CG ASP A 1 0.853 -4.097 11.803 1.00 23.34 C ATOM 7 OD1 ASP A 1 1.312 -2.937 11.897 1.00 23.45 O ATOM 8 OD2 ASP A 1 1.266 -5.052 12.509 1.00 21.37 O ATOM 9 N SER A 2 -0.212 -4.615 7.541 1.00 19.32 N ATOM 10 CA SER A 2 -0.807 -5.258 6.365 1.00 17.01 C ATOM 11 C SER A 2 -0.117 -6.570 6.036 1.00 18.23 C ATOM 12 O SER A 2 1.103 -6.695 6.181 1.00 16.86 O ATOM 13 CB SER A 2 -0.770 -4.340 5.140 1.00 20.81 C ATOM 14 OG SER A 2 0.489 -4.389 4.488 1.00 22.96 O ATOM 15 N VAL A 3 -0.903 -7.547 5.589 1.00 15.43 N ATOM 16 CA VAL A 3 -0.351 -8.816 5.147 1.00 15.59 C ATOM 17 C VAL A 3 -0.951 -9.208 3.795 1.00 16.60 C ATOM 18 O VAL A 3 -2.161 -9.083 3.598 1.00 14.52 O ATOM 19 CB VAL A 3 -0.666 -9.944 6.156 1.00 15.87 C ATOM 20 CG1 VAL A 3 -0.320 -11.295 5.561 1.00 18.07 C ATOM 21 CG2 VAL A 3 0.062 -9.718 7.473 1.00 15.23 C ATOM 22 N ILE A 4 -0.103 -9.667 2.870 1.00 13.73 N ATOM 23 CA ILE A 4 -0.569 -10.362 1.671 1.00 13.89 C ATOM 24 C ILE A 4 -0.016 -11.774 1.693 1.00 16.10 C ATOM 25 O ILE A 4 1.197 -11.969 1.768 1.00 14.23 O ATOM 26 CB ILE A 4 -0.119 -9.684 0.366 1.00 14.39 C ATOM 27 CG1 ILE A 4 -0.751 -8.298 0.241 1.00 15.53 C ATOM 28 CG2 ILE A 4 -0.508 -10.547 -0.839 1.00 15.49 C ATOM 29 CD1 ILE A 4 -0.252 -7.514 -0.960 1.00 17.74 C ATOM 30 N SER A 5 -0.907 -12.759 1.635 1.00 15.29 N ATOM 31 CA SER A 5 -0.490 -14.149 1.693 1.00 17.76 C ATOM 32 C SER A 5 -1.093 -14.951 0.561 1.00 17.82 C ATOM 33 O SER A 5 -2.318 -15.051 0.455 1.00 16.66 O ATOM 34 CB SER A 5 -0.909 -14.789 3.022 1.00 19.08 C ATOM 35 OG SER A 5 -0.556 -16.164 3.035 1.00 21.03 O ATOM 36 N LEU A 6 -0.228 -15.527 -0.270 1.00 16.86 N ATOM 37 CA LEU A 6 -0.650 -16.487 -1.280 1.00 19.28 C ATOM 38 C LEU A 6 -0.110 -17.859 -0.896 1.00 19.33 C ATOM 39 O LEU A 6 1.091 -18.025 -0.702 1.00 18.71 O ATOM 40 CB LEU A 6 -0.146 -16.087 -2.667 1.00 16.52 C ATOM 41 CG LEU A 6 -0.839 -14.931 -3.390 1.00 23.35 C ATOM 42 CD1 LEU A 6 -0.640 -13.614 -2.656 1.00 20.86 C ATOM 43 CD2 LEU A 6 -0.327 -14.826 -4.832 1.00 24.01 C ATOM 44 N SER A 7 -0.996 -18.841 -0.769 1.00 19.41 N ATOM 45 CA SER A 7 -0.557 -20.177 -0.347 1.00 22.53 C ATOM 46 C SER A 7 -1.191 -21.324 -1.147 1.00 23.93 C ATOM 47 O SER A 7 -0.718 -22.473 -1.105 1.00 22.44 O ATOM 48 CB SER A 7 -0.783 -20.377 1.163 1.00 23.32 C ATOM 49 OG SER A 7 -2.145 -20.169 1.515 1.00 28.39 O ATOM 50 OXT SER A 7 -2.182 -21.133 -1.861 1.00 24.28 O TER 51 SER A 7 HETATM 52 ZN ZN A 101 -0.098 -1.456 12.027 0.55 15.51 ZN2+ HETATM 53 O HOH A 201 1.149 -0.620 13.588 1.00 22.73 O HETATM 54 O HOH A 202 1.199 -0.584 10.679 1.00 22.47 O HETATM 55 O HOH A 203 -1.582 -2.294 13.450 1.00 23.77 O HETATM 56 O HOH A 204 1.870 -17.527 2.405 1.00 22.18 O CONECT 1 52 CONECT 7 52 CONECT 52 1 7 53 54 CONECT 52 55 CONECT 53 52 CONECT 54 52 CONECT 55 52 MASTER 236 0 1 0 0 0 1 6 55 1 7 1 END