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