HEADER UNKNOWN FUNCTION 01-MAR-16 5IIW TITLE CORKSCREW ASSEMBLY OF SOD1 RESIDUES 28-38 WITHOUT POTASSIUM IODIDE COMPND MOL_ID: 1; COMPND 2 MOLECULE: SUPEROXIDE DISMUTASE [CU-ZN]; COMPND 3 CHAIN: A, B, C, D, E, F, G, H; COMPND 4 FRAGMENT: UNP RESIDUES 29-39; COMPND 5 SYNONYM: SUPEROXIDE DISMUTASE 1,HSOD1; COMPND 6 EC: 1.15.1.1; COMPND 7 ENGINEERED: YES; COMPND 8 MUTATION: 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; SOURCE 6 OTHER_DETAILS: SYNTHESIZED KEYWDS AMYLOID-RELATED OLIGOMER, UNKNOWN FUNCTION EXPDTA X-RAY DIFFRACTION AUTHOR S.SANGWAN,A.ZHAO,M.R.SAWAYA,D.EISENBERG REVDAT 6 06-MAR-24 5IIW 1 REMARK REVDAT 5 04-DEC-19 5IIW 1 REMARK REVDAT 4 09-JAN-19 5IIW 1 JRNL REVDAT 3 01-NOV-17 5IIW 1 REMARK REVDAT 2 20-SEP-17 5IIW 1 REMARK REVDAT 1 28-JUN-17 5IIW 0 JRNL AUTH S.SANGWAN,A.ZHAO,K.L.ADAMS,C.K.JAYSON,M.R.SAWAYA, JRNL AUTH 2 E.L.GUENTHER,A.C.PAN,J.NGO,D.M.MOORE,A.B.SORIAGA,T.D.DO, JRNL AUTH 3 L.GOLDSCHMIDT,R.NELSON,M.T.BOWERS,C.M.KOEHLER,D.E.SHAW, JRNL AUTH 4 B.G.NOVITCH,D.S.EISENBERG JRNL TITL ATOMIC STRUCTURE OF A TOXIC, OLIGOMERIC SEGMENT OF SOD1 JRNL TITL 2 LINKED TO AMYOTROPHIC LATERAL SCLEROSIS (ALS). JRNL REF PROC. NATL. ACAD. SCI. V. 114 8770 2017 JRNL REF 2 U.S.A. JRNL REFN ESSN 1091-6490 JRNL PMID 28760994 JRNL DOI 10.1073/PNAS.1705091114 REMARK 2 REMARK 2 RESOLUTION. 2.00 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : BUSTER-TNT REMARK 3 AUTHORS : BRICOGNE,BLANC,BRANDL,FLENSBURG,KELLER, REMARK 3 : PACIOREK,ROVERSI,SMART,VONRHEIN,WOMACK, REMARK 3 : MATTHEWS,TEN EYCK,TRONRUD REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.00 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 35.49 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 97.8 REMARK 3 NUMBER OF REFLECTIONS : 6690 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) : 0.240 REMARK 3 R VALUE (WORKING SET) : 0.239 REMARK 3 FREE R VALUE : 0.252 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.020 REMARK 3 FREE R VALUE TEST SET COUNT : 336 REMARK 3 ESTIMATED ERROR OF FREE R VALUE : NULL REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : 5 REMARK 3 BIN RESOLUTION RANGE HIGH (ANGSTROMS) : 2.00 REMARK 3 BIN RESOLUTION RANGE LOW (ANGSTROMS) : 2.24 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 97.79 REMARK 3 REFLECTIONS IN BIN (WORKING + TEST SET) : 1862 REMARK 3 BIN R VALUE (WORKING + TEST SET) : 0.2051 REMARK 3 REFLECTIONS IN BIN (WORKING SET) : 1769 REMARK 3 BIN R VALUE (WORKING SET) : 0.2043 REMARK 3 BIN FREE R VALUE : 0.2214 REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : 4.99 REMARK 3 BIN FREE R VALUE TEST SET COUNT : 93 REMARK 3 ESTIMATED ERROR OF BIN FREE R VALUE : NULL REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 688 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 0 REMARK 3 SOLVENT ATOMS : 34 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 30.33 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 34.90 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -1.72490 REMARK 3 B22 (A**2) : 5.82360 REMARK 3 B33 (A**2) : -4.09860 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : 0.00000 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM LUZZATI PLOT (A) : 0.256 REMARK 3 DPI (BLOW EQ-10) BASED ON R VALUE (A) : 0.219 REMARK 3 DPI (BLOW EQ-9) BASED ON FREE R VALUE (A) : 0.169 REMARK 3 DPI (CRUICKSHANK) BASED ON R VALUE (A) : 0.210 REMARK 3 DPI (CRUICKSHANK) BASED ON FREE R VALUE (A) : 0.167 REMARK 3 REMARK 3 REFERENCES: BLOW, D. (2002) ACTA CRYST D58, 792-797 REMARK 3 CRUICKSHANK, D.W.J. (1999) ACTA CRYST D55, 583-601 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.927 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.954 REMARK 3 REMARK 3 NUMBER OF GEOMETRIC FUNCTION TERMS DEFINED : 15 REMARK 3 TERM COUNT WEIGHT FUNCTION. REMARK 3 BOND LENGTHS : 696 ; 2.000 ; HARMONIC REMARK 3 BOND ANGLES : 920 ; 2.000 ; HARMONIC REMARK 3 TORSION ANGLES : 248 ; 2.000 ; SINUSOIDAL REMARK 3 TRIGONAL CARBON PLANES : 8 ; 2.000 ; HARMONIC REMARK 3 GENERAL PLANES : 88 ; 5.000 ; HARMONIC REMARK 3 ISOTROPIC THERMAL FACTORS : 696 ; 20.000 ; HARMONIC REMARK 3 BAD NON-BONDED CONTACTS : NULL ; NULL ; NULL REMARK 3 IMPROPER TORSIONS : NULL ; NULL ; NULL REMARK 3 PSEUDOROTATION ANGLES : NULL ; NULL ; NULL REMARK 3 CHIRAL IMPROPER TORSION : 80 ; 5.000 ; SEMIHARMONIC REMARK 3 SUM OF OCCUPANCIES : NULL ; NULL ; NULL REMARK 3 UTILITY DISTANCES : NULL ; NULL ; NULL REMARK 3 UTILITY ANGLES : NULL ; NULL ; NULL REMARK 3 UTILITY TORSION : NULL ; NULL ; NULL REMARK 3 IDEAL-DIST CONTACT TERM : 923 ; 4.000 ; SEMIHARMONIC REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 BOND LENGTHS (A) : 0.010 REMARK 3 BOND ANGLES (DEGREES) : 0.91 REMARK 3 PEPTIDE OMEGA TORSION ANGLES (DEGREES) : 2.61 REMARK 3 OTHER TORSION ANGLES (DEGREES) : 15.23 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 1 REMARK 3 REMARK 3 TLS GROUP : 1 REMARK 3 SELECTION: { *|* } REMARK 3 ORIGIN FOR THE GROUP (A): 9.3142 16.9063 31.6219 REMARK 3 T TENSOR REMARK 3 T11: 0.0281 T22: 0.0525 REMARK 3 T33: -0.1844 T12: -0.0011 REMARK 3 T13: -0.0236 T23: -0.0038 REMARK 3 L TENSOR REMARK 3 L11: 0.6049 L22: 0.4556 REMARK 3 L33: 6.0550 L12: -0.0913 REMARK 3 L13: -1.8857 L23: -0.4244 REMARK 3 S TENSOR REMARK 3 S11: 0.0373 S12: -0.0516 S13: 0.0370 REMARK 3 S21: 0.0213 S22: -0.0155 S23: 0.0070 REMARK 3 S31: 0.0420 S32: 0.0243 S33: -0.0219 REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 5IIW COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 02-MAR-16. REMARK 100 THE DEPOSITION ID IS D_1000218903. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 09-DEC-12 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 5 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) : NULL REMARK 200 WAVELENGTH OR RANGE (A) : 0.9791 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 315 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : XSCALE REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 6691 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.000 REMARK 200 RESOLUTION RANGE LOW (A) : 35.490 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : -3.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 97.8 REMARK 200 DATA REDUNDANCY : 5.100 REMARK 200 R MERGE (I) : 0.12200 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 9.3400 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.00 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.15 REMARK 200 COMPLETENESS FOR SHELL (%) : 97.7 REMARK 200 DATA REDUNDANCY IN SHELL : 5.23 REMARK 200 R MERGE FOR SHELL (I) : 0.59300 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 3.130 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: SIRAS REMARK 200 SOFTWARE USED: SHELX REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 49.43 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.43 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: RESERVOIR CONTAINED 13% PEG 6000, 0.2M REMARK 280 SODIUM CITRATE, PH 5, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE REMARK 280 298K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 21 21 21 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X+1/2,-Y,Z+1/2 REMARK 290 3555 -X,Y+1/2,-Z+1/2 REMARK 290 4555 X+1/2,-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 15.44500 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 35.48500 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 21.61500 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 35.48500 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 15.44500 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 21.61500 REMARK 290 SMTRY3 4 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: AUTHOR STATES THAT THE BIOLOGICAL ASSEMBLY IS VARIABLE BETA- REMARK 300 SHEET ACCORDING TO GEL FILTRATION. ASYMMETRIC UNIT IS ONE WAY OF REMARK 300 REPRESENTING THE VARIABLE BIOLOGICAL ASSEMBLY. 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: OCTAMERIC REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B, C, D, E, F, G, H 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 525 REMARK 525 SOLVENT REMARK 525 REMARK 525 THE SOLVENT MOLECULES HAVE CHAIN IDENTIFIERS THAT REMARK 525 INDICATE THE POLYMER CHAIN WITH WHICH THEY ARE MOST REMARK 525 CLOSELY ASSOCIATED. THE REMARK LISTS ALL THE SOLVENT REMARK 525 MOLECULES WHICH ARE MORE THAN 5A AWAY FROM THE REMARK 525 NEAREST POLYMER CHAIN (M = MODEL NUMBER; REMARK 525 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE REMARK 525 NUMBER; I=INSERTION CODE): REMARK 525 REMARK 525 M RES CSSEQI REMARK 525 HOH A 103 DISTANCE = 13.47 ANGSTROMS REMARK 525 HOH A 104 DISTANCE = 14.05 ANGSTROMS REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 5DLI RELATED DB: PDB REMARK 900 5DLI CONTAINS THE SAME PEPTIDE WITH POTASSIUM IODIDE SOAKED IN FOR REMARK 900 SIRAS PHASING. DBREF 5IIW A 28 38 UNP P00441 SODC_HUMAN 29 39 DBREF 5IIW B 28 38 UNP P00441 SODC_HUMAN 29 39 DBREF 5IIW C 28 38 UNP P00441 SODC_HUMAN 29 39 DBREF 5IIW D 28 38 UNP P00441 SODC_HUMAN 29 39 DBREF 5IIW E 28 38 UNP P00441 SODC_HUMAN 29 39 DBREF 5IIW F 28 38 UNP P00441 SODC_HUMAN 29 39 DBREF 5IIW G 28 38 UNP P00441 SODC_HUMAN 29 39 DBREF 5IIW H 28 38 UNP P00441 SODC_HUMAN 29 39 SEQADV 5IIW LYS A 28 UNP P00441 PRO 29 ENGINEERED MUTATION SEQADV 5IIW LYS B 28 UNP P00441 PRO 29 ENGINEERED MUTATION SEQADV 5IIW LYS C 28 UNP P00441 PRO 29 ENGINEERED MUTATION SEQADV 5IIW LYS D 28 UNP P00441 PRO 29 ENGINEERED MUTATION SEQADV 5IIW LYS E 28 UNP P00441 PRO 29 ENGINEERED MUTATION SEQADV 5IIW LYS F 28 UNP P00441 PRO 29 ENGINEERED MUTATION SEQADV 5IIW LYS G 28 UNP P00441 PRO 29 ENGINEERED MUTATION SEQADV 5IIW LYS H 28 UNP P00441 PRO 29 ENGINEERED MUTATION SEQRES 1 A 11 LYS VAL LYS VAL TRP GLY SER ILE LYS GLY LEU SEQRES 1 B 11 LYS VAL LYS VAL TRP GLY SER ILE LYS GLY LEU SEQRES 1 C 11 LYS VAL LYS VAL TRP GLY SER ILE LYS GLY LEU SEQRES 1 D 11 LYS VAL LYS VAL TRP GLY SER ILE LYS GLY LEU SEQRES 1 E 11 LYS VAL LYS VAL TRP GLY SER ILE LYS GLY LEU SEQRES 1 F 11 LYS VAL LYS VAL TRP GLY SER ILE LYS GLY LEU SEQRES 1 G 11 LYS VAL LYS VAL TRP GLY SER ILE LYS GLY LEU SEQRES 1 H 11 LYS VAL LYS VAL TRP GLY SER ILE LYS GLY LEU FORMUL 9 HOH *34(H2 O) SHEET 1 AA1 8 VAL A 29 GLY A 33 0 SHEET 2 AA1 8 VAL B 29 SER B 34 -1 O TRP B 32 N LYS A 30 SHEET 3 AA1 8 VAL C 29 ILE C 35 -1 O ILE C 35 N VAL B 29 SHEET 4 AA1 8 VAL D 29 SER D 34 -1 O LYS D 30 N TRP C 32 SHEET 5 AA1 8 VAL E 29 ILE E 35 -1 O VAL E 31 N GLY D 33 SHEET 6 AA1 8 VAL F 29 SER F 34 -1 O LYS F 30 N TRP E 32 SHEET 7 AA1 8 VAL G 29 SER G 34 -1 O GLY G 33 N VAL F 31 SHEET 8 AA1 8 VAL H 29 GLY H 33 -1 O TRP H 32 N LYS G 30 CRYST1 30.890 43.230 70.970 90.00 90.00 90.00 P 21 21 21 32 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 0.032373 0.000000 0.000000 0.00000 SCALE2 0.000000 0.023132 0.000000 0.00000 SCALE3 0.000000 0.000000 0.014090 0.00000