HEADER PROTEIN FIBRIL 03-OCT-17 6B79 TITLE CURVED PAIR OF SHEETS FORMED FROM SOD1 RESIDUES 28-38 WITH FAMILIAL TITLE 2 MUTATION G37R. COMPND MOL_ID: 1; COMPND 2 MOLECULE: SUPEROXIDE DISMUTASE [CU-ZN]; COMPND 3 CHAIN: A, B; COMPND 4 SYNONYM: SUPEROXIDE DISMUTASE 1,HSOD1; COMPND 5 EC: 1.15.1.1; 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 AMYLOID FIBRIL, PROTEIN FIBRIL EXPDTA X-RAY DIFFRACTION AUTHOR S.SANGWAN,M.R.SAWAYA,D.S.EISENBERG REVDAT 6 15-NOV-23 6B79 1 LINK REVDAT 5 04-OCT-23 6B79 1 REMARK REVDAT 4 15-JAN-20 6B79 1 REMARK REVDAT 3 20-NOV-19 6B79 1 REMARK REVDAT 2 18-JUL-18 6B79 1 JRNL REVDAT 1 30-MAY-18 6B79 0 JRNL AUTH S.SANGWAN,M.R.SAWAYA,K.A.MURRAY,M.P.HUGHES,D.S.EISENBERG JRNL TITL ATOMIC STRUCTURES OF CORKSCREW-FORMING SEGMENTS OF SOD1 JRNL TITL 2 REVEAL VARIED OLIGOMER CONFORMATIONS. JRNL REF PROTEIN SCI. V. 27 1231 2018 JRNL REFN ESSN 1469-896X JRNL PMID 29453800 JRNL DOI 10.1002/PRO.3391 REMARK 2 REMARK 2 RESOLUTION. 1.80 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : BUSTER 2.10.0 REMARK 3 AUTHORS : BRICOGNE,BLANC,BRANDL,FLENSBURG,KELLER, REMARK 3 : PACIOREK,ROVERSI,SHARFF,SMART,VONRHEIN, REMARK 3 : WOMACK,MATTHEWS,TEN EYCK,TRONRUD REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.80 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 35.73 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 97.9 REMARK 3 NUMBER OF REFLECTIONS : 2327 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) : 0.234 REMARK 3 R VALUE (WORKING SET) : 0.230 REMARK 3 FREE R VALUE : 0.267 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 9.580 REMARK 3 FREE R VALUE TEST SET COUNT : 223 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) : 1.80 REMARK 3 BIN RESOLUTION RANGE LOW (ANGSTROMS) : 2.01 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 97.90 REMARK 3 REFLECTIONS IN BIN (WORKING + TEST SET) : 622 REMARK 3 BIN R VALUE (WORKING + TEST SET) : 0.2764 REMARK 3 REFLECTIONS IN BIN (WORKING SET) : 560 REMARK 3 BIN R VALUE (WORKING SET) : 0.2727 REMARK 3 BIN FREE R VALUE : 0.3159 REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : 9.97 REMARK 3 BIN FREE R VALUE TEST SET COUNT : 62 REMARK 3 ESTIMATED ERROR OF BIN FREE R VALUE : 0.000 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 188 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 27 REMARK 3 SOLVENT ATOMS : 16 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 28.25 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 30.08 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -5.98750 REMARK 3 B22 (A**2) : 7.08830 REMARK 3 B33 (A**2) : -1.10080 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : 7.27710 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM LUZZATI PLOT (A) : 0.298 REMARK 3 DPI (BLOW EQ-10) BASED ON R VALUE (A) : 0.183 REMARK 3 DPI (BLOW EQ-9) BASED ON FREE R VALUE (A) : 0.158 REMARK 3 DPI (CRUICKSHANK) BASED ON R VALUE (A) : 0.168 REMARK 3 DPI (CRUICKSHANK) BASED ON FREE R VALUE (A) : 0.151 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 : 0.909 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.916 REMARK 3 REMARK 3 NUMBER OF GEOMETRIC FUNCTION TERMS DEFINED : 15 REMARK 3 TERM COUNT WEIGHT FUNCTION. REMARK 3 BOND LENGTHS : 219 ; 2.000 ; HARMONIC REMARK 3 BOND ANGLES : 294 ; 2.000 ; HARMONIC REMARK 3 TORSION ANGLES : 80 ; 2.000 ; SINUSOIDAL REMARK 3 TRIGONAL CARBON PLANES : 2 ; 2.000 ; HARMONIC REMARK 3 GENERAL PLANES : 29 ; 5.000 ; HARMONIC REMARK 3 ISOTROPIC THERMAL FACTORS : 219 ; 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 : 22 ; 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 : 274 ; 4.000 ; SEMIHARMONIC REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 BOND LENGTHS (A) : 0.010 REMARK 3 BOND ANGLES (DEGREES) : 1.25 REMARK 3 PEPTIDE OMEGA TORSION ANGLES (DEGREES) : 2.77 REMARK 3 OTHER TORSION ANGLES (DEGREES) : 17.03 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 6B79 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 04-OCT-17. REMARK 100 THE DEPOSITION ID IS D_1000230391. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 03-APR-14 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 7.5 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) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.9792 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 : 2330 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.800 REMARK 200 RESOLUTION RANGE LOW (A) : 35.730 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : -3.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 96.6 REMARK 200 DATA REDUNDANCY : 3.088 REMARK 200 R MERGE (I) : 0.17500 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 4.0600 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.80 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.84 REMARK 200 COMPLETENESS FOR SHELL (%) : 74.1 REMARK 200 DATA REDUNDANCY IN SHELL : 2.40 REMARK 200 R MERGE FOR SHELL (I) : 1.57900 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 0.480 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: PHASER REMARK 200 STARTING MODEL: 5DLI REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 42.06 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.12 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: HEPES PH 7.5, SODIUM CITRATE, 2-METHYL REMARK 280 -2,4-PENTANEDIOL, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 298K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: C 1 2 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,Y,-Z REMARK 290 3555 X+1/2,Y+1/2,Z 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 0.00000 REMARK 290 SMTRY2 2 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 3 1.000000 0.000000 0.000000 28.47000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 5.82000 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 28.47000 REMARK 290 SMTRY2 4 0.000000 1.000000 0.000000 5.82000 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 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 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 0.00000 REMARK 350 BIOMT2 2 0.000000 1.000000 0.000000 11.64000 REMARK 350 BIOMT3 2 0.000000 0.000000 1.000000 0.00000 REMARK 350 BIOMT1 3 -1.000000 0.000000 0.000000 0.00000 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 0.00000 REMARK 350 BIOMT2 4 0.000000 1.000000 0.000000 11.64000 REMARK 350 BIOMT3 4 0.000000 0.000000 -1.000000 0.00000 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue ORA A 101 DBREF 6B79 A 1 11 UNP P00441 SODC_HUMAN 29 39 DBREF 6B79 B 1 11 UNP P00441 SODC_HUMAN 29 39 SEQADV 6B79 LYS A 1 UNP P00441 PRO 29 CONFLICT SEQADV 6B79 ARG A 10 UNP P00441 GLY 38 ENGINEERED MUTATION SEQADV 6B79 LYS B 1 UNP P00441 PRO 29 CONFLICT SEQADV 6B79 ARG B 10 UNP P00441 GLY 38 ENGINEERED MUTATION SEQRES 1 A 11 LYS A8E LYS VAL TRP GLY SER ILE LYS ARG LEU SEQRES 1 B 11 LYS A8E LYS VAL TRP GLY SER ILE LYS ARG LEU MODRES 6B79 A8E A 2 VAL MODIFIED RESIDUE MODRES 6B79 A8E B 2 VAL MODIFIED RESIDUE HET A8E A 2 8 HET A8E B 2 8 HET ORA A 101 27 HETNAM A8E (2S)-2-AMINO-4-BROMOPENT-4-ENOIC ACID HETNAM ORA 7-HYDROXY-8-[(E)-PHENYLDIAZENYL]NAPHTHALENE-1,3- HETNAM 2 ORA DISULFONIC ACID HETSYN ORA ORANGE G FORMUL 1 A8E 2(C5 H8 BR N O2) FORMUL 3 ORA C16 H12 N2 O7 S2 FORMUL 4 HOH *16(H2 O) SHEET 1 AA1 2 VAL A 4 GLY A 6 0 SHEET 2 AA1 2 VAL B 4 GLY B 6 -1 O VAL B 4 N GLY A 6 LINK C LYS A 1 N A8E A 2 1555 1555 1.34 LINK C A8E A 2 N LYS A 3 1555 1555 1.35 LINK C LYS B 1 N A8E B 2 1555 1555 1.33 LINK C A8E B 2 N LYS B 3 1555 1555 1.34 SITE 1 AC1 9 LYS A 3 VAL A 4 TRP A 5 LYS A 9 SITE 2 AC1 9 HOH A 201 HOH A 203 LYS B 3 TRP B 5 SITE 3 AC1 9 GLY B 6 CRYST1 56.940 11.640 44.930 90.00 127.32 90.00 C 1 2 1 8 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 0.017562 0.000000 0.013389 0.00000 SCALE2 0.000000 0.085911 0.000000 0.00000 SCALE3 0.000000 0.000000 0.027987 0.00000