HEADER OXIDOREDUCTASE 04-APR-05 1Z9P TITLE X-RAY STRUCTURE OF A CU-ZN SUPEROXIDE DISMUTASE FROM HAEMOPHILUS TITLE 2 DUCREYI COMPND MOL_ID: 1; COMPND 2 MOLECULE: SUPEROXIDE DISMUTASE [CU-ZN]; COMPND 3 CHAIN: A, B; COMPND 4 FRAGMENT: RESIDUES 45-199; COMPND 5 EC: 1.15.1.1; COMPND 6 ENGINEERED: YES; COMPND 7 OTHER_DETAILS: MATURE PROTEIN WITHOUT BOUND HAEM SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HAEMOPHILUS DUCREYI; SOURCE 3 ORGANISM_TAXID: 730; SOURCE 4 GENE: SODC; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 7 EXPRESSION_SYSTEM_STRAIN: 71/18; SOURCE 8 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 9 EXPRESSION_SYSTEM_PLASMID: PHEN-1 KEYWDS CU-ZN SOD, SOD, METALLOENZYMES, OXIDOREDUCTASE EXPDTA X-RAY DIFFRACTION AUTHOR K.DJINOVIC CARUGO,I.TOEROE REVDAT 4 23-AUG-23 1Z9P 1 REMARK LINK REVDAT 3 26-OCT-11 1Z9P 1 JRNL VERSN REVDAT 2 24-FEB-09 1Z9P 1 VERSN REVDAT 1 12-SEP-06 1Z9P 0 JRNL AUTH I.TORO,C.PETRUTZ,F.PACELLO,M.D'ORAZIO,A.BATTISTONI, JRNL AUTH 2 K.DJINOVIC-CARUGO JRNL TITL STRUCTURAL BASIS OF HEME BINDING IN THE CU,ZN SUPEROXIDE JRNL TITL 2 DISMUTASE FROM HAEMOPHILUS DUCREYI. JRNL REF J.MOL.BIOL. V. 386 406 2009 JRNL REFN ISSN 0022-2836 JRNL PMID 19103206 JRNL DOI 10.1016/J.JMB.2008.12.004 REMARK 2 REMARK 2 RESOLUTION. 1.50 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.2.0001 REMARK 3 AUTHORS : MURSHUDOV,SKUBAK,LEBEDEV,PANNU,STEINER, REMARK 3 : NICHOLLS,WINN,LONG,VAGIN REMARK 3 REMARK 3 REFINEMENT TARGET : MAXIMUM LIKELIHOOD REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.50 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 19.32 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 100.0 REMARK 3 NUMBER OF REFLECTIONS : 44131 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) : 0.172 REMARK 3 R VALUE (WORKING SET) : 0.170 REMARK 3 FREE R VALUE : 0.212 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 2323 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) : 1.50 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.54 REMARK 3 REFLECTION IN BIN (WORKING SET) : 2895 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : NULL REMARK 3 BIN R VALUE (WORKING SET) : 0.2250 REMARK 3 BIN FREE R VALUE SET COUNT : 152 REMARK 3 BIN FREE R VALUE : 0.3060 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 2322 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 4 REMARK 3 SOLVENT ATOMS : 493 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 23.46 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 16.47 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -0.08000 REMARK 3 B22 (A**2) : 0.69000 REMARK 3 B33 (A**2) : -0.35000 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : 0.28000 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED OVERALL COORDINATE ERROR. REMARK 3 ESU BASED ON R VALUE (A): 0.077 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.082 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.053 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 1.442 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.969 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.951 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 2432 ; 0.015 ; 0.021 REMARK 3 BOND LENGTHS OTHERS (A): 2132 ; 0.001 ; 0.020 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 3281 ; 1.539 ; 1.940 REMARK 3 BOND ANGLES OTHERS (DEGREES): 5040 ; 0.832 ; 3.000 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 308 ; 6.332 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 99 ;36.035 ;25.152 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 395 ;12.649 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 4 ;35.064 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 344 ; 0.087 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 2704 ; 0.007 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): 416 ; 0.001 ; 0.020 REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): 459 ; 0.203 ; 0.200 REMARK 3 NON-BONDED CONTACTS OTHERS (A): 2134 ; 0.189 ; 0.200 REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION OTHERS (A): 1330 ; 0.085 ; 0.200 REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): 348 ; 0.198 ; 0.200 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): 30 ; 0.242 ; 0.200 REMARK 3 SYMMETRY VDW OTHERS (A): 52 ; 0.208 ; 0.200 REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): 81 ; 0.349 ; 0.200 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): 1963 ; 1.870 ; 2.000 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): 640 ; 0.301 ; 2.000 REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 2467 ; 2.192 ; 4.000 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 1008 ; 3.066 ; 4.000 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 814 ; 4.098 ; 6.000 REMARK 3 SIDE-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 LONG RANGE B REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 LONG RANGE B OTHER ATOMS (A**2): NULL ; NULL ; NULL 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): 4 ; 7.328 ; 3.000 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 : BABINET MODEL WITH MASK 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 1Z9P COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 07-APR-05. REMARK 100 THE DEPOSITION ID IS D_1000032474. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 10-JAN-01 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 : ELETTRA REMARK 200 BEAMLINE : 5.2R REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.000 REMARK 200 MONOCHROMATOR : DOUBLE-CRYSTAL MONOCHROMATOR IN REMARK 200 NON-DISPERSIVE CONFIGURATION REMARK 200 WITH TWO INTERCHANGEABLE PAIRS REMARK 200 OF CRYSTALS - SI(111) AND SI(220) REMARK 200 OPTICS : MIRRORS REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : MARRESEARCH REMARK 200 INTENSITY-INTEGRATION SOFTWARE : NULL REMARK 200 DATA SCALING SOFTWARE : XDS REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 46454 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.500 REMARK 200 RESOLUTION RANGE LOW (A) : 20.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 0.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 97.4 REMARK 200 DATA REDUNDANCY : 3.930 REMARK 200 R MERGE (I) : 0.05000 REMARK 200 R SYM (I) : 0.05000 REMARK 200 FOR THE DATA SET : 17.9900 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.50 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.59 REMARK 200 COMPLETENESS FOR SHELL (%) : 91.4 REMARK 200 DATA REDUNDANCY IN SHELL : 3.31 REMARK 200 R MERGE FOR SHELL (I) : 0.17800 REMARK 200 R SYM FOR SHELL (I) : 0.17800 REMARK 200 FOR SHELL : 6.620 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: MOLREP REMARK 200 STARTING MODEL: PDB ENTRY 1Z9N REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 45.53 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.26 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: SODIUM CYTRATE, HEPES, PH 7.5, VAPOR REMARK 280 DIFFUSION, HANGING DROP, TEMPERATURE 293.0K 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 35.70500 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 31.99500 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 35.70500 REMARK 290 SMTRY2 4 0.000000 1.000000 0.000000 31.99500 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: THE BIOLOGICAL ASSEMBLY IS A DIMER IN THE ASYMMETRIC UNIT. 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: DIMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 1560 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 13810 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -15.0 KCAL/MOL 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 375 REMARK 375 SPECIAL POSITION REMARK 375 THE FOLLOWING ATOMS ARE FOUND TO BE WITHIN 0.15 ANGSTROMS REMARK 375 OF A SYMMETRY RELATED ATOM AND ARE ASSUMED TO BE ON SPECIAL REMARK 375 POSITIONS. REMARK 375 REMARK 375 ATOM RES CSSEQI REMARK 375 HOH B 264 LIES ON A SPECIAL POSITION. REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS IN SAME ASYMMETRIC UNIT REMARK 500 REMARK 500 THE FOLLOWING ATOMS ARE IN CLOSE CONTACT. REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI DISTANCE REMARK 500 NZ LYS A 99 O HOH A 320 1.60 REMARK 500 O HOH A 242 O HOH A 294 1.72 REMARK 500 O HOH B 231 O HOH B 240 1.74 REMARK 500 O HOH A 236 O HOH B 231 1.75 REMARK 500 O HOH B 252 O HOH B 344 1.90 REMARK 500 O HOH A 246 O HOH A 296 1.95 REMARK 500 NE2 HIS B 124 O HOH B 223 2.00 REMARK 500 O HOH B 290 O HOH B 409 2.09 REMARK 500 NE2 HIS A 64 O HOH B 223 2.11 REMARK 500 O HOH B 327 O HOH B 329 2.12 REMARK 500 O HOH A 278 O HOH B 401 2.12 REMARK 500 O HOH A 300 O HOH A 375 2.13 REMARK 500 O HOH A 296 O HOH B 294 2.13 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS REMARK 500 REMARK 500 THE FOLLOWING ATOMS THAT ARE RELATED BY CRYSTALLOGRAPHIC REMARK 500 SYMMETRY ARE IN CLOSE CONTACT. AN ATOM LOCATED WITHIN 0.15 REMARK 500 ANGSTROMS OF A SYMMETRY RELATED ATOM IS ASSUMED TO BE ON A REMARK 500 SPECIAL POSITION AND IS, THEREFORE, LISTED IN REMARK 375 REMARK 500 INSTEAD OF REMARK 500. ATOMS WITH NON-BLANK ALTERNATE REMARK 500 LOCATION INDICATORS ARE NOT INCLUDED IN THE CALCULATIONS. REMARK 500 REMARK 500 DISTANCE CUTOFF: REMARK 500 2.2 ANGSTROMS FOR CONTACTS NOT INVOLVING HYDROGEN ATOMS REMARK 500 1.6 ANGSTROMS FOR CONTACTS INVOLVING HYDROGEN ATOMS REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI SSYMOP DISTANCE REMARK 500 O HOH A 320 O HOH A 320 2555 1.63 REMARK 500 O HOH A 238 O HOH A 330 2555 2.14 REMARK 500 O HOH B 349 O HOH B 432 2656 2.17 REMARK 500 ND1 HIS A 160 O HOH B 427 4545 2.18 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: COVALENT BOND ANGLES REMARK 500 REMARK 500 THE STEREOCHEMICAL PARAMETERS OF THE FOLLOWING RESIDUES REMARK 500 HAVE VALUES WHICH DEVIATE FROM EXPECTED VALUES BY MORE REMARK 500 THAN 6*RMSD (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 500 IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT: (10X,I3,1X,A3,1X,A1,I4,A1,3(1X,A4,2X),12X,F5.1) REMARK 500 REMARK 500 EXPECTED VALUES PROTEIN: ENGH AND HUBER, 1999 REMARK 500 EXPECTED VALUES NUCLEIC ACID: CLOWNEY ET AL 1996 REMARK 500 REMARK 500 M RES CSSEQI ATM1 ATM2 ATM3 REMARK 500 ASP A 125 CB - CG - OD2 ANGL. DEV. = 5.7 DEGREES REMARK 500 ASP B 83 CB - CG - OD2 ANGL. DEV. = 5.8 DEGREES REMARK 500 ASP B 116 CB - CG - OD2 ANGL. DEV. = 5.8 DEGREES REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: TORSION ANGLES REMARK 500 REMARK 500 TORSION ANGLES OUTSIDE THE EXPECTED RAMACHANDRAN REGIONS: REMARK 500 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 500 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT:(10X,I3,1X,A3,1X,A1,I4,A1,4X,F7.2,3X,F7.2) REMARK 500 REMARK 500 EXPECTED VALUES: GJ KLEYWEGT AND TA JONES (1996). PHI/PSI- REMARK 500 CHOLOGY: RAMACHANDRAN REVISITED. STRUCTURE 4, 1395 - 1400 REMARK 500 REMARK 500 M RES CSSEQI PSI PHI REMARK 500 THR B 129 13.03 -140.20 REMARK 500 REMARK 500 REMARK: NULL 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 CU A 200 CU REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS A 70 ND1 REMARK 620 2 HIS A 72 NE2 142.3 REMARK 620 3 HIS A 151 NE2 99.7 117.4 REMARK 620 N 1 2 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN A 201 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS A 95 ND1 REMARK 620 2 HIS A 104 ND1 102.7 REMARK 620 3 HIS A 113 ND1 104.9 124.8 REMARK 620 4 ASP A 116 OD1 111.5 98.0 114.4 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 CU B 200 CU REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS B 70 ND1 REMARK 620 2 HIS B 72 NE2 145.4 REMARK 620 3 HIS B 151 NE2 98.2 116.0 REMARK 620 N 1 2 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN B 201 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS B 95 ND1 REMARK 620 2 HIS B 104 ND1 102.5 REMARK 620 3 HIS B 113 ND1 104.8 122.3 REMARK 620 4 ASP B 116 OD1 110.4 98.1 117.7 REMARK 620 N 1 2 3 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CU A 200 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ZN A 201 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CU B 200 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ZN B 201 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 2APS RELATED DB: PDB REMARK 900 CU/ZN SUPEROXIDE DISMUTASE FROM ACTINOBACILLUS PLEUROPNEUMONIAE REMARK 900 RELATED ID: 1BZO RELATED DB: PDB REMARK 900 THREE-DIMENSIONAL STRUCTURE OF PROKARYOTIC CU,ZN SUPEROXIDE REMARK 900 DISMUTASE FROM P.LEIOGNATHI, SOLVED BY X-RAY REMARK 900 RELATED ID: 1YAI RELATED DB: PDB REMARK 900 X-RAY STRUCTURE OF A BACTERIAL COPPER,ZINC SUPEROXIDE DISMUTASE DBREF 1Z9P A 23 177 UNP Q59452 SODC_HAEDU 45 199 DBREF 1Z9P B 23 177 UNP Q59452 SODC_HAEDU 45 199 SEQRES 1 A 155 GLU LYS ILE VAL VAL PRO VAL GLN GLN LEU ASP PRO GLN SEQRES 2 A 155 ASN GLY ASN LYS ASP VAL GLY THR VAL GLU ILE THR GLU SEQRES 3 A 155 SER ALA TYR GLY LEU VAL PHE THR PRO LYS LEU HIS ASP SEQRES 4 A 155 LEU ALA HIS GLY LEU HIS GLY PHE HIS ILE HIS GLU LYS SEQRES 5 A 155 PRO SER CYS GLU PRO LYS GLU LYS ASP GLY LYS LEU VAL SEQRES 6 A 155 ALA GLY LEU GLY ALA GLY GLY HIS TRP ASP PRO LYS GLN SEQRES 7 A 155 THR GLN LYS HIS GLY TYR PRO TRP SER ASP ASP ALA HIS SEQRES 8 A 155 MET GLY ASP LEU PRO ALA LEU PHE VAL MET HIS ASP GLY SEQRES 9 A 155 SER ALA THR THR PRO VAL LEU ALA PRO ARG LEU LYS LYS SEQRES 10 A 155 LEU ALA GLU VAL LYS GLY HIS SER LEU MET ILE HIS ALA SEQRES 11 A 155 GLY GLY ASP ASN HIS SER ASP HIS PRO ALA PRO LEU GLY SEQRES 12 A 155 GLY GLY GLY PRO ARG MET ALA CYS GLY VAL ILE LYS SEQRES 1 B 155 GLU LYS ILE VAL VAL PRO VAL GLN GLN LEU ASP PRO GLN SEQRES 2 B 155 ASN GLY ASN LYS ASP VAL GLY THR VAL GLU ILE THR GLU SEQRES 3 B 155 SER ALA TYR GLY LEU VAL PHE THR PRO LYS LEU HIS ASP SEQRES 4 B 155 LEU ALA HIS GLY LEU HIS GLY PHE HIS ILE HIS GLU LYS SEQRES 5 B 155 PRO SER CYS GLU PRO LYS GLU LYS ASP GLY LYS LEU VAL SEQRES 6 B 155 ALA GLY LEU GLY ALA GLY GLY HIS TRP ASP PRO LYS GLN SEQRES 7 B 155 THR GLN LYS HIS GLY TYR PRO TRP SER ASP ASP ALA HIS SEQRES 8 B 155 MET GLY ASP LEU PRO ALA LEU PHE VAL MET HIS ASP GLY SEQRES 9 B 155 SER ALA THR THR PRO VAL LEU ALA PRO ARG LEU LYS LYS SEQRES 10 B 155 LEU ALA GLU VAL LYS GLY HIS SER LEU MET ILE HIS ALA SEQRES 11 B 155 GLY GLY ASP ASN HIS SER ASP HIS PRO ALA PRO LEU GLY SEQRES 12 B 155 GLY GLY GLY PRO ARG MET ALA CYS GLY VAL ILE LYS HET CU A 200 1 HET ZN A 201 1 HET CU B 200 1 HET ZN B 201 1 HETNAM CU COPPER (II) ION HETNAM ZN ZINC ION FORMUL 3 CU 2(CU 2+) FORMUL 4 ZN 2(ZN 2+) FORMUL 7 HOH *493(H2 O) HELIX 1 1 GLY A 89 GLY A 93 5 5 HELIX 2 2 LYS A 139 LYS A 144 1 6 HELIX 3 3 ALA A 162 GLY A 167 5 6 HELIX 4 4 GLY B 89 GLY B 93 5 5 HELIX 5 5 LYS B 139 VAL B 143 5 5 HELIX 6 6 ALA B 162 GLY B 167 5 6 SHEET 1 A 7 PHE A 69 HIS A 72 0 SHEET 2 A 7 HIS A 146 HIS A 151 -1 O MET A 149 N HIS A 70 SHEET 3 A 7 ARG A 170 ILE A 176 -1 O GLY A 174 N LEU A 148 SHEET 4 A 7 ILE A 25 GLN A 31 -1 N GLN A 30 O CYS A 173 SHEET 5 A 7 LYS A 39 SER A 49 -1 O VAL A 44 N VAL A 27 SHEET 6 A 7 GLY A 52 LEU A 59 -1 O LYS A 58 N THR A 43 SHEET 7 A 7 VAL A 132 ALA A 134 -1 O VAL A 132 N PHE A 55 SHEET 1 B 2 GLY A 65 HIS A 67 0 SHEET 2 B 2 LEU A 120 VAL A 122 -1 O VAL A 122 N GLY A 65 SHEET 1 C 2 LYS A 80 LYS A 82 0 SHEET 2 C 2 LYS A 85 VAL A 87 -1 O VAL A 87 N LYS A 80 SHEET 1 D 7 PHE B 69 HIS B 72 0 SHEET 2 D 7 HIS B 146 HIS B 151 -1 O MET B 149 N HIS B 70 SHEET 3 D 7 ARG B 170 ILE B 176 -1 O GLY B 174 N LEU B 148 SHEET 4 D 7 LYS B 24 GLN B 31 -1 N GLN B 30 O CYS B 173 SHEET 5 D 7 LYS B 39 SER B 49 -1 O ILE B 46 N ILE B 25 SHEET 6 D 7 GLY B 52 LEU B 59 -1 O LYS B 58 N THR B 43 SHEET 7 D 7 VAL B 132 ALA B 134 -1 O ALA B 134 N LEU B 53 SHEET 1 E 2 GLY B 65 HIS B 67 0 SHEET 2 E 2 LEU B 120 VAL B 122 -1 O LEU B 120 N HIS B 67 SHEET 1 F 2 LYS B 80 LYS B 82 0 SHEET 2 F 2 LYS B 85 VAL B 87 -1 O LYS B 85 N LYS B 82 SSBOND 1 CYS A 77 CYS A 173 1555 1555 2.06 SSBOND 2 CYS B 77 CYS B 173 1555 1555 2.04 LINK ND1 HIS A 70 CU CU A 200 1555 1555 2.03 LINK NE2 HIS A 72 CU CU A 200 1555 1555 1.99 LINK ND1 HIS A 95 ZN ZN A 201 1555 1555 2.03 LINK ND1 HIS A 104 ZN ZN A 201 1555 1555 2.08 LINK ND1 HIS A 113 ZN ZN A 201 1555 1555 2.05 LINK OD1 ASP A 116 ZN ZN A 201 1555 1555 1.99 LINK NE2 HIS A 151 CU CU A 200 1555 1555 2.04 LINK ND1 HIS B 70 CU CU B 200 1555 1555 1.99 LINK NE2 HIS B 72 CU CU B 200 1555 1555 1.98 LINK ND1 HIS B 95 ZN ZN B 201 1555 1555 2.05 LINK ND1 HIS B 104 ZN ZN B 201 1555 1555 2.08 LINK ND1 HIS B 113 ZN ZN B 201 1555 1555 2.05 LINK OD1 ASP B 116 ZN ZN B 201 1555 1555 1.97 LINK NE2 HIS B 151 CU CU B 200 1555 1555 2.05 CISPEP 1 HIS A 160 PRO A 161 0 -1.21 CISPEP 2 HIS B 160 PRO B 161 0 -1.11 SITE 1 AC1 4 HIS A 70 HIS A 72 HIS A 95 HIS A 151 SITE 1 AC2 4 HIS A 95 HIS A 104 HIS A 113 ASP A 116 SITE 1 AC3 4 HIS B 70 HIS B 72 HIS B 95 HIS B 151 SITE 1 AC4 4 HIS B 95 HIS B 104 HIS B 113 ASP B 116 CRYST1 71.410 63.990 73.970 90.00 118.04 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 0.014004 0.000000 0.007458 0.00000 SCALE2 0.000000 0.015627 0.000000 0.00000 SCALE3 0.000000 0.000000 0.015317 0.00000