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 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,VAGIN,DODSON 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) : 23.45 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 SIDE-CHAIN BOND REFINED ATOMS (A**2): 1008 ; 3.066 ; 4.000 REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 814 ; 4.098 ; 6.000 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. 3.15, 01-DEC-08 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 07-APR-05. REMARK 100 THE RCSB ID CODE IS RCSB032474. 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 WITH REMARK 200 TWO INTERCHANGEABLE PAIRS OF REMARK 200 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 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 446 DISTANCE = 6.50 ANGSTROMS REMARK 525 HOH B 441 DISTANCE = 5.54 ANGSTROMS 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 REMARK 900 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 REMARK 900 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 NE2 HIS A 151 CU CU A 200 1555 1555 2.04 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 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 NE2 HIS B 151 CU CU B 200 1555 1555 2.05 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 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 MASTER 408 0 4 6 22 0 4 6 0 0 0 24 END