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 <I/SIGMA(I)> 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 <I/SIGMA(I)> 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
(ATOM LINES ARE NOT SHOWN.)
END
