HEADER OXIDOREDUCTASE 27-JUN-97 1ESO TITLE MONOMERIC CU,ZN SUPEROXIDE DISMUTASE FROM ESCHERICHIA COLI COMPND MOL_ID: 1; COMPND 2 MOLECULE: CU, ZN SUPEROXIDE DISMUTASE; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: SOD; COMPND 5 EC: 1.15.1.1; COMPND 6 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: ESCHERICHIA COLI; SOURCE 3 ORGANISM_TAXID: 562; SOURCE 4 STRAIN: BMH 71-18; SOURCE 5 CELLULAR_LOCATION: PERIPLASM; SOURCE 6 GENE: SODC; SOURCE 7 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 8 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS OXIDOREDUCTASE, CU, ZN SUPEROXIDE DISMUTASE, MONOMERIC SUPEROXIDE KEYWDS 2 DISMUTASE, COPPER ENZYMES, ENZYME EVOLUTION, X-RAY CRYSTAL STRUCTURE EXPDTA X-RAY DIFFRACTION AUTHOR A.PESCE,C.CAPASSO,A.BATTISTONI,S.FOLCARELLI,G.ROTILIO,A.DESIDERI, AUTHOR 2 M.BOLOGNESI REVDAT 3 03-APR-24 1ESO 1 REMARK LINK REVDAT 2 24-FEB-09 1ESO 1 VERSN REVDAT 1 01-JUL-98 1ESO 0 JRNL AUTH A.PESCE,C.CAPASSO,A.BATTISTONI,S.FOLCARELLI,G.ROTILIO, JRNL AUTH 2 A.DESIDERI,M.BOLOGNESI JRNL TITL UNIQUE STRUCTURAL FEATURES OF THE MONOMERIC CU,ZN SUPEROXIDE JRNL TITL 2 DISMUTASE FROM ESCHERICHIA COLI, REVEALED BY X-RAY JRNL TITL 3 CRYSTALLOGRAPHY. JRNL REF J.MOL.BIOL. V. 274 408 1997 JRNL REFN ISSN 0022-2836 JRNL PMID 9405149 JRNL DOI 10.1006/JMBI.1997.1400 REMARK 2 REMARK 2 RESOLUTION. 2.00 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : TNT 5B REMARK 3 AUTHORS : TRONRUD,TEN EYCK,MATTHEWS REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.00 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 26.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 96.4 REMARK 3 NUMBER OF REFLECTIONS : 9057 REMARK 3 REMARK 3 USING DATA ABOVE SIGMA CUTOFF. REMARK 3 CROSS-VALIDATION METHOD : NULL REMARK 3 FREE R VALUE TEST SET SELECTION : NULL REMARK 3 R VALUE (WORKING + TEST SET) : NULL REMARK 3 R VALUE (WORKING SET) : 0.168 REMARK 3 FREE R VALUE : 0.260 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 433 REMARK 3 REMARK 3 USING ALL DATA, NO SIGMA CUTOFF. REMARK 3 R VALUE (WORKING + TEST SET, NO CUTOFF) : NULL REMARK 3 R VALUE (WORKING SET, NO CUTOFF) : 0.1680 REMARK 3 FREE R VALUE (NO CUTOFF) : 0.263 REMARK 3 FREE R VALUE TEST SET SIZE (%, NO CUTOFF) : 5.00 REMARK 3 FREE R VALUE TEST SET COUNT (NO CUTOFF) : 433 REMARK 3 TOTAL NUMBER OF REFLECTIONS (NO CUTOFF) : 8624 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 1103 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 2 REMARK 3 SOLVENT ATOMS : 75 REMARK 3 REMARK 3 WILSON B VALUE (FROM FCALC, A**2) : NULL REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. RMS WEIGHT COUNT REMARK 3 BOND LENGTHS (A) : 0.018 ; 6.000 ; 1125 REMARK 3 BOND ANGLES (DEGREES) : 2.780 ; 10.500; 1510 REMARK 3 TORSION ANGLES (DEGREES) : 19.360; 0.000 ; 695 REMARK 3 PSEUDOROTATION ANGLES (DEGREES) : NULL ; NULL ; NULL REMARK 3 TRIGONAL CARBON PLANES (A) : 0.018 ; 8.500 ; 32 REMARK 3 GENERAL PLANES (A) : 0.019 ; 28.000; 165 REMARK 3 ISOTROPIC THERMAL FACTORS (A**2) : 4.700 ; 7.000 ; 1125 REMARK 3 NON-BONDED CONTACTS (A) : 0.062 ; 0.062 ; 13 REMARK 3 REMARK 3 INCORRECT CHIRAL-CENTERS (COUNT) : NULL REMARK 3 REMARK 3 BULK SOLVENT MODELING. REMARK 3 METHOD USED : TNT REMARK 3 KSOL : 0.76 REMARK 3 BSOL : 103.3 REMARK 3 REMARK 3 RESTRAINT LIBRARIES. REMARK 3 STEREOCHEMISTRY : TNT: ENGH-HUBER REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS : TNT BCORREL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 1ESO COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY BNL. REMARK 100 THE DEPOSITION ID IS D_1000173152. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 07-APR-96 REMARK 200 TEMPERATURE (KELVIN) : 295 REMARK 200 PH : 8.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : N REMARK 200 RADIATION SOURCE : ROTATING ANODE REMARK 200 BEAMLINE : NULL REMARK 200 X-RAY GENERATOR MODEL : RIGAKU RUH2R REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.5418 REMARK 200 MONOCHROMATOR : GRAPHITE(002) REMARK 200 OPTICS : PINHOLE COLLIMATOR REMARK 200 REMARK 200 DETECTOR TYPE : IMAGE PLATE REMARK 200 DETECTOR MANUFACTURER : RIGAKU RAXIS IIC REMARK 200 INTENSITY-INTEGRATION SOFTWARE : MOSFLM, ROTAVATA, AGROVATA REMARK 200 DATA SCALING SOFTWARE : CCP4 (AGROVATA, ROTAVATA REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 9044 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.000 REMARK 200 RESOLUTION RANGE LOW (A) : 26.300 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 0.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 96.4 REMARK 200 DATA REDUNDANCY : 3.100 REMARK 200 R MERGE (I) : 0.06000 REMARK 200 R SYM (I) : 0.06000 REMARK 200 FOR THE DATA SET : 17.0000 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) : 2.10 REMARK 200 COMPLETENESS FOR SHELL (%) : 87.0 REMARK 200 DATA REDUNDANCY IN SHELL : 2.80 REMARK 200 R MERGE FOR SHELL (I) : 0.18000 REMARK 200 R SYM FOR SHELL (I) : 0.07000 REMARK 200 FOR SHELL : 3.500 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: NULL REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: AMORE REMARK 200 STARTING MODEL: SUPEROXIDE DISMUTASE FROM P.LEIOGNATHI, SOLVED BY REMARK 200 SIRAS IN THE DEPOSITORS' LAB REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 40.00 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.10 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: PROTEIN WAS CRYSTALLIZED FROM 30% PEG REMARK 280 4000, 0.2 M MGCL2, 0.1 M TRIS, PH 8.5 REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 1 21 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,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 26.20000 REMARK 290 SMTRY3 2 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: MONOMERIC REMARK 350 APPLY THE FOLLOWING TO CHAINS: A 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 475 REMARK 475 ZERO OCCUPANCY RESIDUES REMARK 475 THE FOLLOWING RESIDUES WERE MODELED WITH ZERO OCCUPANCY. REMARK 475 THE LOCATION AND PROPERTIES OF THESE RESIDUES MAY NOT REMARK 475 BE RELIABLE. (M=MODEL NUMBER; RES=RESIDUE NAME; REMARK 475 C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE) REMARK 475 M RES C SSEQI REMARK 475 LYS A 54A REMARK 475 ASP A 54B REMARK 475 GLY A 54C REMARK 480 REMARK 480 ZERO OCCUPANCY ATOM REMARK 480 THE FOLLOWING RESIDUES HAVE ATOMS MODELED WITH ZERO REMARK 480 OCCUPANCY. THE LOCATION AND PROPERTIES OF THESE ATOMS REMARK 480 MAY NOT BE RELIABLE. (M=MODEL NUMBER; RES=RESIDUE NAME; REMARK 480 C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE): REMARK 480 M RES C SSEQI ATOMS REMARK 480 GLU A 4 CG CD OE1 OE2 REMARK 480 LYS A 5 CG CD CE NZ REMARK 480 GLU A 7 CG CD OE1 OE2 REMARK 480 GLN A 10D CG CD OE1 NE2 REMARK 480 GLU A 40 CG CD OE1 OE2 REMARK 480 LYS A 48 CE NZ REMARK 480 THR A 54 CA C O CB OG1 CG2 REMARK 480 LYS A 54D CB CG CD CE NZ REMARK 480 GLN A 65 CD OE1 NE2 REMARK 480 ASN A 66 OD1 REMARK 480 ASN A 89 OD1 REMARK 480 ASP A 108 OD2 REMARK 480 LYS A 113 NZ REMARK 480 LYS A 133 CD CE NZ REMARK 480 GLU A 140 CG CD OE1 OE2 REMARK 480 LYS A 148 CG CD CE NZ 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 MET A 124 CG - SD - CE ANGL. DEV. = 10.0 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 ASP A 54B 61.43 124.07 REMARK 500 LYS A 54D -170.12 161.97 REMARK 500 ASP A 63 67.95 -158.82 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 150 CU REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS A 44 ND1 REMARK 620 2 HIS A 46 NE2 148.8 REMARK 620 3 HIS A 61 NE2 72.7 96.8 REMARK 620 4 HIS A 118 NE2 97.6 111.7 126.6 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN A 149 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS A 61 ND1 REMARK 620 2 HIS A 69 ND1 108.8 REMARK 620 3 HIS A 78 ND1 107.4 113.3 REMARK 620 4 ASP A 81 OD1 115.3 106.9 105.4 REMARK 620 N 1 2 3 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: CUL REMARK 800 EVIDENCE_CODE: UNKNOWN REMARK 800 SITE_DESCRIPTION: CU LIGANDS. REMARK 800 REMARK 800 SITE_IDENTIFIER: ZNL REMARK 800 EVIDENCE_CODE: UNKNOWN REMARK 800 SITE_DESCRIPTION: ZN LIGANDS. REMARK 800 REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ZN A 149 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CU A 150 DBREF 1ESO A 2 148 UNP P53635 SODC_ECOLI 20 173 SEQRES 1 A 154 ALA SER GLU LYS VAL GLU MET ASN LEU VAL THR SER GLN SEQRES 2 A 154 GLY VAL GLY GLN SER ILE GLY SER VAL THR ILE THR GLU SEQRES 3 A 154 THR ASP LYS GLY LEU GLU PHE SER PRO ASP LEU LYS ALA SEQRES 4 A 154 LEU PRO PRO GLY GLU HIS GLY PHE HIS ILE HIS ALA LYS SEQRES 5 A 154 GLY SER CYS GLN PRO ALA THR LYS ASP GLY LYS ALA SER SEQRES 6 A 154 ALA ALA GLU SER ALA GLY GLY HIS LEU ASP PRO GLN ASN SEQRES 7 A 154 THR GLY LYS HIS GLU GLY PRO GLU GLY ALA GLY HIS LEU SEQRES 8 A 154 GLY ASP LEU PRO ALA LEU VAL VAL ASN ASN ASP GLY LYS SEQRES 9 A 154 ALA THR ASP ALA VAL ILE ALA PRO ARG LEU LYS SER LEU SEQRES 10 A 154 ASP GLU ILE LYS ASP LYS ALA LEU MET VAL HIS VAL GLY SEQRES 11 A 154 GLY ASP ASN MET SER ASP GLN PRO LYS PRO LEU GLY GLY SEQRES 12 A 154 GLY GLY GLU ARG TYR ALA CYS GLY VAL ILE LYS HET ZN A 149 1 HET CU A 150 1 HETNAM ZN ZINC ION HETNAM CU COPPER (II) ION FORMUL 2 ZN ZN 2+ FORMUL 3 CU CU 2+ FORMUL 4 HOH *75(H2 O) HELIX 1 1 ALA A 55 GLY A 59 5 5 HELIX 2 2 SER A 104 LYS A 111 5 6 HELIX 3 3 PRO A 134 GLY A 137 5 4 SHEET 1 A 4 VAL A 97 ALA A 99 0 SHEET 2 A 4 GLY A 26 LEU A 33 -1 N PHE A 29 O VAL A 97 SHEET 3 A 4 GLY A 10E THR A 23 -1 N THR A 23 O GLY A 26 SHEET 4 A 4 SER A 3 THR A 10B-1 N MET A 8 O ILE A 15 SHEET 1 B 2 GLY A 39 HIS A 46 0 SHEET 2 B 2 LEU A 85 VAL A 87 -1 N VAL A 87 O GLY A 39 SHEET 1 C 2 LYS A 113 HIS A 118 0 SHEET 2 C 2 ARG A 141 ILE A 147 -1 N ILE A 147 O LYS A 113 SSBOND 1 CYS A 50A CYS A 144 1555 1555 1.99 LINK ND1 HIS A 44 CU CU A 150 1555 1555 2.19 LINK NE2 HIS A 46 CU CU A 150 1555 1555 2.09 LINK ND1 HIS A 61 ZN ZN A 149 1555 1555 2.14 LINK NE2 HIS A 61 CU CU A 150 1555 1555 2.65 LINK ND1 HIS A 69 ZN ZN A 149 1555 1555 1.98 LINK ND1 HIS A 78 ZN ZN A 149 1555 1555 1.93 LINK OD1 ASP A 81 ZN ZN A 149 1555 1555 2.07 LINK NE2 HIS A 118 CU CU A 150 1555 1555 2.11 CISPEP 1 GLN A 131 PRO A 132 0 2.33 SITE 1 CUL 4 HIS A 44 HIS A 46 HIS A 61 HIS A 118 SITE 1 ZNL 4 HIS A 61 HIS A 69 HIS A 78 ASP A 81 SITE 1 AC1 4 HIS A 61 HIS A 69 HIS A 78 ASP A 81 SITE 1 AC2 4 HIS A 44 HIS A 46 HIS A 61 HIS A 118 CRYST1 33.000 52.400 43.200 90.00 111.20 90.00 P 1 21 1 2 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 0.030303 0.000000 0.011754 0.00000 SCALE2 0.000000 0.019084 0.000000 0.00000 SCALE3 0.000000 0.000000 0.024828 0.00000