10 20 30 40 50 60 70 80 1DSW - Header ----|----|----|----|----|----|----|----|----|----|----|----|----|----|----|----| Asymmetric UnitHEADER OXIDOREDUCTASE 10-JAN-00 1DSW
TITLE THE SOLUTION STRUCTURE OF A MONOMERIC, REDUCED FORM OF TITLE 2 HUMAN COPPER, ZINC SUPEROXIDE DISMUTASE BEARING THE SAME TITLE 3 CHARGE AS THE NATIVE PROTEIN
CAVEAT 1DSW ONE RESIDUE HAS INCORRECT CHIRALITY
COMPND MOL_ID: 1; COMPND 2 MOLECULE: SUPEROXIDE DISMUTASE (CU-ZN); COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: M4SOD IS A MONOMERIC VARIANT OF HUMAN SOD. THE COMPND 5 MUTANT IS STUDIED IN THE REDUCED FORM, EACH MOLECULE COMPND 6 CONTAINS A CU(I) AND A ZN(II) IONS.; COMPND 7 EC: 1.15.1.1; COMPND 8 ENGINEERED: YES; COMPND 9 MUTATION: YES; COMPND 10 OTHER_DETAILS: COPPER, ZINC SUPEROXIDE DISMUTASE (SOD) IS COMPND 11 AN ENZYME WHICH CATALYZES THE DISMUTATION OF SUPEROXIDE
SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 3 ORGANISM_COMMON: HUMAN; SOURCE 4 ORGANISM_TAXID: 9606; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 7 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 8 EXPRESSION_SYSTEM_PLASMID: PBR322
KEYWDS REDUCED COPPER-ZINC-PROTEIN, BETA BARREL, SINGLE ALPHA KEYWDS 2 HELIX, OXIDOREDUCTASE
EXPDTA SOLUTION NMR
AUTHOR L.BANCI,I.BERTINI,R.DEL CONTE,R.FADIN,S.MANGANI,M.S.VIEZZOLI
REVDAT 2 24-FEB-09 1DSW 1 VERSN REVDAT 1 22-MAR-00 1DSW 0
JRNL AUTH L.BANCI,I.BERTINI,R.DEL CONTE,R.FADIN,S.MANGANI, JRNL AUTH 2 M.S.VIEZZOLI JRNL TITL THE SOLUTION STRUCTURE OF A MONOMERIC, REDUCED JRNL TITL 2 FORM OF HUMAN COPPER,ZINC SUPEROXIDE DISMUTASE JRNL TITL 3 BEARING THE SAME CHARGE AS THE NATIVE PROTEIN. JRNL REF J.BIOL.INORG.CHEM. V. 4 795 1999 JRNL REFN ISSN 0949-8257 JRNL PMID 10631612 JRNL DOI 10.1007/S007750050353
REMARK 1
REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE.
REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : AMBER 4.0 REMARK 3 AUTHORS : PEALRMAN, DA, ET AL. (1991) REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: INTENSITIES OF DIPOLAR REMARK 3 CONNECTIVITIES IN 3D NOESY-HSQC, 3D HNHA AND 2D NOESY WERE REMARK 3 MEASURED WITH THE INTEGRATION ROUTINES OF THE PROGRAM XEASY. REMARK 3 PEAK VOLUMES WERE CONVERTED INTO UPPER DISTANCE LIMITS BY REMARK 3 FOLLOWING THE METHODOLOGY OF THE PROGRAM CALIBA. 3JHNHA REMARK 3 COUPLING CONSTANTS WERE OBTAINED FROM THE RATIO BETWEEN THE REMARK 3 INTENSITY OF THE DIAGONAL PEAK AND THAT OF THE CROSS PEAK OF REMARK 3 THE 3D HNHA EXPERIMENT. THE 3D STRUCTURE WAS CALCULATED WITH REMARK 3 THE PROGRAM DYANA; THE FINAL DYANA FAMILY WAS FORMED BY THE 36 REMARK 3 CONFORMERS WITH THE LOWEST TARGET FUNCTION. REFINEMENT WAS REMARK 3 PERFORMED THROUGH RESTRAINED ENERGY MINIMIZATION WITH THE REMARK 3 SANDER MODULE OF THE PROGRAM AMBER. NOESY CROSS PEAKS WERE REMARK 3 BACK -CALCULATED ON THE FINAL STRUCTURE WITH THE PROGRAM CORMA.
REMARK 4 REMARK 4 1DSW COMPLIES WITH FORMAT V. 3.15, 01-DEC-08
REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 10-FEB-00. REMARK 100 THE RCSB ID CODE IS RCSB010336.
REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 298.00 REMARK 210 PH : 5.00 REMARK 210 IONIC STRENGTH : NULL REMARK 210 PRESSURE : ATMOSPHERIC ATM REMARK 210 SAMPLE CONTENTS : 2MM M4SOD FULLY ENRICHED IN REMARK 210 15N; 20MM PHOSPHATE BUFFER PH REMARK 210 5.0; 90% H2O, 10% D2O. THE REMARK 210 PROTEIN WAS REDUCED WITH REMARK 210 SODIUM ISOASCORBATE UNDER REMARK 210 UNAEROBIC CONDITIONS. REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : 3D 15N NOESY-HSQC, 3D HNHA, REMARK 210 2D NOESY REMARK 210 SPECTROMETER FIELD STRENGTH : 800 MHZ, 600 MHZ REMARK 210 SPECTROMETER MODEL : AVANCE REMARK 210 SPECTROMETER MANUFACTURER : BRUKER REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : XWINNMR 2.1, CALIBA 1.5, REMARK 210 DYANA 1.4, CORMA REMARK 210 METHOD USED : THE NMR STRUCTURE CALCULATION REMARK 210 PROGRAM USED DYANA THAT USES REMARK 210 SIMULATED ANNEALING COMBINED REMARK 210 WITH MOLECULAR DYNAMICS IN REMARK 210 TORSION ANGLE SPACE (TORSION REMARK 210 ANGLE DYNAMICS) REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : NULL REMARK 210 CONFORMERS, NUMBER SUBMITTED : 1 REMARK 210 CONFORMERS, SELECTION CRITERIA : NULL REMARK 210 REMARK 210 BEST REPRESENTATIVE CONFORMER IN THIS ENSEMBLE : 1 REMARK 210 REMARK 210 REMARK: NULL
REMARK 215 REMARK 215 NMR STUDY REMARK 215 THE COORDINATES IN THIS ENTRY WERE GENERATED FROM SOLUTION REMARK 215 NMR DATA. PROTEIN DATA BANK CONVENTIONS REQUIRE THAT REMARK 215 CRYST1 AND SCALE RECORDS BE INCLUDED, BUT THE VALUES ON REMARK 215 THESE RECORDS ARE MEANINGLESS.
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 GLU A 24 -169.37 -174.91 REMARK 500 GLU A 50 -77.11 -163.69 REMARK 500 GLU A 51 -44.96 62.20 REMARK 500 ALA A 55 -50.48 -120.56 REMARK 500 THR A 58 -72.16 -79.06 REMARK 500 SER A 59 43.48 -100.28 REMARK 500 PRO A 62 -175.24 -65.14 REMARK 500 LEU A 67 -80.72 -144.16 REMARK 500 LYS A 75 -53.59 -146.35 REMARK 500 VAL A 81 -49.87 171.44 REMARK 500 SER A 98 95.23 -166.31 REMARK 500 ASP A 109 -67.48 -23.31 REMARK 500 SER A 111 66.85 33.55 REMARK 500 ARG A 115 142.67 -35.83 REMARK 500 ARG A 143 70.72 52.99 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: PLANAR GROUPS REMARK 500 REMARK 500 PLANAR GROUPS IN THE FOLLOWING RESIDUES HAVE A TOTAL REMARK 500 RMS DISTANCE OF ALL ATOMS FROM THE BEST-FIT PLANE REMARK 500 BY MORE THAN AN EXPECTED VALUE OF 6*RMSD, WITH AN REMARK 500 RMSD 0.02 ANGSTROMS, OR AT LEAST ONE ATOM HAS REMARK 500 AN RMSD GREATER THAN THIS VALUE REMARK 500 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 500 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 M RES CSSEQI RMS TYPE REMARK 500 HIS A 43 0.11 SIDE_CHAIN REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CHIRAL CENTERS REMARK 500 REMARK 500 UNEXPECTED CONFIGURATION OF THE FOLLOWING CHIRAL REMARK 500 CENTER(S) USING IMPROPER CA--C--CB--N CHIRALITY REMARK 500 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: (11X,I3,1X,A3,1X,A1,I4,A1,6X,F5.1,6X,A1,10X,A1,3X,A16) REMARK 500 REMARK 500 M RES CSSEQI IMPROPER EXPECTED FOUND DETAILS REMARK 500 ALA A 1 122.0 ALPHA-CARBON 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 154 CU REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS A 46 ND1 REMARK 620 2 HIS A 48 NE2 151.2 REMARK 620 3 HIS A 120 NE2 81.4 110.4 REMARK 620 N 1 2 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN A 155 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS A 63 ND1 REMARK 620 2 HIS A 71 ND1 97.6 REMARK 620 3 HIS A 80 ND1 104.8 118.2 REMARK 620 4 ASP A 83 OD1 85.7 121.8 116.8 REMARK 620 5 ASP A 83 OD2 150.7 91.9 94.8 65.9 REMARK 620 N 1 2 3 4
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 154 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ZN A 155
DBREF 1DSW A 1 153 UNP P00441 SODC_HUMAN 2 154
SEQRES 1 A 153 ALA THR LYS ALA VAL ALA VAL LEU LYS GLY ASP GLY PRO SEQRES 2 A 153 VAL GLN GLY ILE ILE ASN PHE GLU GLN LYS GLU SER ASN SEQRES 3 A 153 GLY PRO VAL LYS VAL TRP GLY SER ILE LYS GLY LEU THR SEQRES 4 A 153 GLU GLY LEU HIS GLY PHE HIS VAL HIS GLU GLU GLU ASP SEQRES 5 A 153 ASN THR ALA GLY CYS THR SER ALA GLY PRO HIS PHE ASN SEQRES 6 A 153 PRO LEU SER ARG LYS HIS GLY GLY PRO LYS ASP GLU GLU SEQRES 7 A 153 ARG HIS VAL GLY ASP LEU GLY ASN VAL THR ALA ASP LYS SEQRES 8 A 153 ASP GLY VAL ALA ASP VAL SER ILE GLU ASP SER VAL ILE SEQRES 9 A 153 SER LEU SER GLY ASP HIS SER ILE ILE GLY ARG THR LEU SEQRES 10 A 153 VAL VAL HIS GLU LYS ALA ASP ASP LEU GLY LYS GLY GLY SEQRES 11 A 153 ASN GLU GLU SER THR LYS THR GLY ASN ALA GLY SER ARG SEQRES 12 A 153 LEU ALA CYS GLY LYS ILE GLY LYS ALA GLN
HET CU A 154 1 HET ZN A 155 1
HETNAM CU COPPER (II) ION HETNAM ZN ZINC ION
FORMUL 2 CU CU 2+ FORMUL 3 ZN ZN 2+
HELIX 1 1 ASN A 131 GLY A 138 1 8
SHEET 1 A 5 VAL A 94 ASP A 101 0 SHEET 2 A 5 VAL A 29 LYS A 36 -1 N VAL A 29 O ASP A 101 SHEET 3 A 5 GLN A 15 GLN A 22 -1 O GLN A 15 N LYS A 36 SHEET 4 A 5 LYS A 3 LYS A 9 -1 O ALA A 4 N PHE A 20 SHEET 5 A 5 ILE A 149 LYS A 151 -1 N GLY A 150 O VAL A 5 SHEET 1 B 4 ASP A 83 ALA A 89 0 SHEET 2 B 4 GLY A 41 HIS A 48 -1 N GLY A 41 O ALA A 89 SHEET 3 B 4 THR A 116 VAL A 119 -1 O THR A 116 N HIS A 48 SHEET 4 B 4 ALA A 145 CYS A 146 -1 O ALA A 145 N VAL A 119
SSBOND 1 CYS A 57 CYS A 146 1555 1555 2.05
LINK ND1 HIS A 46 CU CU A 154 1555 1555 2.13 LINK NE2 HIS A 48 CU CU A 154 1555 1555 2.01 LINK ND1 HIS A 63 ZN ZN A 155 1555 1555 2.10 LINK ND1 HIS A 71 ZN ZN A 155 1555 1555 2.10 LINK ND1 HIS A 80 ZN ZN A 155 1555 1555 2.14 LINK OD1 ASP A 83 ZN ZN A 155 1555 1555 2.03 LINK OD2 ASP A 83 ZN ZN A 155 1555 1555 1.99 LINK NE2 HIS A 120 CU CU A 154 1555 1555 2.18
SITE 1 AC1 5 HIS A 46 HIS A 48 HIS A 63 VAL A 118 SITE 2 AC1 5 HIS A 120 SITE 1 AC2 4 HIS A 63 HIS A 71 HIS A 80 ASP A 83
CRYST1 1.000 1.000 1.000 90.00 90.00 90.00 P 1 1
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 1.000000 0.000000 0.000000 0.00000
SCALE2 0.000000 1.000000 0.000000 0.00000
SCALE3 0.000000 0.000000 1.000000 0.00000