HEADER OXIDOREDUCTASE 19-MAY-05 1ZRR TITLE RESIDUAL DIPOLAR COUPLING REFINEMENT OF ACIREDUCTONE DIOXYGENASE FROM TITLE 2 KLEBSIELLA COMPND MOL_ID: 1; COMPND 2 MOLECULE: E-2/E-2' PROTEIN; COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: KLEBSIELLA OXYTOCA; SOURCE 3 ORGANISM_TAXID: 571; SOURCE 4 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3); SOURCE 5 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 6 EXPRESSION_SYSTEM_STRAIN: BL21(DE3); SOURCE 7 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 8 EXPRESSION_SYSTEM_PLASMID: PET3A KEYWDS NICKEL, CUPIN, BETA HELIX, METHIONINE SALVAGE, OXIDOREDUCTASE EXPDTA SOLUTION NMR NUMMDL 17 AUTHOR T.C.POCHAPSKY,S.S.POCHAPSKY,T.JU,C.HOEFLER,J.LIANG REVDAT 6 22-MAY-24 1ZRR 1 REMARK REVDAT 5 02-MAR-22 1ZRR 1 REMARK LINK REVDAT 4 24-FEB-09 1ZRR 1 VERSN REVDAT 3 24-OCT-06 1ZRR 1 SPRSDE REVDAT 2 14-MAR-06 1ZRR 1 JRNL REVDAT 1 06-DEC-05 1ZRR 0 SPRSDE 24-OCT-06 1ZRR 1M4O JRNL AUTH T.C.POCHAPSKY,S.S.POCHAPSKY,T.JU,C.HOEFLER,J.LIANG JRNL TITL A REFINED MODEL FOR THE STRUCTURE OF ACIREDUCTONE JRNL TITL 2 DIOXYGENASE FROM KLEBSIELLA ATCC 8724 INCORPORATING RESIDUAL JRNL TITL 3 DIPOLAR COUPLINGS JRNL REF J.BIOMOL.NMR V. 34 117 2006 JRNL REFN ISSN 0925-2738 JRNL PMID 16518698 JRNL DOI 10.1007/S10858-005-5735-8 REMARK 1 REMARK 1 REFERENCE 1 REMARK 1 AUTH T.C.POCHAPSKY,S.S.POCHAPSKY,T.JU,H.MO,F.AL-MJENI,M.J.MARONEY REMARK 1 TITL MODELING AND EXPERIMENT YIELDS THE STRUCTURE OF ACIREDUCTONE REMARK 1 TITL 2 DIOXYGENASE FROM KLEBSIELLA PNEUMONIAE REMARK 1 REF NAT.STRUCT.BIOL. V. 9 966 2002 REMARK 1 REFN ISSN 1072-8368 REMARK 1 PMID 12402029 REMARK 1 DOI 10.1038/NSB863 REMARK 1 REFERENCE 2 REMARK 1 AUTH Y.DAI,T.C.POCHAPSKY,R.H.ABELES REMARK 1 TITL MECHANISTIC STUDIES OF TWO DIOXYGENASES FROM THE METHIONINE REMARK 1 TITL 2 SALVAGE PATHWAY OF KLEBSIELLA PNEUMONIAE REMARK 1 REF BIOCHEMISTRY V. 40 6379 2001 REMARK 1 REFN ISSN 0006-2960 REMARK 1 PMID 11371200 REMARK 1 DOI 10.1021/BI010110Y REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : X-PLOR 2.10 REMARK 3 AUTHORS : BRUNGER REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: REMARK 3 METAL BINDING SITE MODELED FROM XAFS DATA, PARAMAGNETICALLY REMARK 3 BROADENED BACKBONE RESIDUES MODELED FROM REMARK 3 PDB ENTRY 1VR3 (ARD HOMOLOGUE FROM MUS MUSCULUS). REMARK 4 REMARK 4 1ZRR COMPLIES WITH FORMAT V. 3.15, 01-DEC-08 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 26-MAY-05. REMARK 100 THE DEPOSITION ID IS D_1000033041. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : NULL REMARK 210 PH : NULL REMARK 210 IONIC STRENGTH : NULL REMARK 210 PRESSURE : NULL REMARK 210 SAMPLE CONTENTS : 1 MM ARD 15N LABELED IN 5% REMARK 210 ORIENTING MEDIUM (EITHER REMARK 210 FILAMENTOUS PHAGE OR C12E5 REMARK 210 POLYMER) PH 7.4, 20 MM KPI; 90/ REMARK 210 10 H2O/D2O REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : NULL REMARK 210 SPECTROMETER FIELD STRENGTH : 600 MHZ REMARK 210 SPECTROMETER MODEL : INOVA REMARK 210 SPECTROMETER MANUFACTURER : VARIAN REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : NULL REMARK 210 METHOD USED : COMBINED TORSIONAL AND CARTESIAN REMARK 210 DYNAMICS SIMULATED ANNEALING REMARK 210 WITH RESIDUAL DIPOLAR COUPLINGS, REMARK 210 NOE, CHEMICAL SHIFT AND DIHEDRAL REMARK 210 RESTRAINTS REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : NULL REMARK 210 CONFORMERS, NUMBER SUBMITTED : 17 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 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 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS 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 HH12 ARG A 89 OE2 GLU A 90 1.46 REMARK 500 O PRO A 159 H TRP A 162 1.53 REMARK 500 O LEU A 28 H LYS A 31 1.55 REMARK 500 O GLN A 58 H ASP A 62 1.56 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 1 GLN A 12 4.99 -69.63 REMARK 500 1 SER A 77 101.69 -170.13 REMARK 500 1 ALA A 80 2.21 -60.66 REMARK 500 1 HIS A 96 -167.26 -175.90 REMARK 500 1 ASP A 119 79.26 -105.36 REMARK 500 1 ASN A 129 -4.00 -58.68 REMARK 500 1 HIS A 137 10.40 91.94 REMARK 500 1 TRP A 141 -149.76 -136.14 REMARK 500 1 PHE A 142 125.00 -175.08 REMARK 500 1 PRO A 148 40.24 -103.36 REMARK 500 1 ASN A 149 72.32 81.75 REMARK 500 1 GLU A 160 -13.79 -43.98 REMARK 500 1 ALA A 164 -72.67 -57.36 REMARK 500 1 SER A 173 -2.20 -54.54 REMARK 500 2 LEU A 3 114.43 -160.06 REMARK 500 2 GLN A 71 -89.55 -57.21 REMARK 500 2 ASP A 74 -167.42 -174.70 REMARK 500 2 HIS A 96 -165.60 -174.92 REMARK 500 2 ASP A 119 79.11 -109.32 REMARK 500 2 ASN A 129 -3.03 -58.76 REMARK 500 2 HIS A 137 3.92 95.43 REMARK 500 2 TRP A 141 -153.78 -130.06 REMARK 500 2 PHE A 142 125.01 -170.78 REMARK 500 2 ASN A 149 63.79 81.79 REMARK 500 2 GLU A 160 -13.53 -45.92 REMARK 500 2 ALA A 164 -75.54 -66.78 REMARK 500 2 SER A 173 -3.09 -52.46 REMARK 500 3 GLN A 12 7.86 -69.62 REMARK 500 3 GLN A 71 -87.48 -63.20 REMARK 500 3 SER A 77 102.99 -169.56 REMARK 500 3 ALA A 80 1.38 -62.42 REMARK 500 3 HIS A 96 -169.26 -173.17 REMARK 500 3 ASP A 119 79.20 -103.80 REMARK 500 3 ASN A 129 -4.27 -57.12 REMARK 500 3 HIS A 137 11.21 91.31 REMARK 500 3 TRP A 141 -146.94 -134.53 REMARK 500 3 PHE A 142 126.86 -177.90 REMARK 500 3 PRO A 148 40.95 -103.12 REMARK 500 3 ASN A 149 71.71 81.79 REMARK 500 3 GLU A 160 -15.49 -44.09 REMARK 500 3 ALA A 164 -71.10 -66.35 REMARK 500 3 SER A 173 -2.95 -54.62 REMARK 500 4 GLN A 71 -89.05 -57.74 REMARK 500 4 SER A 77 100.06 -167.63 REMARK 500 4 ALA A 80 0.26 -55.97 REMARK 500 4 HIS A 96 -169.24 -173.96 REMARK 500 4 ASP A 119 79.93 -106.19 REMARK 500 4 ASN A 129 -3.32 -58.35 REMARK 500 4 HIS A 137 10.20 92.95 REMARK 500 4 TRP A 141 -147.16 -133.71 REMARK 500 REMARK 500 THIS ENTRY HAS 227 RAMACHANDRAN OUTLIERS. 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 1 ARG A 34 0.17 SIDE CHAIN REMARK 500 1 ARG A 42 0.26 SIDE CHAIN REMARK 500 1 ARG A 79 0.31 SIDE CHAIN REMARK 500 1 ARG A 89 0.31 SIDE CHAIN REMARK 500 1 ARG A 104 0.28 SIDE CHAIN REMARK 500 1 ARG A 154 0.26 SIDE CHAIN REMARK 500 1 ARG A 177 0.27 SIDE CHAIN REMARK 500 2 ARG A 34 0.27 SIDE CHAIN REMARK 500 2 ARG A 37 0.27 SIDE CHAIN REMARK 500 2 ARG A 42 0.31 SIDE CHAIN REMARK 500 2 ARG A 79 0.28 SIDE CHAIN REMARK 500 2 ARG A 89 0.29 SIDE CHAIN REMARK 500 2 ARG A 104 0.24 SIDE CHAIN REMARK 500 2 ARG A 154 0.30 SIDE CHAIN REMARK 500 2 ARG A 177 0.15 SIDE CHAIN REMARK 500 3 ARG A 34 0.28 SIDE CHAIN REMARK 500 3 ARG A 37 0.23 SIDE CHAIN REMARK 500 3 ARG A 42 0.20 SIDE CHAIN REMARK 500 3 ARG A 79 0.15 SIDE CHAIN REMARK 500 3 ARG A 89 0.30 SIDE CHAIN REMARK 500 3 ARG A 104 0.12 SIDE CHAIN REMARK 500 3 ARG A 154 0.31 SIDE CHAIN REMARK 500 3 ARG A 177 0.26 SIDE CHAIN REMARK 500 4 ARG A 34 0.31 SIDE CHAIN REMARK 500 4 ARG A 37 0.21 SIDE CHAIN REMARK 500 4 ARG A 42 0.28 SIDE CHAIN REMARK 500 4 ARG A 79 0.28 SIDE CHAIN REMARK 500 4 ARG A 89 0.31 SIDE CHAIN REMARK 500 4 ARG A 104 0.31 SIDE CHAIN REMARK 500 4 ARG A 154 0.32 SIDE CHAIN REMARK 500 4 ARG A 177 0.31 SIDE CHAIN REMARK 500 5 ARG A 34 0.28 SIDE CHAIN REMARK 500 5 ARG A 37 0.31 SIDE CHAIN REMARK 500 5 ARG A 42 0.22 SIDE CHAIN REMARK 500 5 ARG A 79 0.32 SIDE CHAIN REMARK 500 5 ARG A 89 0.28 SIDE CHAIN REMARK 500 5 ARG A 104 0.18 SIDE CHAIN REMARK 500 5 ARG A 154 0.24 SIDE CHAIN REMARK 500 5 ARG A 177 0.20 SIDE CHAIN REMARK 500 6 ARG A 34 0.25 SIDE CHAIN REMARK 500 6 ARG A 42 0.31 SIDE CHAIN REMARK 500 6 ARG A 79 0.30 SIDE CHAIN REMARK 500 6 ARG A 89 0.13 SIDE CHAIN REMARK 500 6 ARG A 104 0.16 SIDE CHAIN REMARK 500 6 ARG A 154 0.08 SIDE CHAIN REMARK 500 6 ARG A 177 0.17 SIDE CHAIN REMARK 500 7 ARG A 34 0.32 SIDE CHAIN REMARK 500 7 ARG A 42 0.23 SIDE CHAIN REMARK 500 7 ARG A 79 0.32 SIDE CHAIN REMARK 500 7 ARG A 89 0.29 SIDE CHAIN REMARK 500 REMARK 500 THIS ENTRY HAS 130 PLANE DEVIATIONS. 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 NI A 180 NI REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS A 96 NE2 REMARK 620 2 HIS A 98 NE2 91.0 REMARK 620 3 GLU A 102 OE1 179.0 90.0 REMARK 620 4 HIS A 140 NE2 90.6 90.8 89.4 REMARK 620 5 HOH A 181 O 90.0 89.6 90.1 179.3 REMARK 620 6 HOH A 182 O 89.5 179.1 89.5 89.8 89.8 REMARK 620 N 1 2 3 4 5 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE NI A 180 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 1M4O RELATED DB: PDB REMARK 900 NMR STRUCTURE OF ACIREDUCTONE DIOXYGENASE FROM KLEBSIELLA DBREF 1ZRR A 1 179 UNP Q9ZFE7 Q9ZFE7_KLEOX 1 179 SEQRES 1 A 179 SER ALA LEU THR ILE PHE SER VAL LYS ASP PRO GLN ASN SEQRES 2 A 179 SER LEU TRP HIS SER THR ASN ALA GLU GLU ILE GLN GLN SEQRES 3 A 179 GLN LEU ASN ALA LYS GLY VAL ARG PHE GLU ARG TRP GLN SEQRES 4 A 179 ALA ASP ARG ASP LEU GLY ALA ALA PRO THR ALA GLU THR SEQRES 5 A 179 VAL ILE ALA ALA TYR GLN HIS ALA ILE ASP LYS LEU VAL SEQRES 6 A 179 ALA GLU LYS GLY TYR GLN SER TRP ASP VAL ILE SER LEU SEQRES 7 A 179 ARG ALA ASP ASN PRO GLN LYS GLU ALA LEU ARG GLU LYS SEQRES 8 A 179 PHE LEU ASN GLU HIS THR HIS GLY GLU ASP GLU VAL ARG SEQRES 9 A 179 PHE PHE VAL GLU GLY ALA GLY LEU PHE CYS LEU HIS ILE SEQRES 10 A 179 GLY ASP GLU VAL PHE GLN VAL LEU CYS GLU LYS ASN ASP SEQRES 11 A 179 LEU ILE SER VAL PRO ALA HIS THR PRO HIS TRP PHE ASP SEQRES 12 A 179 MET GLY SER GLU PRO ASN PHE THR ALA ILE ARG ILE PHE SEQRES 13 A 179 ASP ASN PRO GLU GLY TRP ILE ALA GLN PHE THR GLY ASP SEQRES 14 A 179 ASP ILE ALA SER ALA TYR PRO ARG LEU ALA HET NI A 180 1 HETNAM NI NICKEL (II) ION FORMUL 2 NI NI 2+ FORMUL 3 HOH *2(H2 O) HELIX 1 1 ALA A 21 LYS A 31 1 11 HELIX 2 2 THR A 49 GLY A 69 1 21 HELIX 3 3 PRO A 83 ASN A 94 1 12 HELIX 4 4 ASN A 158 GLU A 160 5 3 HELIX 5 5 ILE A 171 TYR A 175 5 5 SHEET 1 A 4 SER A 14 SER A 18 0 SHEET 2 A 4 ALA A 2 PHE A 6 -1 N LEU A 3 O SER A 18 SHEET 3 A 4 VAL A 121 LEU A 125 -1 O GLN A 123 N THR A 4 SHEET 4 A 4 LEU A 115 HIS A 116 -1 N LEU A 115 O PHE A 122 SHEET 1 B 4 SER A 72 ILE A 76 0 SHEET 2 B 4 THR A 151 PHE A 156 -1 O ARG A 154 N ASP A 74 SHEET 3 B 4 GLU A 102 GLU A 108 -1 N VAL A 107 O THR A 151 SHEET 4 B 4 LEU A 131 VAL A 134 -1 O VAL A 134 N GLU A 102 SHEET 1 C 2 THR A 97 HIS A 98 0 SHEET 2 C 2 TRP A 162 ILE A 163 -1 O ILE A 163 N THR A 97 LINK NE2 HIS A 96 NI NI A 180 1555 1555 2.08 LINK NE2 HIS A 98 NI NI A 180 1555 1555 2.07 LINK OE1 GLU A 102 NI NI A 180 1555 1555 1.91 LINK NE2 HIS A 140 NI NI A 180 1555 1555 2.07 LINK NI NI A 180 O HOH A 181 1555 1555 1.91 LINK NI NI A 180 O HOH A 182 1555 1555 1.91 SITE 1 AC1 6 HIS A 96 HIS A 98 GLU A 102 HIS A 140 SITE 2 AC1 6 HOH A 181 HOH A 182 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 MODEL 1