Header list of 1zrr.pdb file
Complete list - r 2 2 Bytes
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 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
Complete list - r 2 2 Bytes