Header list of 1puq.pdb file
Complete list - v 20 2 Bytes
HEADER HYDROLASE 25-JUN-03 1PUQ
TITLE SOLUTION STRUCTURE OF THE MUTT PYROPHOSPHOHYDROLASE COMPLEXED WITH
TITLE 2 MG(2+) AND 8-OXO-DGMP, A TIGHTLY-BOUND PRODUCT
COMPND MOL_ID: 1;
COMPND 2 MOLECULE: MUTATOR MUTT PROTEIN;
COMPND 3 CHAIN: A;
COMPND 4 SYNONYM: 7,8-DIHYDRO-8-OXOGUANINE-TRIPHOSPHATASE, 8-OXO-DGTPASE, DGTP
COMPND 5 PYROPHOSPHOHYDROLASE;
COMPND 6 EC: 3.6.1.-;
COMPND 7 ENGINEERED: YES
SOURCE MOL_ID: 1;
SOURCE 2 ORGANISM_SCIENTIFIC: ESCHERICHIA COLI;
SOURCE 3 ORGANISM_TAXID: 562;
SOURCE 4 GENE: MUTT,STRAIN: K12-I7023;
SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI;
SOURCE 6 EXPRESSION_SYSTEM_TAXID: 562;
SOURCE 7 EXPRESSION_SYSTEM_STRAIN: HMS174;
SOURCE 8 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID;
SOURCE 9 EXPRESSION_SYSTEM_PLASMID: PET MUTT, T7 PROMOTER
KEYWDS MUTATOR PROTEIN, NUCLEOSIDE TRIPHOSPHATE PYROPHOSPHOHYDROLASE, MUTT
KEYWDS 2 PYROPHOSPHOHYDROLASE-METAL-PRODUCT COMPLEX, HYDROLASE
EXPDTA SOLUTION NMR
NUMMDL 20
AUTHOR M.A.MASSIAH,V.SARASWAT,H.F.AZURMENDI,A.S.MILDVAN
REVDAT 4 20-NOV-19 1PUQ 1 REMARK LINK
REVDAT 3 24-FEB-09 1PUQ 1 VERSN
REVDAT 2 27-JAN-04 1PUQ 1 JRNL
REVDAT 1 26-AUG-03 1PUQ 0
JRNL AUTH M.A.MASSIAH,V.SARASWAT,H.F.AZURMENDI,A.S.MILDVAN
JRNL TITL SOLUTION STRUCTURE AND NH EXCHANGE STUDIES OF THE MUTT
JRNL TITL 2 PYROPHOSPHOHYDROLASE COMPLEXED WITH MG(2+) AND 8-OXO-DGMP, A
JRNL TITL 3 TIGHTLY BOUND PRODUCT.
JRNL REF BIOCHEMISTRY V. 42 10140 2003
JRNL REFN ISSN 0006-2960
JRNL PMID 12939141
JRNL DOI 10.1021/BI030105P
REMARK 1
REMARK 1 REFERENCE 1
REMARK 1 AUTH J.LIN,C.ABEYGUNAWARDANA,D.N.FRICK,M.J BESSMAN,A.S.MILDVAN
REMARK 1 TITL SOLUTION STRUCTURE OF THE QUATERNARY COMPLEX
REMARK 1 TITL 2 MUTT-M(2+)-AMPCPP-M(2+) COMPLEX AND MECHANISM OF ITS
REMARK 1 TITL 3 PYROPHOSPHOHYDROLASE ACTION
REMARK 1 REF BIOCHEMISTRY V. 36 1199 1997
REMARK 1 REFN ISSN 0006-2960
REMARK 1 DOI 10.1021/BI962619C
REMARK 1 REFERENCE 2
REMARK 1 AUTH D.N.FRICK,D.J.WEBER,C.ABEYGUNAWARDANA,A.G.GITTIS,
REMARK 1 AUTH 2 M.J BESSMAN,A.S.MILDVAN
REMARK 1 TITL NMR STUDIES OF THE CONFORMATIONS AND LOCATION OF NUCLEOTIDES
REMARK 1 TITL 2 BOUND TO THE E.COLI MUTT ENZYME
REMARK 1 REF BIOCHEMISTRY V. 34 5577 1995
REMARK 1 REFN ISSN 0006-2960
REMARK 1 REFERENCE 3
REMARK 1 AUTH C.ABEYGUNAWARDANA,D.J.WEBER,A.G.GITTIS,D.N.FRICK,J.LIN,
REMARK 1 AUTH 2 A.F.MILLER,M.J.BESSMAN,A.S.MILDVAN
REMARK 1 TITL SOLUTION STRUCTURE OF THE MUTT ENZYME, A NUCLEOSIDE
REMARK 1 TITL 2 TRIPHOSPHATE PYROPHOSPHOHYDROLASE
REMARK 1 REF BIOCHEMISTRY V. 34 14997 1995
REMARK 1 REFN ISSN 0006-2960
REMARK 2
REMARK 2 RESOLUTION. NOT APPLICABLE.
REMARK 3
REMARK 3 REFINEMENT.
REMARK 3 PROGRAM : NMRPIPE 2.1, CNS 1.1
REMARK 3 AUTHORS : F. DELAGLIO (NMRPIPE), A. BRUNGER ET AL. (CNS)
REMARK 3
REMARK 3 OTHER REFINEMENT REMARKS: THE STRUCTURES ARE BASED ON 1746 NOE
REMARK 3 -DERIVED DISTANCE CONSTRAINTS, 186 DIHEDRAL ANGLE RESTRAINTS
REMARK 3 DERIVED FROM TALOS, 82 DISTANCE RESTRAINTS FROM HYDROGEN BONDS
REMARK 3 AND 3 ASSUMED DISTANCES LIGAND/PROTEIN (SEE CASE 3, TABLE 1 IN
REMARK 3 REFERENCE).
REMARK 4
REMARK 4 1PUQ COMPLIES WITH FORMAT V. 3.15, 01-DEC-08
REMARK 100
REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 03-JUL-03.
REMARK 100 THE DEPOSITION ID IS D_1000019583.
REMARK 210
REMARK 210 EXPERIMENTAL DETAILS
REMARK 210 EXPERIMENT TYPE : NMR
REMARK 210 TEMPERATURE (KELVIN) : 295
REMARK 210 PH : 7.5
REMARK 210 IONIC STRENGTH : 21 MM NACL
REMARK 210 PRESSURE : AMBIENT
REMARK 210 SAMPLE CONTENTS : 1MM MUTT, 1.3MM 8-OXO-DGMP, 15MM
REMARK 210 MGCL2, 4MM D11-TRIS-HCL, PH 7.5,
REMARK 210 21MM NACL, 0.34MM NAN3.
REMARK 210
REMARK 210 NMR EXPERIMENTS CONDUCTED : 3D_15N-SEPARATED_NOESY; 2D
REMARK 210 NOESY; 2D TOCSY; 3D_13C-
REMARK 210 SEPARATED_NOESY; 12C/13C-
REMARK 210 FILTERED-NOESY-HSQC; HNCA; NHCACB
REMARK 210 SPECTROMETER FIELD STRENGTH : 600 MHZ
REMARK 210 SPECTROMETER MODEL : UNITYPLUS
REMARK 210 SPECTROMETER MANUFACTURER : VARIAN
REMARK 210
REMARK 210 STRUCTURE DETERMINATION.
REMARK 210 SOFTWARE USED : CNS 1.1, TALOS 1999.019.15.47
REMARK 210 METHOD USED : SIMULATED ANNEALING TORSION
REMARK 210 ANGLE DYNAMICS
REMARK 210
REMARK 210 CONFORMERS, NUMBER CALCULATED : 50
REMARK 210 CONFORMERS, NUMBER SUBMITTED : 20
REMARK 210 CONFORMERS, SELECTION CRITERIA : STRUCTURES WITH THE LEAST
REMARK 210 RESTRAINT VIOLATIONS
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 O HOH A 5012 H2 HOH A 5013 0.96
REMARK 500 O HOH A 5011 H1 HOH A 5014 0.96
REMARK 500 O HOH A 5011 H1 HOH A 5013 0.96
REMARK 500 O HOH A 5012 H2 HOH A 5014 0.96
REMARK 500 O GLU A 120 H ALA A 124 1.54
REMARK 500 O ILE A 123 H LYS A 127 1.57
REMARK 500 O PHE A 75 H ARG A 78 1.58
REMARK 500 O THR A 45 H ALA A 49 1.60
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 ASN A 16 24.32 45.78
REMARK 500 1 ARG A 23 26.15 47.71
REMARK 500 1 ALA A 24 -168.78 46.60
REMARK 500 1 ASP A 26 33.62 -162.33
REMARK 500 1 MET A 29 86.57 -60.34
REMARK 500 1 ASN A 31 31.17 -96.37
REMARK 500 1 LEU A 33 74.67 -63.11
REMARK 500 1 LYS A 39 -2.19 86.11
REMARK 500 1 MET A 42 -81.10 9.64
REMARK 500 1 VAL A 58 -45.11 -134.29
REMARK 500 1 PHE A 65 166.91 179.77
REMARK 500 1 SER A 66 155.39 87.31
REMARK 500 1 GLU A 69 144.42 -171.77
REMARK 500 1 PRO A 76 83.79 -50.72
REMARK 500 1 ASP A 77 15.45 93.98
REMARK 500 1 TRP A 95 -62.62 -121.23
REMARK 500 1 LYS A 97 39.43 173.59
REMARK 500 2 ASN A 16 21.17 47.56
REMARK 500 2 ARG A 23 -109.75 47.71
REMARK 500 2 ALA A 24 -170.71 168.40
REMARK 500 2 ASP A 26 -45.94 -132.80
REMARK 500 2 ALA A 27 -166.11 -71.75
REMARK 500 2 HIS A 28 -86.54 -95.62
REMARK 500 2 MET A 29 29.09 46.47
REMARK 500 2 LEU A 33 74.76 -64.01
REMARK 500 2 LYS A 39 0.25 82.29
REMARK 500 2 MET A 42 -80.27 8.05
REMARK 500 2 VAL A 58 -44.01 -133.18
REMARK 500 2 PHE A 65 -133.55 -179.82
REMARK 500 2 SER A 66 167.72 55.23
REMARK 500 2 PRO A 76 81.91 -50.81
REMARK 500 2 ASP A 77 12.88 89.58
REMARK 500 2 TRP A 95 -64.70 -126.24
REMARK 500 2 LYS A 97 37.67 170.99
REMARK 500 3 ARG A 23 -103.18 50.33
REMARK 500 3 ALA A 24 -67.62 179.71
REMARK 500 3 ALA A 25 -40.49 -175.64
REMARK 500 3 ALA A 27 158.23 63.67
REMARK 500 3 MET A 29 41.09 -142.75
REMARK 500 3 GLU A 34 -167.71 -106.73
REMARK 500 3 LYS A 39 -0.18 84.53
REMARK 500 3 MET A 42 -75.33 0.90
REMARK 500 3 VAL A 58 -44.04 -133.81
REMARK 500 3 ILE A 60 -166.80 -114.37
REMARK 500 3 PHE A 65 163.61 179.78
REMARK 500 3 SER A 66 154.57 85.64
REMARK 500 3 GLU A 69 138.26 -171.87
REMARK 500 3 PRO A 76 81.73 -55.63
REMARK 500 3 ASP A 77 6.00 97.08
REMARK 500 3 TRP A 95 -59.75 -132.25
REMARK 500
REMARK 500 THIS ENTRY HAS 348 RAMACHANDRAN OUTLIERS.
REMARK 500
REMARK 500 REMARK: NULL
REMARK 610
REMARK 610 MISSING HETEROATOM
REMARK 610 THE FOLLOWING RESIDUES HAVE MISSING ATOMS (M=MODEL NUMBER;
REMARK 610 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER;
REMARK 610 I=INSERTION CODE):
REMARK 610 M RES C SSEQI
REMARK 610 1 HOH A 5013
REMARK 610 1 HOH A 5014
REMARK 610 2 HOH A 5025
REMARK 610 2 HOH A 5026
REMARK 610 3 HOH A 5037
REMARK 610 3 HOH A 5038
REMARK 610 4 HOH A 5049
REMARK 610 4 HOH A 5050
REMARK 610 5 HOH A 5061
REMARK 610 5 HOH A 5062
REMARK 610 6 HOH A 5073
REMARK 610 6 HOH A 5074
REMARK 610 7 HOH A 5085
REMARK 610 7 HOH A 5086
REMARK 610 8 HOH A 5097
REMARK 610 8 HOH A 5098
REMARK 610 9 HOH A 5109
REMARK 610 9 HOH A 5110
REMARK 610 10 HOH A 5121
REMARK 610 10 HOH A 5122
REMARK 610 11 HOH A 5133
REMARK 610 11 HOH A 5134
REMARK 610 12 HOH A 5145
REMARK 610 12 HOH A 5146
REMARK 610 13 HOH A 5157
REMARK 610 13 HOH A 5158
REMARK 610 14 HOH A 5169
REMARK 610 14 HOH A 5170
REMARK 610 15 HOH A 5181
REMARK 610 15 HOH A 5182
REMARK 610 16 HOH A 5193
REMARK 610 16 HOH A 5194
REMARK 610 17 HOH A 5205
REMARK 610 17 HOH A 5206
REMARK 610 18 HOH A 5217
REMARK 610 18 HOH A 5218
REMARK 610 19 HOH A 5229
REMARK 610 19 HOH A 5230
REMARK 610 20 HOH A 5241
REMARK 610 20 HOH A 5242
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 MG A 130 MG
REMARK 620 N RES CSSEQI ATOM
REMARK 620 1 GLY A 38 O
REMARK 620 2 GLU A 53 OE2 81.6
REMARK 620 3 GLU A 56 OE1 149.3 78.8
REMARK 620 4 GLU A 57 OE1 76.7 87.7 79.0
REMARK 620 5 GLU A 57 OE2 58.7 127.5 118.1 52.9
REMARK 620 6 HOH A5011 O 108.7 82.7 92.1 168.1 139.0
REMARK 620 7 HOH A5012 O 116.0 162.3 85.7 97.7 67.7 89.5
REMARK 620 N 1 2 3 4 5 6
REMARK 800
REMARK 800 SITE
REMARK 800 SITE_IDENTIFIER: AC1
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MG A 130
REMARK 800
REMARK 800 SITE_IDENTIFIER: AC2
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE 8OG A 131
REMARK 900
REMARK 900 RELATED ENTRIES
REMARK 900 RELATED ID: 1PPX RELATED DB: PDB
REMARK 900 SOLUTION STRUCTURE OF THE SAME COMPLEX WITHOUT ASSUMED DISTANCES
REMARK 900 LIGAND/PROTEIN.
REMARK 900 RELATED ID: 1MUT RELATED DB: PDB
REMARK 900 THE FREE SOLUTION STRUCTURE.
REMARK 900 RELATED ID: 1TUM RELATED DB: PDB
REMARK 900 COMPLEXED WITH AMPCPP-MG.
REMARK 900 RELATED ID: 1PUN RELATED DB: PDB
REMARK 900 SOLUTION STRUCTURE OF THE MUTT PYROPHOSPHOHYDROLASE COMPLEXED WITH
REMARK 900 MG(2+) AND 8-OXO-DGMP, A TIGHTLY-BOUND PRODUCT
REMARK 900 RELATED ID: 1PUS RELATED DB: PDB
REMARK 900 SOLUTION STRUCTURE OF THE MUTT PYROPHOSPHOHYDROLASE COMPLEXED WITH
REMARK 900 MG(2+) AND 8-OXO-DGMP, A TIGHTLY-BOUND PRODUCT
DBREF 1PUQ A 1 129 UNP P08337 MUTT_ECOLI 1 129
SEQRES 1 A 129 MET LYS LYS LEU GLN ILE ALA VAL GLY ILE ILE ARG ASN
SEQRES 2 A 129 GLU ASN ASN GLU ILE PHE ILE THR ARG ARG ALA ALA ASP
SEQRES 3 A 129 ALA HIS MET ALA ASN LYS LEU GLU PHE PRO GLY GLY LYS
SEQRES 4 A 129 ILE GLU MET GLY GLU THR PRO GLU GLN ALA VAL VAL ARG
SEQRES 5 A 129 GLU LEU GLN GLU GLU VAL GLY ILE THR PRO GLN HIS PHE
SEQRES 6 A 129 SER LEU PHE GLU LYS LEU GLU TYR GLU PHE PRO ASP ARG
SEQRES 7 A 129 HIS ILE THR LEU TRP PHE TRP LEU VAL GLU ARG TRP GLU
SEQRES 8 A 129 GLY GLU PRO TRP GLY LYS GLU GLY GLN PRO GLY GLU TRP
SEQRES 9 A 129 MET SER LEU VAL GLY LEU ASN ALA ASP ASP PHE PRO PRO
SEQRES 10 A 129 ALA ASN GLU PRO VAL ILE ALA LYS LEU LYS ARG LEU
HET MG A 130 1
HET 8OG A 131 36
HETNAM MG MAGNESIUM ION
HETNAM 8OG 8-OXO-2'-DEOXY-GUANOSINE-5'-MONOPHOSPHATE
HETSYN 8OG 8-OXO-7,8-DIHYDRO-2'-DEOXY-GUANOSINE-5'-MONOPHOSPHATE
FORMUL 2 MG MG 2+
FORMUL 3 8OG C10 H14 N5 O8 P
FORMUL 4 HOH *4(H2 O)
HELIX 1 1 LYS A 39 GLU A 44 5 6
HELIX 2 2 GLU A 47 GLY A 59 1 13
HELIX 3 3 SER A 106 LEU A 110 5 5
HELIX 4 4 PRO A 116 ALA A 118 5 3
HELIX 5 5 ASN A 119 ARG A 128 1 10
SHEET 1 A 5 HIS A 64 TYR A 73 0
SHEET 2 A 5 HIS A 79 VAL A 87 -1 O LEU A 82 N LEU A 71
SHEET 3 A 5 LYS A 3 ARG A 12 1 N VAL A 8 O TRP A 83
SHEET 4 A 5 ILE A 18 THR A 21 -1 O PHE A 19 N ILE A 11
SHEET 5 A 5 GLY A 102 MET A 105 -1 O MET A 105 N ILE A 18
LINK O GLY A 38 MG MG A 130 1555 1555 2.40
LINK OE2 GLU A 53 MG MG A 130 1555 1555 2.41
LINK OE1 GLU A 56 MG MG A 130 1555 1555 2.30
LINK OE1 GLU A 57 MG MG A 130 1555 1555 2.41
LINK OE2 GLU A 57 MG MG A 130 1555 1555 2.52
LINK MG MG A 130 O HOH A5011 1555 1555 2.11
LINK MG MG A 130 O HOH A5012 1555 1555 2.11
SITE 1 AC1 7 GLY A 38 LYS A 39 GLU A 53 GLU A 56
SITE 2 AC1 7 GLU A 57 HOH A5011 HOH A5012
SITE 1 AC2 8 LEU A 4 ILE A 6 GLU A 34 PHE A 75
SITE 2 AC2 8 ARG A 78 ILE A 80 ALA A 118 ASN A 119
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
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