Header list of 1joq.pdb file
Complete list - t 27 2 Bytes
HEADER HYDROLASE 30-JUL-01 1JOQ
TITLE ENSEMBLE STRUCTURES FOR STAPHYLOCOCCAL NUCLEASE-H124L IN TERNARY
TITLE 2 COMPLEX WITH CA2+ AND THYMIDINE-3',5'-BISPHOSPHATE
COMPND MOL_ID: 1;
COMPND 2 MOLECULE: STAPHYLOCOCCAL NUCLEASE;
COMPND 3 CHAIN: A;
COMPND 4 FRAGMENT: NUCLEASE A;
COMPND 5 SYNONYM: THERMONUCLEASE, TNASE, MICROCOCCAL NUCLEASE;
COMPND 6 EC: 3.1.31.1;
COMPND 7 ENGINEERED: YES;
COMPND 8 MUTATION: YES
SOURCE MOL_ID: 1;
SOURCE 2 ORGANISM_SCIENTIFIC: STAPHYLOCOCCUS AUREUS;
SOURCE 3 ORGANISM_TAXID: 1280;
SOURCE 4 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3);
SOURCE 5 EXPRESSION_SYSTEM_TAXID: 469008;
SOURCE 6 EXPRESSION_SYSTEM_STRAIN: BL-21(DE3);
SOURCE 7 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID;
SOURCE 8 EXPRESSION_SYSTEM_PLASMID: PTSN2CC
KEYWDS TERNARY COMPLEX, BETA BARREL, ALPHA HELIX, HYDROLASE
EXPDTA SOLUTION NMR
NUMMDL 30
AUTHOR J.WANG,D.M.TRUCKSES,F.ABILDGAARD,Z.DZAKULA,Z.ZOLNAI,J.L.MARKLEY
REVDAT 4 27-OCT-21 1JOQ 1 REMARK SEQADV
REVDAT 3 24-FEB-09 1JOQ 1 VERSN
REVDAT 2 01-APR-03 1JOQ 1 JRNL
REVDAT 1 22-AUG-01 1JOQ 0
JRNL AUTH J.WANG,D.M.TRUCKSES,F.ABILDGAARD,Z.DZAKULA,Z.ZOLNAI,
JRNL AUTH 2 J.L.MARKLEY
JRNL TITL SOLUTION STRUCTURES OF STAPHYLOCOCCAL NUCLEASE FROM
JRNL TITL 2 MULTIDIMENSIONAL, MULTINUCLEAR NMR: NUCLEASE-H124L AND ITS
JRNL TITL 3 TERNARY COMPLEX WITH CA2+ AND THYMIDINE-3',5'-BISPHOSPHATE.
JRNL REF J.BIOMOL.NMR V. 10 143 1997
JRNL REFN ISSN 0925-2738
JRNL PMID 9369015
JRNL DOI 10.1023/A:1018350004729
REMARK 2
REMARK 2 RESOLUTION. NOT APPLICABLE.
REMARK 3
REMARK 3 REFINEMENT.
REMARK 3 PROGRAM : FELIX, X-PLOR 3.1
REMARK 3 AUTHORS : BIOSYM TECHNOLOGIES INC (FELIX), BRUNGER (X-PLOR)
REMARK 3
REMARK 3 OTHER REFINEMENT REMARKS: 2261 CONSTRAINTS WERE USED TO CALCULATE
REMARK 3 THE STRUCTURE. CA2+ IS BOUND, BUT COORDINATES FOR THE CALCIUM
REMARK 3 ARE NOT PROVIDED.
REMARK 4
REMARK 4 1JOQ COMPLIES WITH FORMAT V. 3.15, 01-DEC-08
REMARK 100
REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 31-JUL-01.
REMARK 100 THE DEPOSITION ID IS D_1000014010.
REMARK 210
REMARK 210 EXPERIMENTAL DETAILS
REMARK 210 EXPERIMENT TYPE : NMR
REMARK 210 TEMPERATURE (KELVIN) : 318; 318
REMARK 210 PH : 5.5; 5.1
REMARK 210 IONIC STRENGTH : 300 NM KCL; 300 NM KCL
REMARK 210 PRESSURE : AMBIENT; AMBIENT
REMARK 210 SAMPLE CONTENTS : 3.5-5 MM NUCLEASE-H124L U-50%
REMARK 210 2H; 300 MM KCL; D2O; 3.5-5 MM
REMARK 210 NUCLEASE-H124L U-95% 15N; 300 MM
REMARK 210 KCL; H2O; 3.5-5 MM NUCLEASE-
REMARK 210 H124L; 300 MM KCL; D2O; 3.5-5 MM
REMARK 210 NUCLEASE-H124L U-50% 2H; 300 MM
REMARK 210 KCL; H2O; 3.5-5 MM NUCLEASE-
REMARK 210 H124L U-98% 13C; 300 MM KCL; H2O;
REMARK 210 3.5-5 MM NUCLEASE-H124L U-98%
REMARK 210 13C U-99% 15N; 300 MM KCL; H2O
REMARK 210
REMARK 210 NMR EXPERIMENTS CONDUCTED : E-COSY; MHQC-J; DQF-COSY; 2D
REMARK 210 NOESY; 3D 1H-15N NOESY-HMQC; 3D
REMARK 210 HMQC-NOESY-HMQC; 2D 1H-13C HMQC;
REMARK 210 HNCO; AND OTHERS
REMARK 210 SPECTROMETER FIELD STRENGTH : 500 MHZ; 600 MHZ
REMARK 210 SPECTROMETER MODEL : AM
REMARK 210 SPECTROMETER MANUFACTURER : BRUKER
REMARK 210
REMARK 210 STRUCTURE DETERMINATION.
REMARK 210 SOFTWARE USED : X-PLOR 3.1, INSIGHT II 2.3,
REMARK 210 HBPLUS
REMARK 210 METHOD USED : DISTANCE, HYDROGEN BOND AND
REMARK 210 TORSION ANGLE CONSTRAINTS
REMARK 210
REMARK 210 CONFORMERS, NUMBER CALCULATED : 90
REMARK 210 CONFORMERS, NUMBER SUBMITTED : 30
REMARK 210 CONFORMERS, SELECTION CRITERIA : STRUCTURES WITH ACCEPTABLE
REMARK 210 COVALENT GEOMETRY,STRUCTURES
REMARK 210 WITH THE LEAST RESTRAINT
REMARK 210 VIOLATIONS
REMARK 210
REMARK 210 BEST REPRESENTATIVE CONFORMER IN THIS ENSEMBLE : NULL
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: 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 LYS A 5 -163.58 -122.39
REMARK 500 1 LEU A 7 -169.42 48.40
REMARK 500 1 LYS A 16 109.96 -166.91
REMARK 500 1 ILE A 18 -68.91 -98.59
REMARK 500 1 ASP A 19 -164.43 -112.77
REMARK 500 1 LYS A 53 32.93 -178.77
REMARK 500 1 PRO A 56 -158.18 -90.08
REMARK 500 1 GLU A 57 52.69 -113.62
REMARK 500 1 MET A 65 -71.77 -61.54
REMARK 500 1 ASP A 83 -169.88 -100.13
REMARK 500 1 ALA A 90 142.68 -170.25
REMARK 500 1 ALA A 112 -173.15 178.02
REMARK 500 1 TYR A 113 75.31 58.47
REMARK 500 1 LYS A 116 154.45 -45.75
REMARK 500 1 PRO A 117 32.84 -87.92
REMARK 500 1 ASN A 119 26.71 -164.88
REMARK 500 1 HIS A 121 56.87 -99.75
REMARK 500 1 ASN A 138 -123.20 66.49
REMARK 500 1 ILE A 139 -35.12 -37.18
REMARK 500 1 TRP A 140 45.55 -86.20
REMARK 500 1 ASP A 143 69.47 -105.72
REMARK 500 1 ASN A 144 90.82 -68.52
REMARK 500 1 SER A 147 152.00 63.67
REMARK 500 2 LYS A 6 110.74 -162.73
REMARK 500 2 LEU A 7 177.01 -59.76
REMARK 500 2 ILE A 15 -68.03 -100.29
REMARK 500 2 ILE A 18 -64.09 -120.16
REMARK 500 2 ASP A 19 -163.93 -122.51
REMARK 500 2 PRO A 42 -165.84 -76.10
REMARK 500 2 THR A 44 57.22 -153.12
REMARK 500 2 LYS A 45 52.18 -108.04
REMARK 500 2 HIS A 46 102.97 -43.08
REMARK 500 2 LYS A 48 -61.57 -170.50
REMARK 500 2 LYS A 49 55.90 -105.39
REMARK 500 2 GLU A 52 -169.78 63.37
REMARK 500 2 GLU A 57 -60.42 177.73
REMARK 500 2 MET A 65 -70.46 -63.37
REMARK 500 2 ASP A 77 -167.36 -69.91
REMARK 500 2 TYR A 113 75.27 57.12
REMARK 500 2 ASN A 119 32.95 -162.42
REMARK 500 2 HIS A 121 48.31 -88.38
REMARK 500 2 GLU A 122 -70.46 -77.17
REMARK 500 2 ASN A 138 -102.95 40.04
REMARK 500 2 ASP A 146 -92.82 55.39
REMARK 500 2 SER A 147 -86.59 -85.95
REMARK 500 3 THR A 2 22.23 -147.80
REMARK 500 3 THR A 4 41.61 -158.89
REMARK 500 3 LYS A 6 -72.69 -74.03
REMARK 500 3 LEU A 7 -164.02 -76.24
REMARK 500 3 LYS A 16 112.82 -179.94
REMARK 500
REMARK 500 THIS ENTRY HAS 639 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 35 0.17 SIDE CHAIN
REMARK 500 1 ARG A 81 0.29 SIDE CHAIN
REMARK 500 1 ARG A 87 0.22 SIDE CHAIN
REMARK 500 1 ARG A 105 0.13 SIDE CHAIN
REMARK 500 1 ARG A 126 0.29 SIDE CHAIN
REMARK 500 2 ARG A 35 0.18 SIDE CHAIN
REMARK 500 2 ARG A 81 0.26 SIDE CHAIN
REMARK 500 2 ARG A 87 0.26 SIDE CHAIN
REMARK 500 2 ARG A 105 0.19 SIDE CHAIN
REMARK 500 2 ARG A 126 0.12 SIDE CHAIN
REMARK 500 3 ARG A 35 0.24 SIDE CHAIN
REMARK 500 3 ARG A 81 0.21 SIDE CHAIN
REMARK 500 3 ARG A 87 0.20 SIDE CHAIN
REMARK 500 3 ARG A 105 0.19 SIDE CHAIN
REMARK 500 3 ARG A 126 0.28 SIDE CHAIN
REMARK 500 4 ARG A 81 0.32 SIDE CHAIN
REMARK 500 4 ARG A 87 0.31 SIDE CHAIN
REMARK 500 4 ARG A 105 0.27 SIDE CHAIN
REMARK 500 4 ARG A 126 0.31 SIDE CHAIN
REMARK 500 5 ARG A 35 0.21 SIDE CHAIN
REMARK 500 5 ARG A 81 0.18 SIDE CHAIN
REMARK 500 5 ARG A 87 0.24 SIDE CHAIN
REMARK 500 5 ARG A 105 0.10 SIDE CHAIN
REMARK 500 5 ARG A 126 0.11 SIDE CHAIN
REMARK 500 6 ARG A 35 0.30 SIDE CHAIN
REMARK 500 6 ARG A 81 0.30 SIDE CHAIN
REMARK 500 6 ARG A 87 0.14 SIDE CHAIN
REMARK 500 6 ARG A 105 0.30 SIDE CHAIN
REMARK 500 6 ARG A 126 0.26 SIDE CHAIN
REMARK 500 7 ARG A 35 0.20 SIDE CHAIN
REMARK 500 7 ARG A 81 0.17 SIDE CHAIN
REMARK 500 7 ARG A 87 0.21 SIDE CHAIN
REMARK 500 7 ARG A 105 0.23 SIDE CHAIN
REMARK 500 7 ARG A 126 0.28 SIDE CHAIN
REMARK 500 8 ARG A 35 0.09 SIDE CHAIN
REMARK 500 8 ARG A 81 0.32 SIDE CHAIN
REMARK 500 8 ARG A 87 0.19 SIDE CHAIN
REMARK 500 8 ARG A 105 0.30 SIDE CHAIN
REMARK 500 8 ARG A 126 0.31 SIDE CHAIN
REMARK 500 9 ARG A 35 0.32 SIDE CHAIN
REMARK 500 9 ARG A 81 0.28 SIDE CHAIN
REMARK 500 9 ARG A 87 0.23 SIDE CHAIN
REMARK 500 9 ARG A 105 0.18 SIDE CHAIN
REMARK 500 9 ARG A 126 0.30 SIDE CHAIN
REMARK 500 10 ARG A 81 0.31 SIDE CHAIN
REMARK 500 10 ARG A 87 0.13 SIDE CHAIN
REMARK 500 10 ARG A 105 0.29 SIDE CHAIN
REMARK 500 10 ARG A 126 0.13 SIDE CHAIN
REMARK 500 11 ARG A 35 0.14 SIDE CHAIN
REMARK 500 11 ARG A 81 0.28 SIDE CHAIN
REMARK 500
REMARK 500 THIS ENTRY HAS 139 PLANE DEVIATIONS.
REMARK 500
REMARK 500 REMARK: NULL
REMARK 800
REMARK 800 SITE
REMARK 800 SITE_IDENTIFIER: AC1
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE THP A 150
REMARK 900
REMARK 900 RELATED ENTRIES
REMARK 900 RELATED ID: 1JOK RELATED DB: PDB
REMARK 900 AVERAGED STRUCTURE FOR STAPHYLOCOCCAL NUCLEASE-H124L IN TERNARY
REMARK 900 COMPLEX WITH CA2+ AND THYMIDINE-3',5'-BISPHOSPHATE
REMARK 900 RELATED ID: 1JOO RELATED DB: PDB
REMARK 900 AVERAGED STRUCTURE FOR UNLIGATED STAPHYLOCOCCAL NUCLEASE-H124L
REMARK 900 RELATED ID: 1JOR RELATED DB: PDB
REMARK 900 ENSEMBLE STRUCTURES FOR UNLIGATED STAPHYLOCOCCAL NUCLEASE-H124L
DBREF 1JOQ A 1 149 UNP P00644 NUC_STAAU 83 231
SEQADV 1JOQ LEU A 124 UNP P00644 HIS 206 ENGINEERED MUTATION
SEQRES 1 A 149 ALA THR SER THR LYS LYS LEU HIS LYS GLU PRO ALA THR
SEQRES 2 A 149 LEU ILE LYS ALA ILE ASP GLY ASP THR VAL LYS LEU MET
SEQRES 3 A 149 TYR LYS GLY GLN PRO MET THR PHE ARG LEU LEU LEU VAL
SEQRES 4 A 149 ASP THR PRO GLU THR LYS HIS PRO LYS LYS GLY VAL GLU
SEQRES 5 A 149 LYS TYR GLY PRO GLU ALA SER ALA PHE THR LYS LYS MET
SEQRES 6 A 149 VAL GLU ASN ALA LYS LYS ILE GLU VAL GLU PHE ASP LYS
SEQRES 7 A 149 GLY GLN ARG THR ASP LYS TYR GLY ARG GLY LEU ALA TYR
SEQRES 8 A 149 ILE TYR ALA ASP GLY LYS MET VAL ASN GLU ALA LEU VAL
SEQRES 9 A 149 ARG GLN GLY LEU ALA LYS VAL ALA TYR VAL TYR LYS PRO
SEQRES 10 A 149 ASN ASN THR HIS GLU GLN LEU LEU ARG LYS SER GLU ALA
SEQRES 11 A 149 GLN ALA LYS LYS GLU LYS LEU ASN ILE TRP SER GLU ASP
SEQRES 12 A 149 ASN ALA ASP SER GLY GLN
HET THP A 150 35
HETNAM THP THYMIDINE-3',5'-DIPHOSPHATE
FORMUL 2 THP C10 H16 N2 O11 P2
HELIX 1 1 GLU A 57 ALA A 69 1 13
HELIX 2 2 VAL A 99 GLN A 106 1 8
HELIX 3 3 HIS A 121 LYS A 136 1 16
HELIX 4 4 LEU A 137 SER A 141 5 5
SHEET 1 A 6 LYS A 9 PRO A 11 0
SHEET 2 A 6 ILE A 72 PHE A 76 -1 N VAL A 74 O GLU A 10
SHEET 3 A 6 GLY A 88 ALA A 94 -1 N TYR A 91 O GLU A 75
SHEET 4 A 6 PRO A 31 ARG A 35 1 O THR A 33 N GLY A 88
SHEET 5 A 6 THR A 22 MET A 26 -1 O VAL A 23 N PHE A 34
SHEET 6 A 6 THR A 13 ASP A 19 -1 O THR A 13 N MET A 26
SHEET 1 B 4 LYS A 9 PRO A 11 0
SHEET 2 B 4 ILE A 72 PHE A 76 -1 N VAL A 74 O GLU A 10
SHEET 3 B 4 GLY A 88 ALA A 94 -1 N TYR A 91 O GLU A 75
SHEET 4 B 4 LYS A 97 MET A 98 -1 O LYS A 97 N ALA A 94
SHEET 1 C 2 VAL A 39 ASP A 40 0
SHEET 2 C 2 LYS A 110 VAL A 111 -1 N LYS A 110 O ASP A 40
CISPEP 1 LYS A 116 PRO A 117 1 -0.25
CISPEP 2 LYS A 116 PRO A 117 2 -0.16
CISPEP 3 LYS A 116 PRO A 117 3 -0.17
CISPEP 4 LYS A 116 PRO A 117 4 -0.22
CISPEP 5 LYS A 116 PRO A 117 5 0.19
CISPEP 6 LYS A 116 PRO A 117 6 0.03
CISPEP 7 LYS A 116 PRO A 117 7 -0.31
CISPEP 8 LYS A 116 PRO A 117 8 0.17
CISPEP 9 LYS A 116 PRO A 117 9 -0.39
CISPEP 10 LYS A 116 PRO A 117 10 -0.11
CISPEP 11 LYS A 116 PRO A 117 11 -0.13
CISPEP 12 LYS A 116 PRO A 117 12 0.08
CISPEP 13 LYS A 116 PRO A 117 13 -0.19
CISPEP 14 LYS A 116 PRO A 117 14 -0.16
CISPEP 15 LYS A 116 PRO A 117 15 -0.57
CISPEP 16 LYS A 116 PRO A 117 16 -0.10
CISPEP 17 LYS A 116 PRO A 117 17 0.08
CISPEP 18 LYS A 116 PRO A 117 18 -0.09
CISPEP 19 LYS A 116 PRO A 117 19 -0.12
CISPEP 20 LYS A 116 PRO A 117 20 0.15
CISPEP 21 LYS A 116 PRO A 117 21 0.22
CISPEP 22 LYS A 116 PRO A 117 22 -0.17
CISPEP 23 LYS A 116 PRO A 117 23 -0.22
CISPEP 24 LYS A 116 PRO A 117 24 -0.44
CISPEP 25 LYS A 116 PRO A 117 25 -0.29
CISPEP 26 LYS A 116 PRO A 117 26 -0.27
CISPEP 27 LYS A 116 PRO A 117 27 -0.02
CISPEP 28 LYS A 116 PRO A 117 28 0.30
CISPEP 29 LYS A 116 PRO A 117 29 -0.56
CISPEP 30 LYS A 116 PRO A 117 30 -0.13
SITE 1 AC1 7 ARG A 35 ASP A 83 LYS A 84 TYR A 85
SITE 2 AC1 7 ARG A 87 TYR A 113 TYR A 115
CRYST1 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 - t 27 2 Bytes