10 20 30 40 50 60 70 80 1JOK - Header ----|----|----|----|----|----|----|----|----|----|----|----|----|----|----|----| Asymmetric UnitHEADER HYDROLASE 30-JUL-01 1JOK
TITLE AVERAGED STRUCTURE FOR STAPHYLOCOCCAL NUCLEASE-H124L IN TITLE 2 TERNARY 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
MDLTYP MINIMIZED AVERAGE
AUTHOR J.WANG,D.M.TRUCKSES,F.ABILDGAARD,Z.DZAKULA,Z.ZOLNAI, AUTHOR 2 J.L.MARKLEY
REVDAT 3 24-FEB-09 1JOK 1 VERSN REVDAT 2 01-APR-03 1JOK 1 JRNL REVDAT 1 22-AUG-01 1JOK 0
JRNL AUTH J.WANG,D.M.TRUCKSES,F.ABILDGAARD,Z.DZAKULA, JRNL AUTH 2 Z.ZOLNAI,J.L.MARKLEY JRNL TITL SOLUTION STRUCTURES OF STAPHYLOCOCCAL NUCLEASE JRNL TITL 2 FROM MULTIDIMENSIONAL, MULTINUCLEAR NMR: JRNL TITL 3 NUCLEASE-H124L AND ITS TERNARY COMPLEX WITH CA2+ JRNL TITL 4 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 1
REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE.
REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : X-PLOR 3.1 REMARK 3 AUTHORS : BRUNGER REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: 2261 CONSTRAINTS WERE USED TO REMARK 3 CALCULATE THE STRUCTURE. CA2+ IS BOUND, BUT COORDINATES FOR REMARK 3 THE CALCIUM ARE NOT PROVIDED.
REMARK 4 REMARK 4 1JOK 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 RCSB ID CODE IS RCSB014007.
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 REMARK 210 MM KCL; H2O; 3.5-5 MM NUCLEASE REMARK 210 -H124L; 300 MM KCL; D2O; 3.5-5 REMARK 210 MM NUCLEASE-H124L U-50% 2H; REMARK 210 300 MM KCL; H2O; 3.5-5 MM REMARK 210 NUCLEASE-H124L U-98% 13C; 300 REMARK 210 MM KCL; H2O; 3.5-5 MM NUCLEASE REMARK 210 -H124L U-98% 13C U-99% 15N; REMARK 210 300 MM KCL; H2O REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : E-COSY, HMQC-J, DQF-COSY, 2D REMARK 210 NOESY, 3D 1H-15N NOESY-HMQC, REMARK 210 3D HMQC-NOESY-HMQC, 2D 1H-13C REMARK 210 HMQC, 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 : FELIX, X-PLOR 3.1, INSIGHTII REMARK 210 2.3, HBPLUS REMARK 210 METHOD USED : DISTANCE, HYDROGEN BOND AND REMARK 210 TORSION ANGLE CONSTRAINTS 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 : 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 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 LYS A 5 -76.89 -133.46 REMARK 500 LYS A 6 -96.37 -105.01 REMARK 500 ILE A 15 -61.10 -123.91 REMARK 500 LEU A 25 -158.03 -119.12 REMARK 500 GLU A 43 93.44 55.58 REMARK 500 HIS A 46 73.80 42.59 REMARK 500 LYS A 48 -82.60 -163.72 REMARK 500 LYS A 53 -80.60 -125.53 REMARK 500 GLU A 57 -56.91 -160.96 REMARK 500 LYS A 63 -70.64 -60.47 REMARK 500 MET A 65 -78.26 -53.08 REMARK 500 ASN A 119 27.69 -165.31 REMARK 500 ASN A 138 -106.73 69.05 REMARK 500 TRP A 140 46.70 -85.23 REMARK 500 SER A 141 -81.91 -106.52 REMARK 500 ASP A 143 70.48 -164.81 REMARK 500 ASN A 144 165.34 177.01 REMARK 500 ALA A 145 76.94 -118.44 REMARK 500 SER A 147 71.47 56.98 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 ARG A 35 0.30 SIDE_CHAIN REMARK 500 ARG A 81 0.25 SIDE_CHAIN REMARK 500 ARG A 87 0.22 SIDE_CHAIN REMARK 500 ARG A 105 0.26 SIDE_CHAIN REMARK 500 ARG A 126 0.24 SIDE_CHAIN 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: 1JOO RELATED DB: PDB REMARK 900 AVERAGED STRUCTURE FOR UNLIGATED STAPHYLOCOCCAL NUCLEASE- REMARK 900 H124L REMARK 900 RELATED ID: 1JOQ RELATED DB: PDB REMARK 900 ENSEMBLE STRUCTURES FOR STAPHYLOCOCCAL NUCLEASE-H124L IN REMARK 900 TERNARY COMPLEX WITH CA2+ AND THYMIDINE-3',5'-BISPHOSPHATE REMARK 900 RELATED ID: 1JOR RELATED DB: PDB REMARK 900 ENSEMBLE STRUCTURES FOR UNLIGATED STAPHYLOCOCCAL NUCLEASE- REMARK 900 H124L
DBREF 1JOK A 1 149 UNP P00644 NUC_STAAU 83 231
SEQADV 1JOK LEU A 124 UNP P00644 HIS 206 ENGINEERED
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 37
HETNAM THP THYMIDINE-3',5'-DIPHOSPHATE
FORMUL 2 THP C10 H16 N2 O11 P2
HELIX 1 1 TYR A 54 ALA A 69 1 16 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 16 ALA A 17 0 SHEET 2 A 6 THR A 22 TYR A 27 -1 N LYS A 24 O LYS A 16 SHEET 3 A 6 GLN A 30 LEU A 36 -1 O GLN A 30 N TYR A 27 SHEET 4 A 6 GLY A 88 ALA A 94 1 N GLY A 88 O THR A 33 SHEET 5 A 6 ILE A 72 PHE A 76 -1 O GLU A 73 N TYR A 93 SHEET 6 A 6 HIS A 8 ALA A 12 -1 N HIS A 8 O PHE A 76 SHEET 1 B 5 LYS A 16 ALA A 17 0 SHEET 2 B 5 THR A 22 TYR A 27 -1 N LYS A 24 O LYS A 16 SHEET 3 B 5 GLN A 30 LEU A 36 -1 O GLN A 30 N TYR A 27 SHEET 4 B 5 GLY A 88 ALA A 94 1 N GLY A 88 O THR A 33 SHEET 5 B 5 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 0 -0.47
SITE 1 AC1 8 ARG A 35 LEU A 37 ASP A 83 LYS A 84 SITE 2 AC1 8 TYR A 85 ARG A 87 TYR A 113 TYR A 115
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