PDB Short entry for 2P3M HEADER TRANSFERASE 09-MAR-07 2P3M TITLE SOLUTION STRUCTURE OF MJ0056 COMPND MOL_ID: 1; COMPND 2 MOLECULE: RIBOFLAVIN KINASE MJ0056; COMPND 3 CHAIN: A; COMPND 4 EC: 2.7.1.161; COMPND 5 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: METHANOCALDOCOCCUS JANNASCHII; SOURCE 3 ORGANISM_TAXID: 2190; SOURCE 4 GENE: MJ0056; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 7 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 8 EXPRESSION_SYSTEM_PLASMID: PET30B KEYWDS RIFT BARREL, PHOSPHOTRANSFERASE, RIBOFLAVIN KINASE, TRANSFERASE EXPDTA SOLUTION NMR NUMMDL 20 MDLTYP MINIMIZED AVERAGE AUTHOR M.COLES,V.TRUFFAULT,S.DJURANOVIC,J.MARTIN,A.N.LUPAS REVDAT 5 16-MAR-22 2P3M 1 REMARK REVDAT 4 24-FEB-09 2P3M 1 VERSN REVDAT 3 03-JUN-08 2P3M 1 COMPND REVDAT 2 25-DEC-07 2P3M 1 JRNL REVDAT 1 09-OCT-07 2P3M 0 JRNL AUTH M.AMMELBURG,M.D.HARTMANN,S.DJURANOVIC,V.ALVA,K.K.KORETKE, JRNL AUTH 2 J.MARTIN,G.SAUER,V.TRUFFAULT,K.ZETH,A.N.LUPAS,M.COLES JRNL TITL A CTP-DEPENDENT ARCHAEAL RIBOFLAVIN KINASE FORMS A BRIDGE IN JRNL TITL 2 THE EVOLUTION OF CRADLE-LOOP BARRELS. JRNL REF STRUCTURE V. 15 1577 2007 JRNL REFN ISSN 0969-2126 JRNL PMID 18073108 JRNL DOI 10.1016/J.STR.2007.09.027 REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : X-PLOR NIH 2.9.4 REMARK 3 AUTHORS : BRUNGER REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: STRUCTURE SOLVED USING 839, DISTANCE REMARK 3 RESTRAINTS, 56 HBOND RESTRAINTS, 399 DIHEDRAL RESTRAINTS AND 180 REMARK 3 J-COUPLING RESTRAINTS. REMARK 4 REMARK 4 2P3M COMPLIES WITH FORMAT V. 3.15, 01-DEC-08 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 12-MAR-07. REMARK 100 THE DEPOSITION ID IS D_1000041923. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 300 REMARK 210 PH : 7.4 REMARK 210 IONIC STRENGTH : 150 MM REMARK 210 PRESSURE : AMBIENT REMARK 210 SAMPLE CONTENTS : 0.65 MM MJ0056 UNLABELLED MM REMARK 210 PHOSPHATE BUFFER; 150 MM NAC 90% REMARK 210 H2O,10% D2O; 0.65 MM MJ0056 U- REMARK 210 15N; 30 MM PHOSPHATE BUFFER; 150 REMARK 210 MM 90% H2O, 10% D2O; 0.65 MM REMARK 210 MJ005 15N,13C; 30 MM PHOSPHATE REMARK 210 BUFFER 150 MM NACL REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : 2D NOESY; 3D_15N-SEPARATED_ REMARK 210 NOESY; 3D_NNH_NOESY; HNHA; HNHB; REMARK 210 3D_13C-SEPARATED_NOESY; 3D_CNH_ REMARK 210 NOESY REMARK 210 SPECTROMETER FIELD STRENGTH : 600 MHZ; 750 MHZ; 900 MHZ REMARK 210 SPECTROMETER MODEL : DMX; AVANCE REMARK 210 SPECTROMETER MANUFACTURER : BRUKER REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : XWINNMR 3.1, SPARKY, X-PLOR NIH REMARK 210 2.9.4 REMARK 210 METHOD USED : SIMULATED ANNEALING REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : 50 REMARK 210 CONFORMERS, NUMBER SUBMITTED : 20 REMARK 210 CONFORMERS, SELECTION CRITERIA : TARGET FUNCTION REMARK 210 REMARK 210 BEST REPRESENTATIVE CONFORMER IN THIS ENSEMBLE : 1 REMARK 210 REMARK 210 REMARK: REPRESENTATIVE CONFORMER IS THE REGULARISED AVERAGE REMARK 210 STRUCTURE 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 LEU A 15 -46.69 -155.16 REMARK 500 2 TYR A 100 -60.01 -94.90 REMARK 500 3 LEU A 15 -47.45 -154.97 REMARK 500 3 PHE A 21 33.67 -148.24 REMARK 500 3 LYS A 134 -59.82 -154.27 REMARK 500 4 PHE A 21 35.35 -154.81 REMARK 500 4 ASP A 133 -60.05 -155.04 REMARK 500 5 LEU A 15 -52.57 -155.07 REMARK 500 6 LEU A 15 -49.04 -143.04 REMARK 500 7 ASP A 133 33.31 -154.99 REMARK 500 8 LEU A 15 -60.05 -153.55 REMARK 500 9 LEU A 15 30.76 -99.40 REMARK 500 10 ASP A 133 78.86 -155.07 REMARK 500 11 LEU A 15 -45.69 -155.11 REMARK 500 12 GLU A 17 100.50 -163.53 REMARK 500 13 GLU A 17 32.48 -99.77 REMARK 500 14 LEU A 15 -46.84 -155.11 REMARK 500 14 ASP A 135 -48.26 -138.34 REMARK 500 15 VAL A 2 68.50 -152.53 REMARK 500 15 LEU A 15 -47.80 -155.11 REMARK 500 16 ARG A 19 38.69 -141.79 REMARK 500 17 GLU A 17 32.64 -99.95 REMARK 500 18 SER A 23 31.25 -94.65 REMARK 500 19 LYS A 3 50.58 -140.84 REMARK 500 20 LEU A 15 -48.68 -143.39 REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 2VBS RELATED DB: PDB REMARK 900 RELATED ID: 2VBU RELATED DB: PDB REMARK 900 RELATED ID: 2VBT RELATED DB: PDB REMARK 900 RELATED ID: 2VBV RELATED DB: PDB DBREF 2P3M A 1 136 UNP Q60365 Y056_METJA 1 136 SEQRES 1 A 136 MET VAL LYS LEU MET ILE ILE GLU GLY GLU VAL VAL SER SEQRES 2 A 136 GLY LEU GLY GLU GLY ARG TYR PHE LEU SER LEU PRO PRO SEQRES 3 A 136 TYR LYS GLU ILE PHE LYS LYS ILE LEU GLY PHE GLU PRO SEQRES 4 A 136 TYR GLU GLY THR LEU ASN LEU LYS LEU ASP ARG GLU PHE SEQRES 5 A 136 ASP ILE ASN LYS PHE LYS TYR ILE GLU THR GLU ASP PHE SEQRES 6 A 136 GLU PHE ASN GLY LYS ARG PHE PHE GLY VAL LYS VAL LEU SEQRES 7 A 136 PRO ILE LYS ILE LEU ILE GLY ASN LYS LYS ILE ASP GLY SEQRES 8 A 136 ALA ILE VAL VAL PRO LYS LYS THR TYR HIS SER SER GLU SEQRES 9 A 136 ILE ILE GLU ILE ILE ALA PRO MET LYS LEU ARG GLU GLN SEQRES 10 A 136 PHE ASN LEU LYS ASP GLY ASP VAL ILE LYS ILE LEU ILE SEQRES 11 A 136 LYS GLY ASP LYS ASP GLU HELIX 1 1 LEU A 24 GLY A 36 1 13 HELIX 2 2 ASP A 53 PHE A 57 5 5 HELIX 3 3 LYS A 113 PHE A 118 1 6 SHEET 1 A 8 ILE A 60 THR A 62 0 SHEET 2 A 8 VAL A 75 ILE A 84 -1 O VAL A 77 N ILE A 60 SHEET 3 A 8 VAL A 125 ILE A 130 -1 O LYS A 127 N LEU A 83 SHEET 4 A 8 MET A 5 VAL A 12 -1 N ILE A 7 O ILE A 128 SHEET 5 A 8 LEU A 44 LYS A 47 -1 O ASN A 45 N VAL A 12 SHEET 6 A 8 ILE A 105 ILE A 109 -1 O ILE A 106 N LEU A 46 SHEET 7 A 8 LYS A 87 PRO A 96 -1 N VAL A 94 O GLU A 107 SHEET 8 A 8 VAL A 75 ILE A 84 -1 N LYS A 76 O VAL A 95 SHEET 1 B 2 PHE A 65 PHE A 67 0 SHEET 2 B 2 LYS A 70 PHE A 72 -1 O LYS A 70 N PHE A 67 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