HEADER SIGNALING PROTEIN,TRANSFERASE 27-JUL-06 2HUR TITLE ESCHERICHIA COLI NUCLEOSIDE DIPHOSPHATE KINASE COMPND MOL_ID: 1; COMPND 2 MOLECULE: NUCLEOSIDE DIPHOSPHATE KINASE; COMPND 3 CHAIN: A, B, C, D, E, F; COMPND 4 SYNONYM: NDK; NDP KINASE; NUCLEOSIDE-2-P KINASE; COMPND 5 EC: 2.7.4.6; COMPND 6 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: ESCHERICHIA COLI; SOURCE 3 ORGANISM_TAXID: 562; SOURCE 4 GENE: NDK; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 7 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 8 EXPRESSION_SYSTEM_PLASMID: PJC20 KEYWDS TYPE II TETRAMER, SIGNALING PROTEIN, TRANSFERASE EXPDTA X-RAY DIFFRACTION AUTHOR L.MOYNIE,M.-F.GIRAUD,F.GEORGESCAULD,I.LASCU,A.DAUTANT REVDAT 5 30-AUG-23 2HUR 1 REMARK REVDAT 4 13-JUL-11 2HUR 1 VERSN REVDAT 3 24-FEB-09 2HUR 1 VERSN REVDAT 2 05-JUN-07 2HUR 1 JRNL REVDAT 1 10-APR-07 2HUR 0 JRNL AUTH L.MOYNIE,M.-F.GIRAUD,F.GEORGESCAULD,I.LASCU,A.DAUTANT JRNL TITL THE STRUCTURE OF THE ESCHERICHIA COLI NUCLEOSIDE DIPHOSPHATE JRNL TITL 2 KINASE REVEALS A NEW QUATERNARY ARCHITECTURE FOR THIS ENZYME JRNL TITL 3 FAMILY JRNL REF PROTEINS V. 67 755 2007 JRNL REFN ISSN 0887-3585 JRNL PMID 17330300 JRNL DOI 10.1002/PROT.21316 REMARK 1 REMARK 1 REFERENCE 1 REMARK 1 AUTH N.ALMAULA,Q.LU,J.DELGADO,S.BELKIN,M.INOUYE REMARK 1 TITL NUCLEOSIDE DIPHOSPHATE KINASE FROM ESCHERICHIA COLI REMARK 1 REF J.BACTERIOL. V. 177 2524 1995 REMARK 1 REFN ISSN 0021-9193 REMARK 1 PMID 7730286 REMARK 1 REFERENCE 2 REMARK 1 AUTH R.L.WILLIAMS,D.A.OREN,S.INOUYE,M.INOUYE,E.ARNOLD REMARK 1 TITL CRYSTAL STRUCTURE OF MYXOCOCCUS XANTHUS NUCLEOSIDE REMARK 1 TITL 2 DIPHOSPHATE KINASE AND ITS INTERACTION WITH A NUCLEOTIDE REMARK 1 TITL 3 SUBSTRATE AT 2.0 A RESOLUTION REMARK 1 REF J.MOL.BIOL. V. 234 1230 1993 REMARK 1 REFN ISSN 0022-2836 REMARK 1 PMID 8263923 REMARK 1 DOI 10.1006/JMBI.1993.1673 REMARK 1 REFERENCE 3 REMARK 1 AUTH G.LEBRAS,I.LASCU,M.L.LACOMBE,J.JANIN REMARK 1 TITL REFINED X-RAY STRUCTURE OF DICTYOSTELIUM DISCOIDEUM REMARK 1 TITL 2 NUCLEOSIDE DIPHOSPHATE KINASE AT 1.8 A RESOLUTION. REMARK 1 REF J.MOL.BIOL. V. 243 873 1994 REMARK 1 REFN ISSN 0022-2836 REMARK 1 PMID 7966307 REMARK 1 DOI 10.1006/JMBI.1994.1689 REMARK 2 REMARK 2 RESOLUTION. 1.62 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : CNS 1.1 REMARK 3 AUTHORS : BRUNGER,ADAMS,CLORE,DELANO,GROS,GROSSE- REMARK 3 : KUNSTLEVE,JIANG,KUSZEWSKI,NILGES,PANNU, REMARK 3 : READ,RICE,SIMONSON,WARREN REMARK 3 REMARK 3 REFINEMENT TARGET : NULL REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.62 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 38.05 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 DATA CUTOFF HIGH (ABS(F)) : 2343463.170 REMARK 3 DATA CUTOFF LOW (ABS(F)) : 0.0000 REMARK 3 COMPLETENESS (WORKING+TEST) (%) : 99.7 REMARK 3 NUMBER OF REFLECTIONS : 108681 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 CROSS-VALIDATION METHOD : THROUGHOUT REMARK 3 FREE R VALUE TEST SET SELECTION : RANDOM REMARK 3 R VALUE (WORKING SET) : 0.191 REMARK 3 FREE R VALUE : 0.215 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 5451 REMARK 3 ESTIMATED ERROR OF FREE R VALUE : 0.003 REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : 6 REMARK 3 BIN RESOLUTION RANGE HIGH (A) : 1.62 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.72 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 98.70 REMARK 3 REFLECTIONS IN BIN (WORKING SET) : 16974 REMARK 3 BIN R VALUE (WORKING SET) : 0.2630 REMARK 3 BIN FREE R VALUE : 0.2980 REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : 5.00 REMARK 3 BIN FREE R VALUE TEST SET COUNT : 894 REMARK 3 ESTIMATED ERROR OF BIN FREE R VALUE : 0.010 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 6492 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 30 REMARK 3 SOLVENT ATOMS : 717 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 19.50 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 21.40 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -0.81000 REMARK 3 B22 (A**2) : 1.33000 REMARK 3 B33 (A**2) : -0.52000 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : 3.96000 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM LUZZATI PLOT (A) : 0.18 REMARK 3 ESD FROM SIGMAA (A) : 0.16 REMARK 3 LOW RESOLUTION CUTOFF (A) : 5.00 REMARK 3 REMARK 3 CROSS-VALIDATED ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM C-V LUZZATI PLOT (A) : 0.20 REMARK 3 ESD FROM C-V SIGMAA (A) : 0.18 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 BOND LENGTHS (A) : 0.007 REMARK 3 BOND ANGLES (DEGREES) : 1.400 REMARK 3 DIHEDRAL ANGLES (DEGREES) : 22.60 REMARK 3 IMPROPER ANGLES (DEGREES) : 0.790 REMARK 3 REMARK 3 ISOTROPIC THERMAL MODEL : RESTRAINED REMARK 3 REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. RMS SIGMA REMARK 3 MAIN-CHAIN BOND (A**2) : NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE (A**2) : NULL ; NULL REMARK 3 SIDE-CHAIN BOND (A**2) : NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE (A**2) : NULL ; NULL REMARK 3 REMARK 3 BULK SOLVENT MODELING. REMARK 3 METHOD USED : FLAT MODEL REMARK 3 KSOL : 0.37 REMARK 3 BSOL : 45.02 REMARK 3 REMARK 3 NCS MODEL : NULL REMARK 3 REMARK 3 NCS RESTRAINTS. RMS SIGMA/WEIGHT REMARK 3 GROUP 1 POSITIONAL (A) : NULL ; NULL REMARK 3 GROUP 1 B-FACTOR (A**2) : NULL ; NULL REMARK 3 REMARK 3 PARAMETER FILE 1 : PROTEIN_REP.PARAM REMARK 3 PARAMETER FILE 2 : WATER_REP.PARAM REMARK 3 PARAMETER FILE 3 : ION.PARAM REMARK 3 PARAMETER FILE 4 : NULL REMARK 3 TOPOLOGY FILE 1 : PROTEIN.TOP REMARK 3 TOPOLOGY FILE 2 : NULL REMARK 3 TOPOLOGY FILE 3 : NULL REMARK 3 TOPOLOGY FILE 4 : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 2HUR COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 04-AUG-06. REMARK 100 THE DEPOSITION ID IS D_1000038785. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 24-FEB-06 REMARK 200 TEMPERATURE (KELVIN) : 107.0 REMARK 200 PH : 4.6 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : ESRF REMARK 200 BEAMLINE : ID14-1 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.934 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 4 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : MOSFLM REMARK 200 DATA SCALING SOFTWARE : CCP4 (SCALA) REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 108681 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.620 REMARK 200 RESOLUTION RANGE LOW (A) : 38.050 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 0.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.7 REMARK 200 DATA REDUNDANCY : 3.500 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : 0.09000 REMARK 200 FOR THE DATA SET : 16.6000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.62 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.66 REMARK 200 COMPLETENESS FOR SHELL (%) : 97.1 REMARK 200 DATA REDUNDANCY IN SHELL : 2.80 REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : 0.38000 REMARK 200 FOR SHELL : 2.100 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: MOLREP REMARK 200 STARTING MODEL: PDB FILE 2NCK REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 47.50 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.34 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.1 M AMMONIUM SULPHATE, 25% PEG 4000 REMARK 280 0.1 M SODIUM ACETATE/ACETIC ACID, PH 4.6, VAPOR DIFFUSION, REMARK 280 SITTING DROP, TEMPERATURE 293K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: C 1 2 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,Y,-Z REMARK 290 3555 X+1/2,Y+1/2,Z REMARK 290 4555 -X+1/2,Y+1/2,-Z REMARK 290 REMARK 290 WHERE NNN -> OPERATOR NUMBER REMARK 290 MMM -> TRANSLATION VECTOR REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY TRANSFORMATIONS REMARK 290 THE FOLLOWING TRANSFORMATIONS OPERATE ON THE ATOM/HETATM REMARK 290 RECORDS IN THIS ENTRY TO PRODUCE CRYSTALLOGRAPHICALLY REMARK 290 RELATED MOLECULES. REMARK 290 SMTRY1 1 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 1 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 1 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 2 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 2 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 3 1.000000 0.000000 0.000000 59.45200 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 38.04750 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 59.45200 REMARK 290 SMTRY2 4 0.000000 1.000000 0.000000 38.04750 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000 REMARK 290 REMARK 290 REMARK: NULL REMARK 300 REMARK 300 BIOMOLECULE: 1, 2, 3, 4, 5 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: TETRAMERIC REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B, C, D 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 350 REMARK 350 BIOMOLECULE: 2 REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: TETRAMERIC REMARK 350 APPLY THE FOLLOWING TO CHAINS: E, F 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 350 BIOMT1 2 -1.000000 0.000000 0.000000 -40.84898 REMARK 350 BIOMT2 2 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT3 2 0.000000 0.000000 -1.000000 96.28089 REMARK 350 REMARK 350 BIOMOLECULE: 3 REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PQS REMARK 350 TOTAL BURIED SURFACE AREA: 6920 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 23520 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -92.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B 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 350 REMARK 350 BIOMOLECULE: 4 REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PQS REMARK 350 TOTAL BURIED SURFACE AREA: 7980 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 22460 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -91.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: E, F 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 350 REMARK 350 BIOMOLECULE: 5 REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PQS REMARK 350 APPLY THE FOLLOWING TO CHAINS: C, D 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 375 REMARK 375 SPECIAL POSITION REMARK 375 THE FOLLOWING ATOMS ARE FOUND TO BE WITHIN 0.15 ANGSTROMS REMARK 375 OF A SYMMETRY RELATED ATOM AND ARE ASSUMED TO BE ON SPECIAL REMARK 375 POSITIONS. REMARK 375 REMARK 375 ATOM RES CSSEQI REMARK 375 HOH B 261 LIES ON A SPECIAL POSITION. REMARK 375 HOH B 296 LIES ON A SPECIAL POSITION. REMARK 375 HOH B 297 LIES ON A SPECIAL POSITION. REMARK 375 HOH C 219 LIES ON A SPECIAL POSITION. REMARK 375 HOH E 303 LIES ON A SPECIAL POSITION. REMARK 375 HOH F 280 LIES ON A SPECIAL POSITION. REMARK 375 HOH F 323 LIES ON A SPECIAL POSITION. 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 THR A 37 149.09 -171.23 REMARK 500 GLU A 53 -6.06 -59.54 REMARK 500 GLU A 113 64.13 -106.82 REMARK 500 ASP C 55 81.79 -67.45 REMARK 500 GLU C 113 62.57 -107.98 REMARK 500 GLU D 135 109.11 -41.87 REMARK 500 GLU E 113 62.50 -102.28 REMARK 500 GLU F 135 118.74 -38.07 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 SO4 A 200 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SO4 B 200 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SO4 C 200 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SO4 D 200 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SO4 E 200 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SO4 F 200 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 2NCK RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF MYXOCOCCUS XANTHUS NUCLEOSIDE DIPHOSPHATE REMARK 900 KINASE AND ITS INTERACTION WITH A NUCLEOTIDE SUBSTRATE AT 2.0 REMARK 900 ANGSTROMS REMARK 900 RELATED ID: 1NPK RELATED DB: PDB REMARK 900 REFINED X-RAY STRUCTURE OF DICTYOSTELIUM NUCLEOSIDE DIPHOSPHATE REMARK 900 KINASE AT 1.8 ANGSTROMS RESOLUTION DBREF 2HUR A 2 143 UNP P0A763 NDK_ECOLI 1 142 DBREF 2HUR B 2 143 UNP P0A763 NDK_ECOLI 1 142 DBREF 2HUR C 2 143 UNP P0A763 NDK_ECOLI 1 142 DBREF 2HUR D 2 143 UNP P0A763 NDK_ECOLI 1 142 DBREF 2HUR E 2 143 UNP P0A763 NDK_ECOLI 1 142 DBREF 2HUR F 2 143 UNP P0A763 NDK_ECOLI 1 142 SEQRES 1 A 142 ALA ILE GLU ARG THR PHE SER ILE ILE LYS PRO ASN ALA SEQRES 2 A 142 VAL ALA LYS ASN VAL ILE GLY ASN ILE PHE ALA ARG PHE SEQRES 3 A 142 GLU ALA ALA GLY PHE LYS ILE VAL GLY THR LYS MET LEU SEQRES 4 A 142 HIS LEU THR VAL GLU GLN ALA ARG GLY PHE TYR ALA GLU SEQRES 5 A 142 HIS ASP GLY LYS PRO PHE PHE ASP GLY LEU VAL GLU PHE SEQRES 6 A 142 MET THR SER GLY PRO ILE VAL VAL SER VAL LEU GLU GLY SEQRES 7 A 142 GLU ASN ALA VAL GLN ARG HIS ARG ASP LEU LEU GLY ALA SEQRES 8 A 142 THR ASN PRO ALA ASN ALA LEU ALA GLY THR LEU ARG ALA SEQRES 9 A 142 ASP TYR ALA ASP SER LEU THR GLU ASN GLY THR HIS GLY SEQRES 10 A 142 SER ASP SER VAL GLU SER ALA ALA ARG GLU ILE ALA TYR SEQRES 11 A 142 PHE PHE GLY GLU GLY GLU VAL CYS PRO ARG THR ARG SEQRES 1 B 142 ALA ILE GLU ARG THR PHE SER ILE ILE LYS PRO ASN ALA SEQRES 2 B 142 VAL ALA LYS ASN VAL ILE GLY ASN ILE PHE ALA ARG PHE SEQRES 3 B 142 GLU ALA ALA GLY PHE LYS ILE VAL GLY THR LYS MET LEU SEQRES 4 B 142 HIS LEU THR VAL GLU GLN ALA ARG GLY PHE TYR ALA GLU SEQRES 5 B 142 HIS ASP GLY LYS PRO PHE PHE ASP GLY LEU VAL GLU PHE SEQRES 6 B 142 MET THR SER GLY PRO ILE VAL VAL SER VAL LEU GLU GLY SEQRES 7 B 142 GLU ASN ALA VAL GLN ARG HIS ARG ASP LEU LEU GLY ALA SEQRES 8 B 142 THR ASN PRO ALA ASN ALA LEU ALA GLY THR LEU ARG ALA SEQRES 9 B 142 ASP TYR ALA ASP SER LEU THR GLU ASN GLY THR HIS GLY SEQRES 10 B 142 SER ASP SER VAL GLU SER ALA ALA ARG GLU ILE ALA TYR SEQRES 11 B 142 PHE PHE GLY GLU GLY GLU VAL CYS PRO ARG THR ARG SEQRES 1 C 142 ALA ILE GLU ARG THR PHE SER ILE ILE LYS PRO ASN ALA SEQRES 2 C 142 VAL ALA LYS ASN VAL ILE GLY ASN ILE PHE ALA ARG PHE SEQRES 3 C 142 GLU ALA ALA GLY PHE LYS ILE VAL GLY THR LYS MET LEU SEQRES 4 C 142 HIS LEU THR VAL GLU GLN ALA ARG GLY PHE TYR ALA GLU SEQRES 5 C 142 HIS ASP GLY LYS PRO PHE PHE ASP GLY LEU VAL GLU PHE SEQRES 6 C 142 MET THR SER GLY PRO ILE VAL VAL SER VAL LEU GLU GLY SEQRES 7 C 142 GLU ASN ALA VAL GLN ARG HIS ARG ASP LEU LEU GLY ALA SEQRES 8 C 142 THR ASN PRO ALA ASN ALA LEU ALA GLY THR LEU ARG ALA SEQRES 9 C 142 ASP TYR ALA ASP SER LEU THR GLU ASN GLY THR HIS GLY SEQRES 10 C 142 SER ASP SER VAL GLU SER ALA ALA ARG GLU ILE ALA TYR SEQRES 11 C 142 PHE PHE GLY GLU GLY GLU VAL CYS PRO ARG THR ARG SEQRES 1 D 142 ALA ILE GLU ARG THR PHE SER ILE ILE LYS PRO ASN ALA SEQRES 2 D 142 VAL ALA LYS ASN VAL ILE GLY ASN ILE PHE ALA ARG PHE SEQRES 3 D 142 GLU ALA ALA GLY PHE LYS ILE VAL GLY THR LYS MET LEU SEQRES 4 D 142 HIS LEU THR VAL GLU GLN ALA ARG GLY PHE TYR ALA GLU SEQRES 5 D 142 HIS ASP GLY LYS PRO PHE PHE ASP GLY LEU VAL GLU PHE SEQRES 6 D 142 MET THR SER GLY PRO ILE VAL VAL SER VAL LEU GLU GLY SEQRES 7 D 142 GLU ASN ALA VAL GLN ARG HIS ARG ASP LEU LEU GLY ALA SEQRES 8 D 142 THR ASN PRO ALA ASN ALA LEU ALA GLY THR LEU ARG ALA SEQRES 9 D 142 ASP TYR ALA ASP SER LEU THR GLU ASN GLY THR HIS GLY SEQRES 10 D 142 SER ASP SER VAL GLU SER ALA ALA ARG GLU ILE ALA TYR SEQRES 11 D 142 PHE PHE GLY GLU GLY GLU VAL CYS PRO ARG THR ARG SEQRES 1 E 142 ALA ILE GLU ARG THR PHE SER ILE ILE LYS PRO ASN ALA SEQRES 2 E 142 VAL ALA LYS ASN VAL ILE GLY ASN ILE PHE ALA ARG PHE SEQRES 3 E 142 GLU ALA ALA GLY PHE LYS ILE VAL GLY THR LYS MET LEU SEQRES 4 E 142 HIS LEU THR VAL GLU GLN ALA ARG GLY PHE TYR ALA GLU SEQRES 5 E 142 HIS ASP GLY LYS PRO PHE PHE ASP GLY LEU VAL GLU PHE SEQRES 6 E 142 MET THR SER GLY PRO ILE VAL VAL SER VAL LEU GLU GLY SEQRES 7 E 142 GLU ASN ALA VAL GLN ARG HIS ARG ASP LEU LEU GLY ALA SEQRES 8 E 142 THR ASN PRO ALA ASN ALA LEU ALA GLY THR LEU ARG ALA SEQRES 9 E 142 ASP TYR ALA ASP SER LEU THR GLU ASN GLY THR HIS GLY SEQRES 10 E 142 SER ASP SER VAL GLU SER ALA ALA ARG GLU ILE ALA TYR SEQRES 11 E 142 PHE PHE GLY GLU GLY GLU VAL CYS PRO ARG THR ARG SEQRES 1 F 142 ALA ILE GLU ARG THR PHE SER ILE ILE LYS PRO ASN ALA SEQRES 2 F 142 VAL ALA LYS ASN VAL ILE GLY ASN ILE PHE ALA ARG PHE SEQRES 3 F 142 GLU ALA ALA GLY PHE LYS ILE VAL GLY THR LYS MET LEU SEQRES 4 F 142 HIS LEU THR VAL GLU GLN ALA ARG GLY PHE TYR ALA GLU SEQRES 5 F 142 HIS ASP GLY LYS PRO PHE PHE ASP GLY LEU VAL GLU PHE SEQRES 6 F 142 MET THR SER GLY PRO ILE VAL VAL SER VAL LEU GLU GLY SEQRES 7 F 142 GLU ASN ALA VAL GLN ARG HIS ARG ASP LEU LEU GLY ALA SEQRES 8 F 142 THR ASN PRO ALA ASN ALA LEU ALA GLY THR LEU ARG ALA SEQRES 9 F 142 ASP TYR ALA ASP SER LEU THR GLU ASN GLY THR HIS GLY SEQRES 10 F 142 SER ASP SER VAL GLU SER ALA ALA ARG GLU ILE ALA TYR SEQRES 11 F 142 PHE PHE GLY GLU GLY GLU VAL CYS PRO ARG THR ARG HET SO4 A 200 5 HET SO4 B 200 5 HET SO4 C 200 5 HET SO4 D 200 5 HET SO4 E 200 5 HET SO4 F 200 5 HETNAM SO4 SULFATE ION FORMUL 7 SO4 6(O4 S 2-) FORMUL 13 HOH *717(H2 O) HELIX 1 1 LYS A 11 LYS A 17 1ALPHA 0 CHAIN A 7 HELIX 2 2 VAL A 19 ALA A 30 1ALPHA 1 CHAIN A 12 HELIX 3 3 THR A 43 TYR A 51 1ALPHA A CHAIN A 9 HELIX 4 4 ALA A 52 ASP A 55 5 4 HELIX 5 5 PHE A 59 THR A 68 1ALPHA 2 CHAIN A 10 HELIX 6 6 ASN A 81 GLY A 91 1ALPHA 3 CHAIN A 11 HELIX 7 7 THR A 102 ALA A 108 1ALPHA 3' CHAIN A 7 HELIX 8 8 SER A 121 PHE A 133 1ALPHA 4 CHAIN A 13 HELIX 9 9 LYS B 11 LYS B 17 1ALPHA 0 CHAIN B 7 HELIX 10 10 VAL B 19 ALA B 30 1ALPHA 1 CHAIN B 12 HELIX 11 11 THR B 43 TYR B 51 1ALPHA A CHAIN B 9 HELIX 12 12 ALA B 52 ASP B 55 5 4 HELIX 13 13 PHE B 59 THR B 68 1ALPHA 2 CHAIN B 10 HELIX 14 14 ASN B 81 GLY B 91 1ALPHA 3 CHAIN B 11 HELIX 15 15 THR B 102 ALA B 108 1ALPHA 3' CHAIN B 7 HELIX 16 16 SER B 121 PHE B 133 1ALPHA 4 CHAIN B 13 HELIX 17 17 LYS C 11 LYS C 17 1ALPHA 0 CHAIN C 7 HELIX 18 18 VAL C 19 ALA C 30 1ALPHA 1 CHAIN C 12 HELIX 19 19 THR C 43 TYR C 51 1ALPHA A CHAIN C 9 HELIX 20 20 ALA C 52 ASP C 55 5 4 HELIX 21 21 PHE C 59 THR C 68 1ALPHA 2 CHAIN C 10 HELIX 22 22 ASN C 81 GLY C 91 1ALPHA 3 CHAIN C 11 HELIX 23 23 THR C 102 ALA C 108 1ALPHA 3' CHAIN C 7 HELIX 24 24 SER C 121 PHE C 133 1ALPHA 4 CHAIN C 13 HELIX 25 25 LYS D 11 LYS D 17 1ALPHA 0 CHAIN D 7 HELIX 26 26 VAL D 19 ALA D 30 1ALPHA 1 CHAIN D 12 HELIX 27 27 THR D 43 TYR D 51 1ALPHA A CHAIN D 9 HELIX 28 28 ALA D 52 ASP D 55 5 4 HELIX 29 29 PHE D 59 THR D 68 1ALPHA 2 CHAIN D 10 HELIX 30 30 ASN D 81 GLY D 91 1ALPHA 3 CHAIN D 11 HELIX 31 31 ASN D 94 ALA D 98 5 5 HELIX 32 32 THR D 102 ALA D 108 1ALPHA 3' CHAIN D 7 HELIX 33 33 SER D 121 PHE D 133 1ALPHA 4 CHAIN D 13 HELIX 34 34 LYS E 11 LYS E 17 1ALPHA 0 CHAIN E 7 HELIX 35 35 VAL E 19 ALA E 30 1ALPHA 1 CHAIN E 12 HELIX 36 36 THR E 43 TYR E 51 1ALPHA A CHAIN E 9 HELIX 37 37 ALA E 52 ASP E 55 5 4 HELIX 38 38 PHE E 59 THR E 68 1ALPHA 2 CHAIN E 10 HELIX 39 39 ASN E 81 GLY E 91 1ALPHA 3 CHAIN E 11 HELIX 40 40 THR E 102 ALA E 108 1ALPHA 3' CHAIN E 7 HELIX 41 41 SER E 121 PHE E 133 1ALPHA 4 CHAIN E 13 HELIX 42 42 LYS F 11 LYS F 17 1ALPHA 0 CHAIN F 7 HELIX 43 43 VAL F 19 ALA F 30 1ALPHA 1 CHAIN F 12 HELIX 44 44 THR F 43 TYR F 51 1ALPHA A CHAIN F 9 HELIX 45 45 ALA F 52 ASP F 55 5 4 HELIX 46 46 PHE F 59 THR F 68 1ALPHA 2 CHAIN F 10 HELIX 47 47 ASN F 81 GLY F 91 1ALPHA 3 CHAIN F 11 HELIX 48 48 THR F 102 ALA F 108 1ALPHA 3' CHAIN F 7 HELIX 49 49 SER F 121 PHE F 133 1ALPHA 4 CHAIN F 13 SHEET 1 A 4 LYS A 33 LEU A 40 0 SHEET 2 A 4 ILE A 72 GLU A 80 -1 O ILE A 72 N LEU A 40 SHEET 3 A 4 ILE A 3 ILE A 10 -1 N GLU A 4 O GLY A 79 SHEET 4 A 4 THR A 116 GLY A 118 -1 O HIS A 117 N ILE A 9 SHEET 1 B 4 LYS B 33 LEU B 40 0 SHEET 2 B 4 ILE B 72 GLU B 80 -1 O ILE B 72 N LEU B 40 SHEET 3 B 4 ILE B 3 ILE B 10 -1 N GLU B 4 O GLY B 79 SHEET 4 B 4 THR B 116 GLY B 118 -1 O HIS B 117 N ILE B 9 SHEET 1 C 4 LYS C 33 LEU C 40 0 SHEET 2 C 4 ILE C 72 GLU C 80 -1 O GLU C 78 N LYS C 33 SHEET 3 C 4 ILE C 3 ILE C 10 -1 N GLU C 4 O GLY C 79 SHEET 4 C 4 THR C 116 GLY C 118 -1 O HIS C 117 N ILE C 9 SHEET 1 D 4 LYS D 33 LEU D 40 0 SHEET 2 D 4 ILE D 72 GLU D 80 -1 O ILE D 72 N LEU D 40 SHEET 3 D 4 ILE D 3 ILE D 10 -1 N SER D 8 O SER D 75 SHEET 4 D 4 THR D 116 GLY D 118 -1 O HIS D 117 N ILE D 9 SHEET 1 E 4 LYS E 33 LEU E 40 0 SHEET 2 E 4 ILE E 72 GLU E 80 -1 O ILE E 72 N LEU E 40 SHEET 3 E 4 ILE E 3 ILE E 10 -1 N ILE E 10 O VAL E 73 SHEET 4 E 4 THR E 116 GLY E 118 -1 O HIS E 117 N ILE E 9 SHEET 1 F 4 LYS F 33 LEU F 40 0 SHEET 2 F 4 ILE F 72 GLU F 80 -1 O ILE F 72 N LEU F 40 SHEET 3 F 4 ILE F 3 ILE F 10 -1 N THR F 6 O LEU F 77 SHEET 4 F 4 THR F 116 GLY F 118 -1 O HIS F 117 N ILE F 9 SITE 1 AC1 8 LYS A 11 THR A 93 ARG A 104 ASN A 114 SITE 2 AC1 8 HIS A 117 HOH A 226 HOH A 237 HOH A 264 SITE 1 AC2 8 LYS B 11 THR B 93 ARG B 104 ASN B 114 SITE 2 AC2 8 HIS B 117 HOH B 246 HOH B 276 HOH B 322 SITE 1 AC3 7 LYS C 11 THR C 93 ARG C 104 ASN C 114 SITE 2 AC3 7 HIS C 117 HOH C 247 HOH C 258 SITE 1 AC4 11 LYS D 11 THR D 93 ARG D 104 ASN D 114 SITE 2 AC4 11 HIS D 117 HOH D 327 HOH D 334 HOH D 397 SITE 3 AC4 11 HOH D 408 HOH D 443 HOH F 360 SITE 1 AC5 6 LYS E 11 THR E 93 ARG E 104 ASN E 114 SITE 2 AC5 6 HIS E 117 HOH E 287 SITE 1 AC6 11 HOH D 343 LYS F 11 THR F 93 ARG F 104 SITE 2 AC6 11 ASN F 114 HIS F 117 HOH F 290 HOH F 302 SITE 3 AC6 11 HOH F 329 HOH F 332 HOH F 344 CRYST1 118.904 76.095 104.588 90.00 112.99 90.00 C 1 2 1 24 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 0.008410 0.000000 0.003568 0.00000 SCALE2 0.000000 0.013141 0.000000 0.00000 SCALE3 0.000000 0.000000 0.010386 0.00000