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 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) : 1.40
REMARK 3 DIHEDRAL ANGLES (DEGREES) : 22.60
REMARK 3 IMPROPER ANGLES (DEGREES) : 0.79
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 RCSB ID CODE IS RCSB038785.
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 <I/SIGMA(I)> 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 <I/SIGMA(I)> 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 C 219 LIES ON A SPECIAL POSITION.
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 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 525
REMARK 525 SOLVENT
REMARK 525
REMARK 525 THE SOLVENT MOLECULES HAVE CHAIN IDENTIFIERS THAT
REMARK 525 INDICATE THE POLYMER CHAIN WITH WHICH THEY ARE MOST
REMARK 525 CLOSELY ASSOCIATED. THE REMARK LISTS ALL THE SOLVENT
REMARK 525 MOLECULES WHICH ARE MORE THAN 5A AWAY FROM THE
REMARK 525 NEAREST POLYMER CHAIN (M = MODEL NUMBER;
REMARK 525 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE
REMARK 525 NUMBER; I=INSERTION CODE):
REMARK 525
REMARK 525 M RES CSSEQI
REMARK 525 HOH A 254 DISTANCE = 5.19 ANGSTROMS
REMARK 525 HOH A 281 DISTANCE = 6.22 ANGSTROMS
REMARK 525 HOH B 265 DISTANCE = 5.27 ANGSTROMS
REMARK 525 HOH B 360 DISTANCE = 6.19 ANGSTROMS
REMARK 525 HOH C 273 DISTANCE = 5.21 ANGSTROMS
REMARK 525 HOH C 304 DISTANCE = 6.28 ANGSTROMS
REMARK 525 HOH C 321 DISTANCE = 5.93 ANGSTROMS
REMARK 525 HOH D 313 DISTANCE = 6.00 ANGSTROMS
REMARK 525 HOH E 301 DISTANCE = 5.38 ANGSTROMS
REMARK 525 HOH E 336 DISTANCE = 6.16 ANGSTROMS
REMARK 525 HOH E 342 DISTANCE = 5.16 ANGSTROMS
REMARK 525 HOH F 333 DISTANCE = 5.07 ANGSTROMS
REMARK 525 HOH F 376 DISTANCE = 5.29 ANGSTROMS
REMARK 525 HOH F 377 DISTANCE = 6.25 ANGSTROMS
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
REMARK 900 DIPHOSPHATE KINASE AND ITS INTERACTION WITH A NUCLEOTIDE
REMARK 900 SUBSTRATE AT 2.0 ANGSTROMS
REMARK 900 RELATED ID: 1NPK RELATED DB: PDB
REMARK 900 REFINED X-RAY STRUCTURE OF DICTYOSTELIUM NUCLEOSIDE
REMARK 900 DIPHOSPHATE 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
(ATOM LINES ARE NOT SHOWN.)
END
