HEADER TRANSFERASE 20-JAN-04 1S57 TITLE CRYSTAL STRUCTURE OF NUCLEOSIDE DIPHOSPHATE KINASE 2 FROM ARABIDOPSIS COMPND MOL_ID: 1; COMPND 2 MOLECULE: NUCLEOSIDE DIPHOSPHATE KINASE II; COMPND 3 CHAIN: A, B, C, D, E, F; COMPND 4 SYNONYM: NUCLEOSIDE DIPHOSPHATE KINASE 2, NDK II, NDP KINASE II, NDPK COMPND 5 II, NDPK IA; COMPND 6 EC: 2.7.4.6; COMPND 7 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: ARABIDOPSIS THALIANA; SOURCE 3 ORGANISM_COMMON: THALE CRESS; SOURCE 4 ORGANISM_TAXID: 3702; SOURCE 5 GENE: NDPK2; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3); SOURCE 7 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: BL21(DE3); SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 10 EXPRESSION_SYSTEM_PLASMID: PGEX-4T-1 KEYWDS TRANSFERASE, KINASE EXPDTA X-RAY DIFFRACTION AUTHOR Y.J.IM,J.-I.KIM,Y.SHEN,Y.NA,Y.-J.HAN,S.-H.KIM,P.-S.SONG,S.H.EOM REVDAT 3 25-OCT-23 1S57 1 REMARK REVDAT 2 24-FEB-09 1S57 1 VERSN REVDAT 1 30-NOV-04 1S57 0 JRNL AUTH Y.J.IM,J.-I.KIM,Y.SHEN,Y.NA,Y.-J.HAN,S.-H.KIM,P.-S.SONG, JRNL AUTH 2 S.H.EOM JRNL TITL STRUCTURAL ANALYSIS OF ARABIDOPSIS THALIANA NUCLEOSIDE JRNL TITL 2 DIPHOSPHATE KINASE-2 FOR PHYTOCHROME-MEDIATED LIGHT JRNL TITL 3 SIGNALING JRNL REF J.MOL.BIOL. V. 343 659 2004 JRNL REFN ISSN 0022-2836 JRNL PMID 15465053 JRNL DOI 10.1016/J.JMB.2004.08.054 REMARK 2 REMARK 2 RESOLUTION. 1.80 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 : ENGH & HUBER REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.80 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 45.24 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 DATA CUTOFF HIGH (ABS(F)) : 2140958.590 REMARK 3 DATA CUTOFF LOW (ABS(F)) : 0.0000 REMARK 3 COMPLETENESS (WORKING+TEST) (%) : 99.8 REMARK 3 NUMBER OF REFLECTIONS : 84292 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) : 0.212 REMARK 3 FREE R VALUE : 0.241 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.100 REMARK 3 FREE R VALUE TEST SET COUNT : 4284 REMARK 3 ESTIMATED ERROR OF FREE R VALUE : 0.004 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) : 1.80 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.91 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 99.40 REMARK 3 REFLECTIONS IN BIN (WORKING SET) : 13106 REMARK 3 BIN R VALUE (WORKING SET) : 0.2590 REMARK 3 BIN FREE R VALUE : 0.3000 REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : 5.10 REMARK 3 BIN FREE R VALUE TEST SET COUNT : 699 REMARK 3 ESTIMATED ERROR OF BIN FREE R VALUE : 0.011 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 7095 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 180 REMARK 3 SOLVENT ATOMS : 545 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 16.40 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 21.60 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 5.75000 REMARK 3 B22 (A**2) : -0.94000 REMARK 3 B33 (A**2) : -4.81000 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : 0.00000 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM LUZZATI PLOT (A) : 0.22 REMARK 3 ESD FROM SIGMAA (A) : 0.11 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) : 0.26 REMARK 3 ESD FROM C-V SIGMAA (A) : 0.17 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 BOND LENGTHS (A) : 0.005 REMARK 3 BOND ANGLES (DEGREES) : 1.300 REMARK 3 DIHEDRAL ANGLES (DEGREES) : 21.90 REMARK 3 IMPROPER ANGLES (DEGREES) : 0.740 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) : 1.120 ; 1.500 REMARK 3 MAIN-CHAIN ANGLE (A**2) : 1.620 ; 2.000 REMARK 3 SIDE-CHAIN BOND (A**2) : 1.990 ; 2.000 REMARK 3 SIDE-CHAIN ANGLE (A**2) : 2.840 ; 2.500 REMARK 3 REMARK 3 BULK SOLVENT MODELING. REMARK 3 METHOD USED : FLAT MODEL REMARK 3 KSOL : 0.38 REMARK 3 BSOL : 39.97 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 : EPE.PARAM REMARK 3 PARAMETER FILE 3 : ION.PARAM REMARK 3 PARAMETER FILE 4 : WATER_REP.PARAM REMARK 3 PARAMETER FILE 5 : NULL REMARK 3 TOPOLOGY FILE 1 : PROTEIN.TOP REMARK 3 TOPOLOGY FILE 2 : EPE.TOP REMARK 3 TOPOLOGY FILE 3 : ION.TOP REMARK 3 TOPOLOGY FILE 4 : WATER.TOP REMARK 3 TOPOLOGY FILE 5 : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 1S57 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 22-JAN-04. REMARK 100 THE DEPOSITION ID IS D_1000021381. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 25-JUN-03 REMARK 200 TEMPERATURE (KELVIN) : 298.0 REMARK 200 PH : 7.0 REMARK 200 NUMBER OF CRYSTALS USED : NULL REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : PHOTON FACTORY REMARK 200 BEAMLINE : AR-NW12A REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.000 REMARK 200 MONOCHROMATOR : SI 111 CHANNEL REMARK 200 OPTICS : MIRRORS REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 210 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 84434 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.800 REMARK 200 RESOLUTION RANGE LOW (A) : 50.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 2.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.9 REMARK 200 DATA REDUNDANCY : 8.100 REMARK 200 R MERGE (I) : 0.06800 REMARK 200 R SYM (I) : 0.06800 REMARK 200 FOR THE DATA SET : 36.8000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.80 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.83 REMARK 200 COMPLETENESS FOR SHELL (%) : 98.3 REMARK 200 DATA REDUNDANCY IN SHELL : 6.30 REMARK 200 R MERGE FOR SHELL (I) : 0.37300 REMARK 200 R SYM FOR SHELL (I) : 0.37300 REMARK 200 FOR SHELL : 3.600 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: AMORE REMARK 200 STARTING MODEL: PDB ENTRY 1JXV REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 39.77 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.06 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: AMMONIUM SULFATE, PH 7.0, VAPOR REMARK 280 DIFFUSION, HANGING DROP, TEMPERATURE 293K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 21 21 21 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X+1/2,-Y,Z+1/2 REMARK 290 3555 -X,Y+1/2,-Z+1/2 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 34.69700 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 59.66200 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 54.42750 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 59.66200 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 34.69700 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 54.42750 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 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: HEXAMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: HEXAMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 23900 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 33390 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -264.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B, C, D, 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: 2 REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: HEXAMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 16090 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 41200 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -261.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B, C 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 APPLY THE FOLLOWING TO CHAINS: D, E, F REMARK 350 BIOMT1 2 -1.000000 0.000000 0.000000 69.39400 REMARK 350 BIOMT2 2 0.000000 1.000000 0.000000 54.42750 REMARK 350 BIOMT3 2 0.000000 0.000000 -1.000000 59.66200 REMARK 465 REMARK 465 MISSING RESIDUES REMARK 465 THE FOLLOWING RESIDUES WERE NOT LOCATED IN THE REMARK 465 EXPERIMENT. (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 465 IDENTIFIER; SSSEQ=SEQUENCE NUMBER; I=INSERTION CODE.) REMARK 465 REMARK 465 M RES C SSSEQI REMARK 465 SER B 79 REMARK 465 MET B 80 REMARK 465 GLU B 81 REMARK 465 ASP B 82 REMARK 465 SER C 79 REMARK 465 MET C 80 REMARK 465 GLU C 81 REMARK 465 ASP C 82 REMARK 465 SER E 79 REMARK 465 MET E 80 REMARK 465 GLU E 81 REMARK 465 ASP E 82 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 MET A 80 34.34 -99.51 REMARK 500 LYS A 118 140.24 -170.87 REMARK 500 ASP A 133 9.53 -66.32 REMARK 500 ASN A 194 33.69 -99.01 REMARK 500 ILE A 195 -26.54 40.26 REMARK 500 LYS B 118 139.12 -170.10 REMARK 500 ARG B 193 57.86 -145.16 REMARK 500 ASN B 194 32.31 -95.91 REMARK 500 ILE B 195 -21.35 40.06 REMARK 500 GLU B 215 -52.22 -27.74 REMARK 500 LYS C 118 138.96 -173.36 REMARK 500 TYR C 131 44.11 -94.15 REMARK 500 ASN C 194 31.97 -98.01 REMARK 500 ILE C 195 -34.72 49.07 REMARK 500 GLU C 215 -91.53 -46.34 REMARK 500 LYS D 118 138.21 -170.82 REMARK 500 ASN D 194 30.14 -99.53 REMARK 500 ILE D 195 -45.28 58.53 REMARK 500 GLU D 215 -57.78 -28.95 REMARK 500 LYS E 118 139.43 -173.49 REMARK 500 TYR E 131 43.44 -100.75 REMARK 500 ASN E 194 31.62 -97.40 REMARK 500 ILE E 195 -22.93 41.46 REMARK 500 ILE F 195 -46.11 56.50 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 1001 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SO4 A 1002 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SO4 A 1003 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SO4 B 1004 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SO4 B 1005 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SO4 B 1006 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC7 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SO4 C 1007 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC8 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SO4 C 1008 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC9 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SO4 C 1009 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SO4 D 1010 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SO4 D 1011 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SO4 D 1012 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SO4 E 1013 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SO4 E 1014 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SO4 E 1015 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC7 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SO4 F 1016 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC8 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SO4 F 1017 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC9 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SO4 F 1018 REMARK 800 REMARK 800 SITE_IDENTIFIER: CC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE EPE A 1101 REMARK 800 REMARK 800 SITE_IDENTIFIER: CC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE EPE B 1102 REMARK 800 REMARK 800 SITE_IDENTIFIER: CC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE EPE C 1103 REMARK 800 REMARK 800 SITE_IDENTIFIER: CC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE EPE D 1104 REMARK 800 REMARK 800 SITE_IDENTIFIER: CC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE EPE C 1105 REMARK 800 REMARK 800 SITE_IDENTIFIER: CC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE EPE F 1106 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 1S59 RELATED DB: PDB REMARK 900 THE SAME PROTEIN COMPLEXED WITH DGTP DBREF 1S57 A 79 231 UNP O64903 NDK2_ARATH 79 231 DBREF 1S57 B 79 231 UNP O64903 NDK2_ARATH 79 231 DBREF 1S57 C 79 231 UNP O64903 NDK2_ARATH 79 231 DBREF 1S57 D 79 231 UNP O64903 NDK2_ARATH 79 231 DBREF 1S57 E 79 231 UNP O64903 NDK2_ARATH 79 231 DBREF 1S57 F 79 231 UNP O64903 NDK2_ARATH 79 231 SEQRES 1 A 153 SER MET GLU ASP VAL GLU GLU THR TYR ILE MET VAL LYS SEQRES 2 A 153 PRO ASP GLY ILE GLN ARG GLY LEU VAL GLY GLU ILE ILE SEQRES 3 A 153 SER ARG PHE GLU LYS LYS GLY PHE LYS LEU ILE GLY LEU SEQRES 4 A 153 LYS MET PHE GLN CYS PRO LYS GLU LEU ALA GLU GLU HIS SEQRES 5 A 153 TYR LYS ASP LEU SER ALA LYS SER PHE PHE PRO ASN LEU SEQRES 6 A 153 ILE GLU TYR ILE THR SER GLY PRO VAL VAL CYS MET ALA SEQRES 7 A 153 TRP GLU GLY VAL GLY VAL VAL ALA SER ALA ARG LYS LEU SEQRES 8 A 153 ILE GLY LYS THR ASP PRO LEU GLN ALA GLU PRO GLY THR SEQRES 9 A 153 ILE ARG GLY ASP LEU ALA VAL GLN THR GLY ARG ASN ILE SEQRES 10 A 153 VAL HIS GLY SER ASP SER PRO GLU ASN GLY LYS ARG GLU SEQRES 11 A 153 ILE GLY LEU TRP PHE LYS GLU GLY GLU LEU CYS LYS TRP SEQRES 12 A 153 ASP SER ALA LEU ALA THR TRP LEU ARG GLU SEQRES 1 B 153 SER MET GLU ASP VAL GLU GLU THR TYR ILE MET VAL LYS SEQRES 2 B 153 PRO ASP GLY ILE GLN ARG GLY LEU VAL GLY GLU ILE ILE SEQRES 3 B 153 SER ARG PHE GLU LYS LYS GLY PHE LYS LEU ILE GLY LEU SEQRES 4 B 153 LYS MET PHE GLN CYS PRO LYS GLU LEU ALA GLU GLU HIS SEQRES 5 B 153 TYR LYS ASP LEU SER ALA LYS SER PHE PHE PRO ASN LEU SEQRES 6 B 153 ILE GLU TYR ILE THR SER GLY PRO VAL VAL CYS MET ALA SEQRES 7 B 153 TRP GLU GLY VAL GLY VAL VAL ALA SER ALA ARG LYS LEU SEQRES 8 B 153 ILE GLY LYS THR ASP PRO LEU GLN ALA GLU PRO GLY THR SEQRES 9 B 153 ILE ARG GLY ASP LEU ALA VAL GLN THR GLY ARG ASN ILE SEQRES 10 B 153 VAL HIS GLY SER ASP SER PRO GLU ASN GLY LYS ARG GLU SEQRES 11 B 153 ILE GLY LEU TRP PHE LYS GLU GLY GLU LEU CYS LYS TRP SEQRES 12 B 153 ASP SER ALA LEU ALA THR TRP LEU ARG GLU SEQRES 1 C 153 SER MET GLU ASP VAL GLU GLU THR TYR ILE MET VAL LYS SEQRES 2 C 153 PRO ASP GLY ILE GLN ARG GLY LEU VAL GLY GLU ILE ILE SEQRES 3 C 153 SER ARG PHE GLU LYS LYS GLY PHE LYS LEU ILE GLY LEU SEQRES 4 C 153 LYS MET PHE GLN CYS PRO LYS GLU LEU ALA GLU GLU HIS SEQRES 5 C 153 TYR LYS ASP LEU SER ALA LYS SER PHE PHE PRO ASN LEU SEQRES 6 C 153 ILE GLU TYR ILE THR SER GLY PRO VAL VAL CYS MET ALA SEQRES 7 C 153 TRP GLU GLY VAL GLY VAL VAL ALA SER ALA ARG LYS LEU SEQRES 8 C 153 ILE GLY LYS THR ASP PRO LEU GLN ALA GLU PRO GLY THR SEQRES 9 C 153 ILE ARG GLY ASP LEU ALA VAL GLN THR GLY ARG ASN ILE SEQRES 10 C 153 VAL HIS GLY SER ASP SER PRO GLU ASN GLY LYS ARG GLU SEQRES 11 C 153 ILE GLY LEU TRP PHE LYS GLU GLY GLU LEU CYS LYS TRP SEQRES 12 C 153 ASP SER ALA LEU ALA THR TRP LEU ARG GLU SEQRES 1 D 153 SER MET GLU ASP VAL GLU GLU THR TYR ILE MET VAL LYS SEQRES 2 D 153 PRO ASP GLY ILE GLN ARG GLY LEU VAL GLY GLU ILE ILE SEQRES 3 D 153 SER ARG PHE GLU LYS LYS GLY PHE LYS LEU ILE GLY LEU SEQRES 4 D 153 LYS MET PHE GLN CYS PRO LYS GLU LEU ALA GLU GLU HIS SEQRES 5 D 153 TYR LYS ASP LEU SER ALA LYS SER PHE PHE PRO ASN LEU SEQRES 6 D 153 ILE GLU TYR ILE THR SER GLY PRO VAL VAL CYS MET ALA SEQRES 7 D 153 TRP GLU GLY VAL GLY VAL VAL ALA SER ALA ARG LYS LEU SEQRES 8 D 153 ILE GLY LYS THR ASP PRO LEU GLN ALA GLU PRO GLY THR SEQRES 9 D 153 ILE ARG GLY ASP LEU ALA VAL GLN THR GLY ARG ASN ILE SEQRES 10 D 153 VAL HIS GLY SER ASP SER PRO GLU ASN GLY LYS ARG GLU SEQRES 11 D 153 ILE GLY LEU TRP PHE LYS GLU GLY GLU LEU CYS LYS TRP SEQRES 12 D 153 ASP SER ALA LEU ALA THR TRP LEU ARG GLU SEQRES 1 E 153 SER MET GLU ASP VAL GLU GLU THR TYR ILE MET VAL LYS SEQRES 2 E 153 PRO ASP GLY ILE GLN ARG GLY LEU VAL GLY GLU ILE ILE SEQRES 3 E 153 SER ARG PHE GLU LYS LYS GLY PHE LYS LEU ILE GLY LEU SEQRES 4 E 153 LYS MET PHE GLN CYS PRO LYS GLU LEU ALA GLU GLU HIS SEQRES 5 E 153 TYR LYS ASP LEU SER ALA LYS SER PHE PHE PRO ASN LEU SEQRES 6 E 153 ILE GLU TYR ILE THR SER GLY PRO VAL VAL CYS MET ALA SEQRES 7 E 153 TRP GLU GLY VAL GLY VAL VAL ALA SER ALA ARG LYS LEU SEQRES 8 E 153 ILE GLY LYS THR ASP PRO LEU GLN ALA GLU PRO GLY THR SEQRES 9 E 153 ILE ARG GLY ASP LEU ALA VAL GLN THR GLY ARG ASN ILE SEQRES 10 E 153 VAL HIS GLY SER ASP SER PRO GLU ASN GLY LYS ARG GLU SEQRES 11 E 153 ILE GLY LEU TRP PHE LYS GLU GLY GLU LEU CYS LYS TRP SEQRES 12 E 153 ASP SER ALA LEU ALA THR TRP LEU ARG GLU SEQRES 1 F 153 SER MET GLU ASP VAL GLU GLU THR TYR ILE MET VAL LYS SEQRES 2 F 153 PRO ASP GLY ILE GLN ARG GLY LEU VAL GLY GLU ILE ILE SEQRES 3 F 153 SER ARG PHE GLU LYS LYS GLY PHE LYS LEU ILE GLY LEU SEQRES 4 F 153 LYS MET PHE GLN CYS PRO LYS GLU LEU ALA GLU GLU HIS SEQRES 5 F 153 TYR LYS ASP LEU SER ALA LYS SER PHE PHE PRO ASN LEU SEQRES 6 F 153 ILE GLU TYR ILE THR SER GLY PRO VAL VAL CYS MET ALA SEQRES 7 F 153 TRP GLU GLY VAL GLY VAL VAL ALA SER ALA ARG LYS LEU SEQRES 8 F 153 ILE GLY LYS THR ASP PRO LEU GLN ALA GLU PRO GLY THR SEQRES 9 F 153 ILE ARG GLY ASP LEU ALA VAL GLN THR GLY ARG ASN ILE SEQRES 10 F 153 VAL HIS GLY SER ASP SER PRO GLU ASN GLY LYS ARG GLU SEQRES 11 F 153 ILE GLY LEU TRP PHE LYS GLU GLY GLU LEU CYS LYS TRP SEQRES 12 F 153 ASP SER ALA LEU ALA THR TRP LEU ARG GLU HET SO4 A1001 5 HET SO4 A1002 5 HET SO4 A1003 5 HET EPE A1101 15 HET SO4 B1004 5 HET SO4 B1005 5 HET SO4 B1006 5 HET EPE B1102 15 HET SO4 C1007 5 HET SO4 C1008 5 HET SO4 C1009 5 HET EPE C1103 15 HET EPE C1105 15 HET SO4 D1010 5 HET SO4 D1011 5 HET SO4 D1012 5 HET EPE D1104 15 HET SO4 E1013 5 HET SO4 E1014 5 HET SO4 E1015 5 HET SO4 F1016 5 HET SO4 F1017 5 HET SO4 F1018 5 HET EPE F1106 15 HETNAM SO4 SULFATE ION HETNAM EPE 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID HETSYN EPE HEPES FORMUL 7 SO4 18(O4 S 2-) FORMUL 10 EPE 6(C8 H18 N2 O4 S) FORMUL 31 HOH *545(H2 O) HELIX 1 1 LYS A 91 ARG A 97 1 7 HELIX 2 2 LEU A 99 GLY A 111 1 13 HELIX 3 3 PRO A 123 TYR A 131 1 9 HELIX 4 4 LYS A 132 SER A 135 5 4 HELIX 5 5 PHE A 139 THR A 148 1 10 HELIX 6 6 GLY A 161 GLY A 171 1 11 HELIX 7 7 THR A 182 ALA A 188 1 7 HELIX 8 8 GLN A 190 ASN A 194 5 5 HELIX 9 9 SER A 201 PHE A 213 1 13 HELIX 10 10 LEU A 225 ARG A 230 1 6 HELIX 11 11 LYS B 91 ARG B 97 1 7 HELIX 12 12 LEU B 99 GLY B 111 1 13 HELIX 13 13 PRO B 123 TYR B 131 1 9 HELIX 14 14 LYS B 132 SER B 135 5 4 HELIX 15 15 PHE B 139 THR B 148 1 10 HELIX 16 16 GLY B 161 GLY B 171 1 11 HELIX 17 17 THR B 182 ALA B 188 1 7 HELIX 18 18 GLN B 190 ASN B 194 5 5 HELIX 19 19 SER B 201 PHE B 213 1 13 HELIX 20 20 LYS B 214 LEU B 218 5 5 HELIX 21 21 LEU B 225 ARG B 230 1 6 HELIX 22 22 LYS C 91 ARG C 97 1 7 HELIX 23 23 LEU C 99 GLY C 111 1 13 HELIX 24 24 PRO C 123 TYR C 131 1 9 HELIX 25 25 LYS C 132 SER C 135 5 4 HELIX 26 26 PHE C 139 THR C 148 1 10 HELIX 27 27 GLY C 161 GLY C 171 1 11 HELIX 28 28 THR C 182 ALA C 188 1 7 HELIX 29 29 GLN C 190 ASN C 194 5 5 HELIX 30 30 SER C 201 PHE C 213 1 13 HELIX 31 31 LYS C 214 LEU C 218 5 5 HELIX 32 32 LEU C 225 LEU C 229 5 5 HELIX 33 33 LYS D 91 ARG D 97 1 7 HELIX 34 34 LEU D 99 GLY D 111 1 13 HELIX 35 35 PRO D 123 TYR D 131 1 9 HELIX 36 36 LYS D 132 SER D 135 5 4 HELIX 37 37 PHE D 139 THR D 148 1 10 HELIX 38 38 GLY D 161 GLY D 171 1 11 HELIX 39 39 THR D 182 ALA D 188 1 7 HELIX 40 40 GLN D 190 ASN D 194 5 5 HELIX 41 41 SER D 201 PHE D 213 1 13 HELIX 42 42 LYS D 214 LEU D 218 5 5 HELIX 43 43 LEU D 225 ARG D 230 1 6 HELIX 44 44 LYS E 91 ARG E 97 1 7 HELIX 45 45 LEU E 99 GLY E 111 1 13 HELIX 46 46 PRO E 123 TYR E 131 1 9 HELIX 47 47 LYS E 132 SER E 135 5 4 HELIX 48 48 PHE E 139 SER E 149 1 11 HELIX 49 49 GLY E 161 GLY E 171 1 11 HELIX 50 50 THR E 182 ALA E 188 1 7 HELIX 51 51 GLN E 190 ASN E 194 5 5 HELIX 52 52 SER E 201 PHE E 213 1 13 HELIX 53 53 LEU E 225 ARG E 230 1 6 HELIX 54 54 LYS F 91 ARG F 97 1 7 HELIX 55 55 LEU F 99 GLY F 111 1 13 HELIX 56 56 PRO F 123 TYR F 131 1 9 HELIX 57 57 LYS F 132 SER F 135 5 4 HELIX 58 58 PHE F 139 THR F 148 1 10 HELIX 59 59 GLY F 161 GLY F 171 1 11 HELIX 60 60 THR F 182 ALA F 188 1 7 HELIX 61 61 GLN F 190 ASN F 194 5 5 HELIX 62 62 SER F 201 PHE F 213 1 13 HELIX 63 63 LEU F 225 ARG F 230 1 6 SHEET 1 A 4 LYS A 113 PHE A 120 0 SHEET 2 A 4 VAL A 152 GLY A 159 -1 O VAL A 152 N PHE A 120 SHEET 3 A 4 GLU A 84 VAL A 90 -1 N VAL A 90 O VAL A 153 SHEET 4 A 4 VAL A 196 GLY A 198 -1 O HIS A 197 N MET A 89 SHEET 1 B 4 LYS B 113 PHE B 120 0 SHEET 2 B 4 VAL B 152 GLU B 158 -1 O VAL B 152 N PHE B 120 SHEET 3 B 4 GLU B 85 VAL B 90 -1 N VAL B 90 O VAL B 153 SHEET 4 B 4 VAL B 196 GLY B 198 -1 O HIS B 197 N MET B 89 SHEET 1 C 4 LYS C 113 PHE C 120 0 SHEET 2 C 4 VAL C 152 GLU C 158 -1 O VAL C 152 N PHE C 120 SHEET 3 C 4 GLU C 85 VAL C 90 -1 N ILE C 88 O MET C 155 SHEET 4 C 4 VAL C 196 GLY C 198 -1 O HIS C 197 N MET C 89 SHEET 1 D 4 LYS D 113 PHE D 120 0 SHEET 2 D 4 VAL D 152 GLY D 159 -1 O CYS D 154 N LYS D 118 SHEET 3 D 4 GLU D 84 VAL D 90 -1 N VAL D 90 O VAL D 153 SHEET 4 D 4 VAL D 196 GLY D 198 -1 O HIS D 197 N MET D 89 SHEET 1 E 4 LYS E 113 PHE E 120 0 SHEET 2 E 4 VAL E 152 GLU E 158 -1 O VAL E 152 N PHE E 120 SHEET 3 E 4 GLU E 85 VAL E 90 -1 N THR E 86 O TRP E 157 SHEET 4 E 4 VAL E 196 GLY E 198 -1 O HIS E 197 N MET E 89 SHEET 1 F 4 LYS F 113 PHE F 120 0 SHEET 2 F 4 VAL F 152 GLY F 159 -1 O VAL F 152 N PHE F 120 SHEET 3 F 4 GLU F 84 VAL F 90 -1 N THR F 86 O TRP F 157 SHEET 4 F 4 VAL F 196 GLY F 198 -1 O HIS F 197 N MET F 89 SITE 1 AC1 1 ARG A 167 SITE 1 AC2 6 ARG A 167 THR A 173 ARG A 184 HIS A 197 SITE 2 AC2 6 HOH A1137 HOH A1176 SITE 1 AC3 4 LYS A 172 THR A 173 HOH A1114 HOH A1164 SITE 1 AC4 3 ARG B 167 HOH B1179 LYS D 206 SITE 1 AC5 6 LYS B 91 ARG B 167 THR B 173 ARG B 184 SITE 2 AC5 6 HIS B 197 HOH B1134 SITE 1 AC6 7 LYS B 172 THR B 173 HOH B1178 HOH B1179 SITE 2 AC6 7 ASP D 82 LYS D 206 HOH D1193 SITE 1 AC7 3 ARG C 167 HOH C1156 HOH C1161 SITE 1 AC8 3 LYS C 91 ARG C 184 HIS C 197 SITE 1 AC9 3 LYS C 172 THR C 173 HOH C1128 SITE 1 BC1 3 ARG D 167 HOH D1185 HOH D1189 SITE 1 BC2 7 LYS D 91 ARG D 167 ARG D 184 HIS D 197 SITE 2 BC2 7 HOH D1134 HOH D1188 HOH D1212 SITE 1 BC3 3 LYS D 172 THR D 173 HOH D1108 SITE 1 BC4 3 ARG E 167 HOH E1061 HOH E1082 SITE 1 BC5 5 ARG E 167 THR E 173 ARG E 184 HOH E1062 SITE 2 BC5 5 HOH E1076 SITE 1 BC6 5 LYS E 172 THR E 173 HOH E1028 HOH E1058 SITE 2 BC6 5 HOH E1074 SITE 1 BC7 2 ARG F 167 HOH F1162 SITE 1 BC8 5 ARG F 167 ARG F 184 HIS F 197 HOH F1159 SITE 2 BC8 5 HOH F1179 SITE 1 BC9 3 LYS F 172 THR F 173 HOH F1117 SITE 1 CC1 15 GLU A 108 GLY A 111 PHE A 112 LYS A 113 SITE 2 CC1 15 TRP A 221 SER A 223 ALA A 226 ARG A 230 SITE 3 CC1 15 HOH A1106 HOH A1110 HOH A1111 HOH A1152 SITE 4 CC1 15 GLN D 96 ARG D 97 GLY D 98 SITE 1 CC2 15 GLU B 108 GLY B 111 TRP B 221 SER B 223 SITE 2 CC2 15 ALA B 226 ARG B 230 HOH B1133 HOH B1138 SITE 3 CC2 15 HOH B1143 HOH B1147 HOH B1165 HOH B1170 SITE 4 CC2 15 GLN F 96 ARG F 97 GLY F 98 SITE 1 CC3 17 GLU C 108 GLY C 111 PHE C 112 LYS C 113 SITE 2 CC3 17 TRP C 221 SER C 223 LEU C 229 ARG C 230 SITE 3 CC3 17 HOH C1110 HOH C1131 HOH C1134 HOH C1142 SITE 4 CC3 17 HOH C1148 HOH C1164 GLN E 96 ARG E 97 SITE 5 CC3 17 GLY E 98 SITE 1 CC4 18 GLN A 96 ARG A 97 GLY A 98 GLU D 108 SITE 2 CC4 18 GLY D 111 PHE D 112 LYS D 113 TRP D 221 SITE 3 CC4 18 SER D 223 ALA D 226 LEU D 229 ARG D 230 SITE 4 CC4 18 HOH D1114 HOH D1115 HOH D1128 HOH D1200 SITE 5 CC4 18 HOH D1204 HOH E1035 SITE 1 CC5 14 GLN C 96 ARG C 97 GLY C 98 HOH C1127 SITE 2 CC5 14 HOH C1132 HOH C1160 GLU E 108 GLY E 111 SITE 3 CC5 14 PHE E 112 TRP E 221 SER E 223 ALA E 226 SITE 4 CC5 14 HOH E1067 HOH E1085 SITE 1 CC6 13 GLN B 96 ARG B 97 GLY B 98 GLU F 108 SITE 2 CC6 13 GLY F 111 PHE F 112 TRP F 221 SER F 223 SITE 3 CC6 13 LEU F 229 HOH F1114 HOH F1116 HOH F1142 SITE 4 CC6 13 HOH F1184 CRYST1 69.394 108.855 119.324 90.00 90.00 90.00 P 21 21 21 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 0.014410 0.000000 0.000000 0.00000 SCALE2 0.000000 0.009187 0.000000 0.00000 SCALE3 0.000000 0.000000 0.008381 0.00000