HEADER TRANSFERASE 03-SEP-14 4WBF TITLE ACINETOBACTER BAUMANNII SDF NDK COMPND MOL_ID: 1; COMPND 2 MOLECULE: NUCLEOSIDE DIPHOSPHATE KINASE; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: UNP RESIDUES 1-140; COMPND 5 SYNONYM: NDP KINASE,NUCLEOSIDE-2-P KINASE; COMPND 6 EC: 2.7.4.6; COMPND 7 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: ACINETOBACTER BAUMANNII; SOURCE 3 ORGANISM_TAXID: 509170; SOURCE 4 STRAIN: SDF; SOURCE 5 GENE: NDK, ABSDF3006; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 8 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID KEYWDS KINASE, TRANSFERASE EXPDTA X-RAY DIFFRACTION AUTHOR Y.HU,Y.LIU REVDAT 2 08-NOV-23 4WBF 1 SOURCE REMARK REVDAT 1 17-JUN-15 4WBF 0 JRNL AUTH Y.HU,F.FENG,Y.LIU JRNL TITL STRUCTURAL AND FUNCTIONAL CHARACTERIZATION OF ACINETOBACTER JRNL TITL 2 BAUMANNII NUCLEOSIDE DIPHOSPHATE KINASE JRNL REF PROG.BIOCHEM.BIOPHYS. V. 42 260 2015 JRNL REFN ISSN 1000-3282 JRNL DOI 10.16476/J.PIBB.2014.0319 REMARK 2 REMARK 2 RESOLUTION. 2.64 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX (PHENIX.REFINE: 1.9_1692) REMARK 3 AUTHORS : PAUL ADAMS,PAVEL AFONINE,VINCENT CHEN,IAN REMARK 3 : DAVIS,KRESHNA GOPAL,RALF GROSSE-KUNSTLEVE, REMARK 3 : LI-WEI HUNG,ROBERT IMMORMINO,TOM IOERGER, REMARK 3 : AIRLIE MCCOY,ERIK MCKEE,NIGEL MORIARTY, REMARK 3 : REETAL PAI,RANDY READ,JANE RICHARDSON, REMARK 3 : DAVID RICHARDSON,TOD ROMO,JIM SACCHETTINI, REMARK 3 : NICHOLAS SAUTER,JACOB SMITH,LAURENT REMARK 3 : STORONI,TOM TERWILLIGER,PETER ZWART REMARK 3 REMARK 3 REFINEMENT TARGET : ML REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.64 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 47.11 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 98.3 REMARK 3 NUMBER OF REFLECTIONS : 5655 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.207 REMARK 3 R VALUE (WORKING SET) : 0.201 REMARK 3 FREE R VALUE : 0.258 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 9.730 REMARK 3 FREE R VALUE TEST SET COUNT : 550 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT (IN BINS). REMARK 3 BIN RESOLUTION RANGE COMPL. NWORK NFREE RWORK RFREE REMARK 3 1 47.1142 - 4.1906 0.99 1352 150 0.1785 0.2018 REMARK 3 2 4.1906 - 3.3265 0.99 1269 134 0.1742 0.2402 REMARK 3 3 3.3265 - 2.9061 0.99 1271 138 0.2304 0.3317 REMARK 3 4 2.9061 - 2.6404 0.97 1213 128 0.2539 0.3149 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : FLAT BULK SOLVENT MODEL REMARK 3 SOLVENT RADIUS : 1.11 REMARK 3 SHRINKAGE RADIUS : 0.90 REMARK 3 K_SOL : NULL REMARK 3 B_SOL : NULL REMARK 3 REMARK 3 ERROR ESTIMATES. REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : 0.340 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 23.880 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : NULL REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : NULL REMARK 3 B22 (A**2) : NULL REMARK 3 B33 (A**2) : NULL REMARK 3 B12 (A**2) : NULL REMARK 3 B13 (A**2) : NULL REMARK 3 B23 (A**2) : NULL REMARK 3 REMARK 3 TWINNING INFORMATION. REMARK 3 FRACTION: NULL REMARK 3 OPERATOR: NULL REMARK 3 REMARK 3 DEVIATIONS FROM IDEAL VALUES. REMARK 3 RMSD COUNT REMARK 3 BOND : 0.009 1086 REMARK 3 ANGLE : 1.102 1465 REMARK 3 CHIRALITY : 0.042 163 REMARK 3 PLANARITY : 0.004 194 REMARK 3 DIHEDRAL : 15.058 389 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : NULL REMARK 3 REMARK 3 NCS DETAILS REMARK 3 NUMBER OF NCS GROUPS : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 4WBF COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 16-SEP-14. REMARK 100 THE DEPOSITION ID IS D_1000203524. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 01-SEP-14 REMARK 200 TEMPERATURE (KELVIN) : 180 REMARK 200 PH : 7.0 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : N REMARK 200 RADIATION SOURCE : ROTATING ANODE REMARK 200 BEAMLINE : NULL REMARK 200 X-RAY GENERATOR MODEL : RIGAKU MICROMAX-007 HF REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.5419 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : RIGAKU SATURN 944 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : NULL REMARK 200 DATA SCALING SOFTWARE : NULL REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 6880 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.490 REMARK 200 RESOLUTION RANGE LOW (A) : 47.110 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 100.0 REMARK 200 DATA REDUNDANCY : 6.200 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 7.3000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : NULL REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : NULL REMARK 200 COMPLETENESS FOR SHELL (%) : NULL REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : NULL REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: NULL REMARK 200 STARTING MODEL: 4W98 REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 60.11 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 3.08 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: SODIUM MALONATE, HEPES, JEFFAMINE ED REMARK 280 -2001, PH 7.0, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 289K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: I 2 2 2 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,Y,-Z REMARK 290 4555 X,-Y,-Z REMARK 290 5555 X+1/2,Y+1/2,Z+1/2 REMARK 290 6555 -X+1/2,-Y+1/2,Z+1/2 REMARK 290 7555 -X+1/2,Y+1/2,-Z+1/2 REMARK 290 8555 X+1/2,-Y+1/2,-Z+1/2 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 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 5 1.000000 0.000000 0.000000 30.16500 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 37.70000 REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 41.06000 REMARK 290 SMTRY1 6 -1.000000 0.000000 0.000000 30.16500 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 37.70000 REMARK 290 SMTRY3 6 0.000000 0.000000 1.000000 41.06000 REMARK 290 SMTRY1 7 -1.000000 0.000000 0.000000 30.16500 REMARK 290 SMTRY2 7 0.000000 1.000000 0.000000 37.70000 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 41.06000 REMARK 290 SMTRY1 8 1.000000 0.000000 0.000000 30.16500 REMARK 290 SMTRY2 8 0.000000 -1.000000 0.000000 37.70000 REMARK 290 SMTRY3 8 0.000000 0.000000 -1.000000 41.06000 REMARK 290 REMARK 290 REMARK: NULL 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: DIMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 1500 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 13330 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -8.0 KCAL/MOL 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 350 BIOMT1 2 -1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 2 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT3 2 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 A 212 LIES ON A SPECIAL POSITION. REMARK 375 HOH A 215 LIES ON A SPECIAL POSITION. 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 CYS A 139 REMARK 465 PRO A 140 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 PHE A 0 -41.92 -137.20 REMARK 500 THR A 37 147.94 -173.65 REMARK 500 ALA A 115 -45.62 65.96 REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 4W98 RELATED DB: PDB REMARK 900 4W98 IS WILD TYPE OF NDK DBREF 4WBF A 1 140 UNP B0VKS3 NDK_ACIBS 1 140 SEQADV 4WBF GLU A -1 UNP B0VKS3 EXPRESSION TAG SEQADV 4WBF PHE A 0 UNP B0VKS3 EXPRESSION TAG SEQRES 1 A 142 GLU PHE MET ALA ILE GLU ARG THR LEU SER ILE VAL LYS SEQRES 2 A 142 PRO ASP ALA VAL SER LYS ASN HIS ILE GLY GLU ILE PHE SEQRES 3 A 142 ALA ARG PHE GLU LYS ALA GLY LEU LYS ILE VAL ALA THR SEQRES 4 A 142 LYS MET LYS HIS LEU SER GLN ALA ASP ALA GLU GLY PHE SEQRES 5 A 142 TYR ALA GLU HIS LYS GLU ARG GLY PHE PHE GLY ASP LEU SEQRES 6 A 142 VAL ALA PHE MET THR SER GLY PRO VAL VAL VAL SER VAL SEQRES 7 A 142 LEU GLU GLY GLU ASN ALA VAL LEU ALA HIS ARG GLU ILE SEQRES 8 A 142 LEU GLY ALA THR ASN PRO LYS GLU ALA ALA PRO GLY THR SEQRES 9 A 142 ILE ARG ALA ASP PHE ALA VAL SER ILE ASP GLU ASN ALA SEQRES 10 A 142 ALA HIS GLY SER ASP SER VAL ALA SER ALA GLU ARG GLU SEQRES 11 A 142 ILE ALA TYR PHE PHE ALA ASP ASN GLU ILE CYS PRO FORMUL 2 HOH *34(H2 O) HELIX 1 AA1 LYS A 11 LYS A 17 1 7 HELIX 2 AA2 HIS A 19 ALA A 30 1 12 HELIX 3 AA3 SER A 43 TYR A 51 1 9 HELIX 4 AA4 ALA A 52 LYS A 55 5 4 HELIX 5 AA5 PHE A 59 THR A 68 1 10 HELIX 6 AA6 ASN A 81 GLY A 91 1 11 HELIX 7 AA7 ASN A 94 ALA A 98 5 5 HELIX 8 AA8 THR A 102 ALA A 108 1 7 HELIX 9 AA9 SER A 121 PHE A 133 1 13 HELIX 10 AB1 ALA A 134 ILE A 138 5 5 SHEET 1 AA1 4 LYS A 33 LYS A 40 0 SHEET 2 AA1 4 VAL A 72 GLU A 80 -1 O VAL A 72 N LYS A 40 SHEET 3 AA1 4 ILE A 3 VAL A 10 -1 N SER A 8 O SER A 75 SHEET 4 AA1 4 ALA A 116 GLY A 118 -1 O HIS A 117 N ILE A 9 CRYST1 60.330 75.400 82.120 90.00 90.00 90.00 I 2 2 2 8 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 0.016576 0.000000 0.000000 0.00000 SCALE2 0.000000 0.013263 0.000000 0.00000 SCALE3 0.000000 0.000000 0.012177 0.00000