HEADER TRANSFERASE 22-MAR-13 3W90 TITLE CRYSTAL STRUCTURE OF CMP KINASE FROM THERMUS THERMOPHILUS HB8 COMPND MOL_ID: 1; COMPND 2 MOLECULE: CYTIDYLATE KINASE; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: CK, CYTIDINE MONOPHOSPHATE KINASE, CMP KINASE; COMPND 5 EC: 2.7.4.25; COMPND 6 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: THERMUS THERMOPHILUS; SOURCE 3 ORGANISM_TAXID: 300852; SOURCE 4 STRAIN: HB8; SOURCE 5 GENE: TTHA0458; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: BL21(DE3); SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 10 EXPRESSION_SYSTEM_PLASMID: PET-11A KEYWDS STRUCTURAL GENOMICS, NPPSFA, NATIONAL PROJECT ON PROTEIN STRUCTURAL KEYWDS 2 AND FUNCTIONAL ANALYSES, RIKEN STRUCTURAL GENOMICS/PROTEOMICS KEYWDS 3 INITIATIVE, RSGI, KINASE, CMP, TRANSFERASE EXPDTA X-RAY DIFFRACTION AUTHOR N.NAKAGAWA,R.MEGA,R.MASUI,S.KURAMITSU,RIKEN STRUCTURAL AUTHOR 2 GENOMICS/PROTEOMICS INITIATIVE (RSGI) REVDAT 3 08-NOV-23 3W90 1 REMARK REVDAT 2 22-NOV-17 3W90 1 REMARK REVDAT 1 25-SEP-13 3W90 0 JRNL AUTH R.MEGA,N.NAKAGAWA,R.MASUI,S.KURAMITSU JRNL TITL CRYSTAL STRUCTURE OF CMP KINASE: INSIGHTS INTO INITIAL JRNL TITL 2 SUBSTRATE RECOGNITION AND REACTION MECHANISMS JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. 1.65 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : CNS 1.3 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) : 1.65 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 44.29 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 DATA CUTOFF HIGH (ABS(F)) : 868369.000 REMARK 3 DATA CUTOFF LOW (ABS(F)) : 0.0000 REMARK 3 COMPLETENESS (WORKING+TEST) (%) : 98.7 REMARK 3 NUMBER OF REFLECTIONS : 23431 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) : 0.214 REMARK 3 FREE R VALUE : 0.245 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 9.900 REMARK 3 FREE R VALUE TEST SET COUNT : 2308 REMARK 3 ESTIMATED ERROR OF FREE R VALUE : 0.005 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) : 1.65 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.75 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 96.70 REMARK 3 REFLECTIONS IN BIN (WORKING SET) : 3383 REMARK 3 BIN R VALUE (WORKING SET) : 0.2340 REMARK 3 BIN FREE R VALUE : 0.2790 REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : 9.80 REMARK 3 BIN FREE R VALUE TEST SET COUNT : 367 REMARK 3 ESTIMATED ERROR OF BIN FREE R VALUE : 0.015 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 1506 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 0 REMARK 3 SOLVENT ATOMS : 170 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 21.47 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 1.60000 REMARK 3 B22 (A**2) : -0.52000 REMARK 3 B33 (A**2) : -1.08000 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) : 0.20 REMARK 3 ESD FROM SIGMAA (A) : 0.08 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) : 0.23 REMARK 3 ESD FROM C-V SIGMAA (A) : 0.13 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 BOND LENGTHS (A) : 0.020 REMARK 3 BOND ANGLES (DEGREES) : 1.900 REMARK 3 DIHEDRAL ANGLES (DEGREES) : 22.20 REMARK 3 IMPROPER ANGLES (DEGREES) : 1.840 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) : 2.030 ; 1.500 REMARK 3 MAIN-CHAIN ANGLE (A**2) : 2.900 ; 2.000 REMARK 3 SIDE-CHAIN BOND (A**2) : 3.120 ; 2.000 REMARK 3 SIDE-CHAIN ANGLE (A**2) : 4.370 ; 2.500 REMARK 3 REMARK 3 BULK SOLVENT MODELING. REMARK 3 METHOD USED : FLAT MODEL REMARK 3 KSOL : 0.36 REMARK 3 BSOL : 36.88 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.PARAM REMARK 3 PARAMETER FILE 2 : DNA-RNA.PARAM REMARK 3 PARAMETER FILE 3 : WATER.PARAM REMARK 3 PARAMETER FILE 4 : ION.PARAM REMARK 3 PARAMETER FILE 5 : CARBOHYDRATE.PARAM REMARK 3 PARAMETER FILE 6 : NULL REMARK 3 TOPOLOGY FILE 1 : PROTEIN.TOP REMARK 3 TOPOLOGY FILE 2 : DNA-RNA.TOP REMARK 3 TOPOLOGY FILE 3 : WATER.TOP REMARK 3 TOPOLOGY FILE 4 : ION.TOP REMARK 3 TOPOLOGY FILE 5 : CARBOHYDRATE.TOP REMARK 3 TOPOLOGY FILE 6 : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: BULK SOLVENT MODEL USED REMARK 4 REMARK 4 3W90 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 27-MAR-13. REMARK 100 THE DEPOSITION ID IS D_1000096037. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 03-NOV-03 REMARK 200 TEMPERATURE (KELVIN) : 90 REMARK 200 PH : 4.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : SPRING-8 REMARK 200 BEAMLINE : BL45PX REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.9794 REMARK 200 MONOCHROMATOR : TRANSPARENT DOUBLE CRYSTAL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : IMAGE PLATE REMARK 200 DETECTOR MANUFACTURER : RIGAKU RAXIS V REMARK 200 INTENSITY-INTEGRATION SOFTWARE : DENZO, HKL-2000 REMARK 200 DATA SCALING SOFTWARE : SCALEPACK, HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 26020 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.600 REMARK 200 RESOLUTION RANGE LOW (A) : 50.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : -3.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.9 REMARK 200 DATA REDUNDANCY : 6.600 REMARK 200 R MERGE (I) : 0.06200 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 28.4000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.60 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.66 REMARK 200 COMPLETENESS FOR SHELL (%) : 99.6 REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : 0.27700 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: MOLREP REMARK 200 STARTING MODEL: 3W8N REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 41.58 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.11 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 60MM SODIUM ACETATE, 40% ETHYLENE REMARK 280 GLYCOL, 15% PEG1000, PH 4.5, VAPOR DIFFUSION, HANGING DROP, REMARK 280 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 17.86350 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 55.01700 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 24.19100 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 55.01700 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 17.86350 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 24.19100 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000 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: MONOMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC REMARK 350 SOFTWARE USED: PISA 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 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 MET A 1 REMARK 465 ARG A 2 REMARK 465 ASP A 50 REMARK 465 PRO A 51 REMARK 465 GLY A 52 REMARK 465 ASP A 53 REMARK 465 GLU A 54 REMARK 465 ARG A 157 REMARK 465 PRO A 158 REMARK 465 ARG A 208 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 3AKC RELATED DB: PDB REMARK 900 THE SAME PROTEIN COMPLEXED WITH CDP AND ADP REMARK 900 RELATED ID: 3AKD RELATED DB: PDB REMARK 900 THE SAME PROTEIN COMPLEXED WITH CDP REMARK 900 RELATED ID: 3AKE RELATED DB: PDB REMARK 900 THE SAME PROTEIN COMPLEXED WITH CMP REMARK 900 RELATED ID: 3W8N RELATED DB: PDB REMARK 900 THE SAME PROTEIN COMPLEXED WITH CMP REMARK 900 RELATED ID: RSGI-TTK003000091.1 RELATED DB: TARGETTRACK DBREF 3W90 A 1 208 UNP Q5SL35 KCY_THET8 1 208 SEQRES 1 A 208 MET ARG GLY ILE VAL THR ILE ASP GLY PRO SER ALA SER SEQRES 2 A 208 GLY LYS SER SER VAL ALA ARG ARG VAL ALA ALA ALA LEU SEQRES 3 A 208 GLY VAL PRO TYR LEU SER SER GLY LEU LEU TYR ARG ALA SEQRES 4 A 208 ALA ALA PHE LEU ALA LEU ARG ALA GLY VAL ASP PRO GLY SEQRES 5 A 208 ASP GLU GLU GLY LEU LEU ALA LEU LEU GLU GLY LEU GLY SEQRES 6 A 208 VAL ARG LEU LEU ALA GLN ALA GLU GLY ASN ARG VAL LEU SEQRES 7 A 208 ALA ASP GLY GLU ASP LEU THR SER PHE LEU HIS THR PRO SEQRES 8 A 208 GLU VAL ASP ARG VAL VAL SER ALA VAL ALA ARG LEU PRO SEQRES 9 A 208 GLY VAL ARG ALA TRP VAL ASN ARG ARG LEU LYS GLU VAL SEQRES 10 A 208 PRO PRO PRO PHE VAL ALA GLU GLY ARG ASP MET GLY THR SEQRES 11 A 208 ALA VAL PHE PRO GLU ALA ALA HIS LYS PHE TYR LEU THR SEQRES 12 A 208 ALA SER PRO GLU VAL ARG ALA TRP ARG ARG ALA ARG GLU SEQRES 13 A 208 ARG PRO GLN ALA TYR GLU GLU VAL LEU ARG ASP LEU LEU SEQRES 14 A 208 ARG ARG ASP GLU ARG ASP LYS ALA GLN SER ALA PRO ALA SEQRES 15 A 208 PRO ASP ALA LEU VAL LEU ASP THR GLY GLY MET THR LEU SEQRES 16 A 208 ASP GLU VAL VAL ALA TRP VAL LEU ALA HIS ILE ARG ARG FORMUL 2 HOH *170(H2 O) HELIX 1 1 GLY A 14 GLY A 27 1 14 HELIX 2 2 SER A 33 GLY A 48 1 16 HELIX 3 3 GLY A 56 GLY A 65 1 10 HELIX 4 4 THR A 85 LEU A 88 5 4 HELIX 5 5 THR A 90 ARG A 102 1 13 HELIX 6 6 LEU A 103 LYS A 115 1 13 HELIX 7 7 SER A 145 GLU A 156 1 12 HELIX 8 8 ALA A 160 SER A 179 1 20 HELIX 9 9 THR A 194 HIS A 205 1 12 SHEET 1 A 5 TYR A 30 LEU A 31 0 SHEET 2 A 5 PHE A 121 GLY A 125 1 O VAL A 122 N LEU A 31 SHEET 3 A 5 ILE A 4 ASP A 8 1 N VAL A 5 O ALA A 123 SHEET 4 A 5 HIS A 138 THR A 143 1 O LEU A 142 N ASP A 8 SHEET 5 A 5 LEU A 186 ASP A 189 1 O LEU A 188 N THR A 143 SHEET 1 B 3 VAL A 66 LEU A 69 0 SHEET 2 B 3 ARG A 76 ALA A 79 -1 O ARG A 76 N LEU A 69 SHEET 3 B 3 GLU A 82 ASP A 83 -1 O GLU A 82 N ALA A 79 CISPEP 1 PRO A 119 PRO A 120 0 -0.32 CRYST1 35.727 48.382 110.034 90.00 90.00 90.00 P 21 21 21 4 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 0.027990 0.000000 0.000000 0.00000 SCALE2 0.000000 0.020669 0.000000 0.00000 SCALE3 0.000000 0.000000 0.009088 0.00000