HEADER TRANSFERASE 17-JUL-20 7CKJ TITLE CRYSTAL STRUCTURE OF CMP KINASE IN COMPLEX WITH CMP FROM THERMUS TITLE 2 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 HB8; SOURCE 3 ORGANISM_TAXID: 300852; SOURCE 4 STRAIN: HB8; SOURCE 5 GENE: CMK, TTHA0458; 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: PET-11A KEYWDS CMP KINASE, CMP COMPLEX, OPEN CONFORMATION, NUCLEOTIDE METABOLISM, KEYWDS 2 STRUCTURAL GENOMICS, PSI-2, PROTEIN STRUCTURE INITIATIVE, RIKEN KEYWDS 3 STRUCTURAL GENOMICS/PROTEOMICS INITIATIVE, RSGI, TRANSFERASE EXPDTA X-RAY DIFFRACTION AUTHOR R.MEGA,N.NAKAGAWA,S.KURAMITSU,R.MASUI,RIKEN STRUCTURAL AUTHOR 2 GENOMICS/PROTEOMICS INITIATIVE (RSGI) REVDAT 2 29-NOV-23 7CKJ 1 REMARK REVDAT 1 29-JUL-20 7CKJ 0 SPRSDE 29-JUL-20 7CKJ 3AKE JRNL AUTH R.MEGA,N.NAKAGAWA,S.KURAMITSU,R.MASUI JRNL TITL THE CRYSTAL STRUCTURES OF THERMUS THERMOPHILUS CMP KINASE JRNL TITL 2 COMPLEXED WITH A PHOSPHORYL GROUP ACCEPTOR AND DONOR. JRNL REF PLOS ONE V. 15 33689 2020 JRNL REFN ESSN 1932-6203 JRNL PMID 32469932 JRNL DOI 10.1371/JOURNAL.PONE.0233689 REMARK 2 REMARK 2 RESOLUTION. 1.50 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : CNS 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) : 1.50 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 50.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 DATA CUTOFF HIGH (ABS(F)) : NULL REMARK 3 DATA CUTOFF LOW (ABS(F)) : NULL REMARK 3 COMPLETENESS (WORKING+TEST) (%) : 99.9 REMARK 3 NUMBER OF REFLECTIONS : 38329 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) : 0.206 REMARK 3 FREE R VALUE : 0.229 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 10.000 REMARK 3 FREE R VALUE TEST SET COUNT : 3834 REMARK 3 ESTIMATED ERROR OF FREE R VALUE : NULL REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : NULL REMARK 3 BIN RESOLUTION RANGE HIGH (A) : 1.50 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.59 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 99.60 REMARK 3 REFLECTIONS IN BIN (WORKING SET) : 5677 REMARK 3 BIN R VALUE (WORKING SET) : 0.2310 REMARK 3 BIN FREE R VALUE : 0.2520 REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : 10.50 REMARK 3 BIN FREE R VALUE TEST SET COUNT : 667 REMARK 3 ESTIMATED ERROR OF BIN FREE R VALUE : 0.001 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 1577 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 21 REMARK 3 SOLVENT ATOMS : 135 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 19.50 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 3.07000 REMARK 3 B22 (A**2) : 3.07000 REMARK 3 B33 (A**2) : -6.13900 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) : NULL REMARK 3 ESD FROM SIGMAA (A) : NULL REMARK 3 LOW RESOLUTION CUTOFF (A) : NULL REMARK 3 REMARK 3 CROSS-VALIDATED ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM C-V LUZZATI PLOT (A) : NULL REMARK 3 ESD FROM C-V SIGMAA (A) : NULL REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 BOND LENGTHS (A) : NULL REMARK 3 BOND ANGLES (DEGREES) : NULL REMARK 3 DIHEDRAL ANGLES (DEGREES) : NULL REMARK 3 IMPROPER ANGLES (DEGREES) : NULL REMARK 3 REMARK 3 ISOTROPIC THERMAL MODEL : NULL REMARK 3 REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. RMS SIGMA REMARK 3 MAIN-CHAIN BOND (A**2) : 1.327 ; 1.500 REMARK 3 MAIN-CHAIN ANGLE (A**2) : 1.994 ; 2.000 REMARK 3 SIDE-CHAIN BOND (A**2) : 1.908 ; 2.000 REMARK 3 SIDE-CHAIN ANGLE (A**2) : 2.806 ; 2.500 REMARK 3 REMARK 3 BULK SOLVENT MODELING. REMARK 3 METHOD USED : NULL REMARK 3 KSOL : NULL REMARK 3 BSOL : 45.92 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 : CNS_TOPPAR:PROTEIN_REP.PARAM REMARK 3 PARAMETER FILE 2 : CNS_TOPPAR:DNA-RNA_REP.PARAM REMARK 3 PARAMETER FILE 3 : CNS_TOPPAR:WATER_REP.PARAM REMARK 3 PARAMETER FILE 4 : CNS_TOPPAR:ION.PARAM REMARK 3 PARAMETER FILE 5 : CNS_TOPPAR:CARBOHYDRATE.PARAM REMARK 3 PARAMETER FILE 6 : C5P.PARAM REMARK 3 PARAMETER FILE 7 : NULL REMARK 3 TOPOLOGY FILE 1 : NULL REMARK 3 TOPOLOGY FILE 2 : NULL REMARK 3 TOPOLOGY FILE 3 : NULL REMARK 3 TOPOLOGY FILE 4 : NULL REMARK 3 TOPOLOGY FILE 5 : NULL REMARK 3 TOPOLOGY FILE 6 : NULL REMARK 3 TOPOLOGY FILE 7 : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 7CKJ COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 20-JUL-20. REMARK 100 THE DEPOSITION ID IS D_1300017788. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 19-JUL-06 REMARK 200 TEMPERATURE (KELVIN) : 90 REMARK 200 PH : 7.0 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : SPRING-8 REMARK 200 BEAMLINE : BL45XU REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.00000 REMARK 200 MONOCHROMATOR : TRANSPARENT DIAMOND DOUBLE REMARK 200 CRYSTAL REMARK 200 OPTICS : NULL 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 : HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 38410 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.500 REMARK 200 RESOLUTION RANGE LOW (A) : 50.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.9 REMARK 200 DATA REDUNDANCY : 8.100 REMARK 200 R MERGE (I) : 0.06600 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 28.0000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.50 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.55 REMARK 200 COMPLETENESS FOR SHELL (%) : 99.8 REMARK 200 DATA REDUNDANCY IN SHELL : 7.80 REMARK 200 R MERGE FOR SHELL (I) : 0.34300 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: 2CMK REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 54.66 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.71 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.1M BIS-TRIS, 3.5M SODIUM FORMATE, PH REMARK 280 7.0, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 293K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 65 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -Y,X-Y,Z+2/3 REMARK 290 3555 -X+Y,-X,Z+1/3 REMARK 290 4555 -X,-Y,Z+1/2 REMARK 290 5555 Y,-X+Y,Z+1/6 REMARK 290 6555 X-Y,X,Z+5/6 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 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 2 0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 74.22133 REMARK 290 SMTRY1 3 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 3 -0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 37.11067 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 55.66600 REMARK 290 SMTRY1 5 0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 5 -0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 18.55533 REMARK 290 SMTRY1 6 0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 6 0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 6 0.000000 0.000000 1.000000 92.77667 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 TOTAL BURIED SURFACE AREA: 610 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 10000 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -4.0 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 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 LYS A 176 REMARK 465 ALA A 177 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 HIS A 89 64.48 -106.36 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 C5P A 301 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 3AKC RELATED DB: PDB REMARK 900 RELATED ID: 3AKD RELATED DB: PDB REMARK 900 RELATED ID: 3W90 RELATED DB: PDB REMARK 900 RELATED ID: 3W8N RELATED DB: PDB DBREF 7CKJ 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 HET C5P A 301 21 HETNAM C5P CYTIDINE-5'-MONOPHOSPHATE FORMUL 2 C5P C9 H14 N3 O8 P FORMUL 3 HOH *135(H2 O) HELIX 1 AA1 GLY A 14 GLY A 27 1 14 HELIX 2 AA2 SER A 33 GLY A 48 1 16 HELIX 3 AA3 ASP A 53 LEU A 64 1 12 HELIX 4 AA4 THR A 85 LEU A 88 5 4 HELIX 5 AA5 THR A 90 ARG A 102 1 13 HELIX 6 AA6 LEU A 103 VAL A 117 1 15 HELIX 7 AA7 SER A 145 GLU A 156 1 12 HELIX 8 AA8 ALA A 160 ARG A 174 1 15 HELIX 9 AA9 THR A 194 ARG A 208 1 15 SHEET 1 AA1 5 TYR A 30 SER A 32 0 SHEET 2 AA1 5 PHE A 121 GLY A 125 1 O GLU A 124 N LEU A 31 SHEET 3 AA1 5 ILE A 4 ASP A 8 1 N VAL A 5 O ALA A 123 SHEET 4 AA1 5 HIS A 138 THR A 143 1 O LEU A 142 N ASP A 8 SHEET 5 AA1 5 LEU A 186 ASP A 189 1 O LEU A 186 N TYR A 141 SHEET 1 AA2 3 ARG A 67 LEU A 69 0 SHEET 2 AA2 3 ARG A 76 ALA A 79 -1 O ARG A 76 N LEU A 69 SHEET 3 AA2 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 0.03 SITE 1 AC1 16 SER A 11 LYS A 15 SER A 33 GLY A 34 SITE 2 AC1 16 TYR A 37 ARG A 38 VAL A 97 ALA A 101 SITE 3 AC1 16 ARG A 107 GLY A 125 ARG A 126 ASP A 127 SITE 4 AC1 16 MET A 128 HOH A 411 HOH A 414 HOH A 439 CRYST1 61.746 61.746 111.332 90.00 90.00 120.00 P 65 6 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 0.016195 0.009350 0.000000 0.00000 SCALE2 0.000000 0.018701 0.000000 0.00000 SCALE3 0.000000 0.000000 0.008982 0.00000