HEADER SIGNALING PROTEIN,TRANSFERASE 16-DEC-05 2FEM TITLE MUTANT R188M OF THE CYTIDINE MONOPHOSPHATE KINASE FROM E. COLI COMPND MOL_ID: 1; COMPND 2 MOLECULE: CYTIDYLATE KINASE; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: CYTIDINE MONOPHOSPHATE KINASE; CK; CMP KINASE; PROTEIN MSSA; COMPND 5 P25; COMPND 6 EC: 2.7.4.14; COMPND 7 ENGINEERED: YES; COMPND 8 MUTATION: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: ESCHERICHIA COLI; SOURCE 3 ORGANISM_TAXID: 562; SOURCE 4 GENE: CMK, MSSA; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 7 EXPRESSION_SYSTEM_STRAIN: CJ236; SOURCE 8 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 9 EXPRESSION_SYSTEM_PLASMID: PHS210; SOURCE 10 OTHER_DETAILS: USED HELPER PHAGE M13K07 TO PERFORM THE SINGLE SOURCE 11 MUTATION KEYWDS NUCLEOTIDE MONOPHOSPHATE KINASE; TRANSFERASE, SIGNALING PROTEIN, KEYWDS 2 TRANSFERASE EXPDTA X-RAY DIFFRACTION AUTHOR A.OFITERU,N.BUCURENCI,E.ALEXOV,T.BERTRAND,P.BRIOZZO,H.MUNIER-LEHMANN, AUTHOR 2 L.TOURNEUX,O.BARZU,A.M.GILLES REVDAT 5 14-FEB-24 2FEM 1 REMARK REVDAT 4 20-OCT-21 2FEM 1 SEQADV REVDAT 3 14-APR-09 2FEM 1 JRNL REVDAT 2 24-FEB-09 2FEM 1 VERSN REVDAT 1 10-JAN-06 2FEM 0 JRNL AUTH A.OFITERU,N.BUCURENCI,E.ALEXOV,T.BERTRAND,P.BRIOZZO, JRNL AUTH 2 H.MUNIER-LEHMANN,A.M.GILLES JRNL TITL STRUCTURAL AND FUNCTIONAL CONSEQUENCES OF SINGLE AMINO ACID JRNL TITL 2 SUBSTITUTIONS IN THE PYRIMIDINE BASE BINDING POCKET OF JRNL TITL 3 ESCHERICHIA COLI CMP KINASE. JRNL REF FEBS J. V. 274 3363 2007 JRNL REFN ISSN 1742-464X JRNL PMID 17542990 JRNL DOI 10.1111/J.1742-4658.2007.05870.X REMARK 2 REMARK 2 RESOLUTION. 1.90 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) : 1.90 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 15.00 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) (%) : NULL REMARK 3 NUMBER OF REFLECTIONS : 18054 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) : 0.231 REMARK 3 FREE R VALUE : 0.242 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 10.500 REMARK 3 FREE R VALUE TEST SET COUNT : 1770 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) : NULL REMARK 3 BIN RESOLUTION RANGE LOW (A) : NULL REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : NULL REMARK 3 REFLECTIONS IN BIN (WORKING SET) : NULL REMARK 3 BIN R VALUE (WORKING SET) : NULL REMARK 3 BIN FREE R VALUE : NULL REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : NULL REMARK 3 BIN FREE R VALUE TEST SET COUNT : NULL REMARK 3 ESTIMATED ERROR OF BIN FREE R VALUE : NULL REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 1614 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 0 REMARK 3 SOLVENT ATOMS : 0 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) : -0.80000 REMARK 3 B22 (A**2) : -0.80000 REMARK 3 B33 (A**2) : 1.60100 REMARK 3 B12 (A**2) : -3.14900 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) : 0.007 REMARK 3 BOND ANGLES (DEGREES) : 1.270 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) : 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 : NULL REMARK 3 KSOL : NULL REMARK 3 BSOL : NULL 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 : NULL REMARK 3 TOPOLOGY FILE 1 : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 2FEM COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 27-DEC-05. REMARK 100 THE DEPOSITION ID IS D_1000035785. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 14-JUN-01 REMARK 200 TEMPERATURE (KELVIN) : 173 REMARK 200 PH : 7.4 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 REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.5418 REMARK 200 MONOCHROMATOR : GRAPHITE REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : IMAGE PLATE REMARK 200 DETECTOR MANUFACTURER : MARRESEARCH REMARK 200 INTENSITY-INTEGRATION SOFTWARE : DENZO REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 18054 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.900 REMARK 200 RESOLUTION RANGE LOW (A) : 15.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 1.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 97.9 REMARK 200 DATA REDUNDANCY : NULL REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : NULL REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.90 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.00 REMARK 200 COMPLETENESS FOR SHELL (%) : 86.1 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 <I/SIGMA(I)> 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: AMORE REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 48.53 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.39 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: TRIS-HCL 50 MM PH 7.4, AMMONIUM REMARK 280 SULFATE 1.3 M, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 293K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 63 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -Y,X-Y,Z REMARK 290 3555 -X+Y,-X,Z REMARK 290 4555 -X,-Y,Z+1/2 REMARK 290 5555 Y,-X+Y,Z+1/2 REMARK 290 6555 X-Y,X,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 -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 0.00000 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 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 30.36300 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 30.36300 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 30.36300 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 300 REMARK: THE BIOLOGICAL ASSEMBLY IS A MONOMER 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 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 THR A 2 REMARK 465 GLU A 180 REMARK 465 ARG A 181 REMARK 465 ASP A 182 REMARK 465 ASP A 183 REMARK 465 ARG A 184 REMARK 465 ASP A 185 REMARK 465 ARG A 186 REMARK 465 ASN A 187 REMARK 465 MET A 188 REMARK 465 ALA A 189 REMARK 465 VAL A 190 REMARK 465 ALA A 191 REMARK 465 PRO A 192 REMARK 470 REMARK 470 MISSING ATOM REMARK 470 THE FOLLOWING RESIDUES HAVE MISSING ATOMS (M=MODEL NUMBER; REMARK 470 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; REMARK 470 I=INSERTION CODE): REMARK 470 M RES CSSEQI ATOMS REMARK 470 GLU A 164 CD OE1 OE2 REMARK 480 REMARK 480 ZERO OCCUPANCY ATOM REMARK 480 THE FOLLOWING RESIDUES HAVE ATOMS MODELED WITH ZERO REMARK 480 OCCUPANCY. THE LOCATION AND PROPERTIES OF THESE ATOMS REMARK 480 MAY NOT BE RELIABLE. (M=MODEL NUMBER; RES=RESIDUE NAME; REMARK 480 C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE): REMARK 480 M RES C SSEQI ATOMS REMARK 480 ARG A 173 CG CD NE CZ NH1 NH2 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 ILE A 4 -64.52 99.07 REMARK 500 ALA A 225 -125.46 -148.33 REMARK 500 LEU A 226 159.46 47.70 REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 2FEO RELATED DB: PDB DBREF 2FEM A 1 227 UNP P0A6I0 KCY_ECOLI 1 227 SEQADV 2FEM MET A 188 UNP P0A6I0 ARG 188 ENGINEERED MUTATION SEQRES 1 A 227 MET THR ALA ILE ALA PRO VAL ILE THR ILE ASP GLY PRO SEQRES 2 A 227 SER GLY ALA GLY LYS GLY THR LEU CYS LYS ALA MET ALA SEQRES 3 A 227 GLU ALA LEU GLN TRP HIS LEU LEU ASP SER GLY ALA ILE SEQRES 4 A 227 TYR ARG VAL LEU ALA LEU ALA ALA LEU HIS HIS HIS VAL SEQRES 5 A 227 ASP VAL ALA SER GLU ASP ALA LEU VAL PRO LEU ALA SER SEQRES 6 A 227 HIS LEU ASP VAL ARG PHE VAL SER THR ASN GLY ASN LEU SEQRES 7 A 227 GLU VAL ILE LEU GLU GLY GLU ASP VAL SER GLY GLU ILE SEQRES 8 A 227 ARG THR GLN GLU VAL ALA ASN ALA ALA SER GLN VAL ALA SEQRES 9 A 227 ALA PHE PRO ARG VAL ARG GLU ALA LEU LEU ARG ARG GLN SEQRES 10 A 227 ARG ALA PHE ARG GLU LEU PRO GLY LEU ILE ALA ASP GLY SEQRES 11 A 227 ARG ASP MET GLY THR VAL VAL PHE PRO ASP ALA PRO VAL SEQRES 12 A 227 LYS ILE PHE LEU ASP ALA SER SER GLU GLU ARG ALA HIS SEQRES 13 A 227 ARG ARG MET LEU GLN LEU GLN GLU LYS GLY PHE SER VAL SEQRES 14 A 227 ASN PHE GLU ARG LEU LEU ALA GLU ILE LYS GLU ARG ASP SEQRES 15 A 227 ASP ARG ASP ARG ASN MET ALA VAL ALA PRO LEU VAL PRO SEQRES 16 A 227 ALA ALA ASP ALA LEU VAL LEU ASP SER THR THR LEU SER SEQRES 17 A 227 ILE GLU GLN VAL ILE GLU LYS ALA LEU GLN TYR ALA ARG SEQRES 18 A 227 GLN LYS LEU ALA LEU ALA HELIX 1 1 GLY A 17 GLN A 30 1 14 HELIX 2 2 SER A 36 HIS A 51 1 16 HELIX 3 3 SER A 56 HIS A 66 1 11 HELIX 4 4 GLY A 89 ARG A 92 5 4 HELIX 5 5 THR A 93 ALA A 105 1 13 HELIX 6 6 PHE A 106 ALA A 119 1 14 HELIX 7 7 SER A 150 LYS A 165 1 16 HELIX 8 8 ASN A 170 LYS A 179 1 10 HELIX 9 9 SER A 208 ALA A 225 1 18 SHEET 1 A 5 HIS A 32 ASP A 35 0 SHEET 2 A 5 LEU A 126 GLY A 130 1 O ILE A 127 N HIS A 32 SHEET 3 A 5 VAL A 7 ASP A 11 1 N ILE A 8 O LEU A 126 SHEET 4 A 5 VAL A 143 ASP A 148 1 O LEU A 147 N ASP A 11 SHEET 5 A 5 LEU A 200 ASP A 203 1 O LEU A 200 N LYS A 144 SHEET 1 B 3 VAL A 69 THR A 74 0 SHEET 2 B 3 ASN A 77 LEU A 82 -1 O GLU A 79 N VAL A 72 SHEET 3 B 3 GLU A 85 ASP A 86 -1 O GLU A 85 N LEU A 82 CISPEP 1 LEU A 123 PRO A 124 0 -0.11 CRYST1 82.167 82.167 60.726 90.00 90.00 120.00 P 63 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 0.012170 0.007027 0.000000 0.00000 SCALE2 0.000000 0.014053 0.000000 0.00000 SCALE3 0.000000 0.000000 0.016467 0.00000