HEADER TRANSFERASE 05-MAY-05 2BRI TITLE UMP KINASE FROM PYROCOCCUS FURIOSUS COMPLEXED WITH ITS TITLE 2 SUBSTRATE ANALOG AMPPNP COMPND MOL_ID: 1; COMPND 2 MOLECULE: URIDYLATE KINASE; COMPND 3 CHAIN: A, B; COMPND 4 SYNONYM: UK, URIDINE MONOPHOSPHATE KINASE, UMP KINASE; COMPND 5 EC: 2.7.4.-; COMPND 6 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: PYROCOCCUS FURIOSUS; SOURCE 3 ORGANISM_TAXID: 2261; SOURCE 4 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 5 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 6 EXPRESSION_SYSTEM_STRAIN: BL21(DE3); SOURCE 7 EXPRESSION_SYSTEM_VECTOR: PET15B; SOURCE 8 EXPRESSION_SYSTEM_PLASMID: PUKPFU KEYWDS UMP KINASE, AMINO ACID KINASE, PHOSPHORYL GROUP TRANSFER, KEYWDS 2 PYRIMIDINE BIOSYNTHESIS, TRANSFERASE EXPDTA X-RAY DIFFRACTION AUTHOR C.MARCO-MARIN,F.GIL-ORTIZ,V.RUBIO REVDAT 3 24-FEB-09 2BRI 1 VERSN REVDAT 2 09-NOV-05 2BRI 1 JRNL REVDAT 1 25-JUL-05 2BRI 0 JRNL AUTH C.MARCO-MARIN,F.GIL-ORTIZ,V.RUBIO JRNL TITL THE CRYSTAL STRUCTURE OF PYROCOCCUS FURIOSUS UMP JRNL TITL 2 KINASE PROVIDES INSIGHT INTO CATALYSIS AND JRNL TITL 3 REGULATION IN MICROBIAL PYRIMIDINE NUCLEOTIDE JRNL TITL 4 BIOSYNTHESIS. JRNL REF J.MOL.BIOL. V. 352 438 2005 JRNL REFN ISSN 0022-2836 JRNL PMID 16095620 JRNL DOI 10.1016/J.JMB.2005.07.045 REMARK 2 REMARK 2 RESOLUTION. 3.0 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : CNS 1.0 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 : MAXIMUN LIKELIHOOD REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 3.00 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 19.96 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.0 REMARK 3 DATA CUTOFF HIGH (ABS(F)) : 5157585.20 REMARK 3 DATA CUTOFF LOW (ABS(F)) : NULL REMARK 3 COMPLETENESS (WORKING+TEST) (%) : 100.0 REMARK 3 NUMBER OF REFLECTIONS : 10646 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) : 0.217 REMARK 3 FREE R VALUE : 0.282 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.1 REMARK 3 FREE R VALUE TEST SET COUNT : 541 REMARK 3 ESTIMATED ERROR OF FREE R VALUE : 0.012 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) : 3.00 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 3.19 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 100.0 REMARK 3 REFLECTIONS IN BIN (WORKING SET) : 1654 REMARK 3 BIN R VALUE (WORKING SET) : 0.314 REMARK 3 BIN FREE R VALUE : 0.364 REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : 5.9 REMARK 3 BIN FREE R VALUE TEST SET COUNT : 103 REMARK 3 ESTIMATED ERROR OF BIN FREE R VALUE : 0.036 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 3466 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 128 REMARK 3 SOLVENT ATOMS : 14 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 47.6 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 0.00 REMARK 3 B22 (A**2) : 0.00 REMARK 3 B33 (A**2) : 0.00 REMARK 3 B12 (A**2) : 0.00 REMARK 3 B13 (A**2) : 0.00 REMARK 3 B23 (A**2) : 0.00 REMARK 3 REMARK 3 ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM LUZZATI PLOT (A) : 0.35 REMARK 3 ESD FROM SIGMAA (A) : 0.48 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) : 0.45 REMARK 3 ESD FROM C-V SIGMAA (A) : 0.53 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 BOND LENGTHS (A) : 0.006 REMARK 3 BOND ANGLES (DEGREES) : 1.2 REMARK 3 DIHEDRAL ANGLES (DEGREES) : 20.7 REMARK 3 IMPROPER ANGLES (DEGREES) : 0.84 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) : 1.22 ; 1.50 REMARK 3 MAIN-CHAIN ANGLE (A**2) : 2.15 ; 2.00 REMARK 3 SIDE-CHAIN BOND (A**2) : 5.23 ; 2.00 REMARK 3 SIDE-CHAIN ANGLE (A**2) : 6.68 ; 2.50 REMARK 3 REMARK 3 BULK SOLVENT MODELING. REMARK 3 METHOD USED : FLAT MODEL REMARK 3 KSOL : 0.338637 REMARK 3 BSOL : 32.9638 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 : ANP2.PARAM REMARK 3 PARAMETER FILE 3 : WATER_REP.PARAM REMARK 3 PARAMETER FILE 4 : ION.PARAM REMARK 3 PARAMETER FILE 5 : NULL REMARK 3 TOPOLOGY FILE 1 : PROTEIN.TOP REMARK 3 TOPOLOGY FILE 2 : ANP2.TOP REMARK 3 TOPOLOGY FILE 3 : WATER.TOP REMARK 3 TOPOLOGY FILE 4 : ION.TOP REMARK 3 TOPOLOGY FILE 5 : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 2BRI COMPLIES WITH FORMAT V. 3.15, 01-DEC-08 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 06-MAY-05. REMARK 100 THE PDBE ID CODE IS EBI-23917. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 08-OCT-03 REMARK 200 TEMPERATURE (KELVIN) : 100.0 REMARK 200 PH : 8.00 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : ESRF REMARK 200 BEAMLINE : BM16 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.979471 REMARK 200 MONOCHROMATOR : SILICON (111) CRYSTAL REMARK 200 OPTICS : TOROIDAL MIRRORS REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : MARRESEARCH REMARK 200 INTENSITY-INTEGRATION SOFTWARE : MOSFLM REMARK 200 DATA SCALING SOFTWARE : CCP4 (SCALA) REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 10646 REMARK 200 RESOLUTION RANGE HIGH (A) : 3.000 REMARK 200 RESOLUTION RANGE LOW (A) : 20.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 0.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 100.0 REMARK 200 DATA REDUNDANCY : 6.900 REMARK 200 R MERGE (I) : 0.09000 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 7.1000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 3.00 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 3.19 REMARK 200 COMPLETENESS FOR SHELL (%) : 100.0 REMARK 200 DATA REDUNDANCY IN SHELL : 7.00 REMARK 200 R MERGE FOR SHELL (I) : 0.42000 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 1.800 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: NULL REMARK 200 REMARK 200 REMARK: NOT DEPOSITED YET REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 53.83 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.68 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 3.5 M SODIUM FORMATE REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: I 2 3 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 Z,X,Y REMARK 290 6555 Z,-X,-Y REMARK 290 7555 -Z,-X,Y REMARK 290 8555 -Z,X,-Y REMARK 290 9555 Y,Z,X REMARK 290 10555 -Y,Z,-X REMARK 290 11555 Y,-Z,-X REMARK 290 12555 -Y,-Z,X REMARK 290 13555 X+1/2,Y+1/2,Z+1/2 REMARK 290 14555 -X+1/2,-Y+1/2,Z+1/2 REMARK 290 15555 -X+1/2,Y+1/2,-Z+1/2 REMARK 290 16555 X+1/2,-Y+1/2,-Z+1/2 REMARK 290 17555 Z+1/2,X+1/2,Y+1/2 REMARK 290 18555 Z+1/2,-X+1/2,-Y+1/2 REMARK 290 19555 -Z+1/2,-X+1/2,Y+1/2 REMARK 290 20555 -Z+1/2,X+1/2,-Y+1/2 REMARK 290 21555 Y+1/2,Z+1/2,X+1/2 REMARK 290 22555 -Y+1/2,Z+1/2,-X+1/2 REMARK 290 23555 Y+1/2,-Z+1/2,-X+1/2 REMARK 290 24555 -Y+1/2,-Z+1/2,X+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 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY2 5 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 5 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY1 6 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY2 6 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 6 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY1 7 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY2 7 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 7 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY1 8 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY2 8 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 8 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY1 9 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY2 9 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY3 9 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY1 10 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY2 10 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY3 10 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY1 11 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY2 11 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY3 11 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY1 12 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY2 12 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY3 12 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY1 13 1.000000 0.000000 0.000000 73.34200 REMARK 290 SMTRY2 13 0.000000 1.000000 0.000000 73.34200 REMARK 290 SMTRY3 13 0.000000 0.000000 1.000000 73.34200 REMARK 290 SMTRY1 14 -1.000000 0.000000 0.000000 73.34200 REMARK 290 SMTRY2 14 0.000000 -1.000000 0.000000 73.34200 REMARK 290 SMTRY3 14 0.000000 0.000000 1.000000 73.34200 REMARK 290 SMTRY1 15 -1.000000 0.000000 0.000000 73.34200 REMARK 290 SMTRY2 15 0.000000 1.000000 0.000000 73.34200 REMARK 290 SMTRY3 15 0.000000 0.000000 -1.000000 73.34200 REMARK 290 SMTRY1 16 1.000000 0.000000 0.000000 73.34200 REMARK 290 SMTRY2 16 0.000000 -1.000000 0.000000 73.34200 REMARK 290 SMTRY3 16 0.000000 0.000000 -1.000000 73.34200 REMARK 290 SMTRY1 17 0.000000 0.000000 1.000000 73.34200 REMARK 290 SMTRY2 17 1.000000 0.000000 0.000000 73.34200 REMARK 290 SMTRY3 17 0.000000 1.000000 0.000000 73.34200 REMARK 290 SMTRY1 18 0.000000 0.000000 1.000000 73.34200 REMARK 290 SMTRY2 18 -1.000000 0.000000 0.000000 73.34200 REMARK 290 SMTRY3 18 0.000000 -1.000000 0.000000 73.34200 REMARK 290 SMTRY1 19 0.000000 0.000000 -1.000000 73.34200 REMARK 290 SMTRY2 19 -1.000000 0.000000 0.000000 73.34200 REMARK 290 SMTRY3 19 0.000000 1.000000 0.000000 73.34200 REMARK 290 SMTRY1 20 0.000000 0.000000 -1.000000 73.34200 REMARK 290 SMTRY2 20 1.000000 0.000000 0.000000 73.34200 REMARK 290 SMTRY3 20 0.000000 -1.000000 0.000000 73.34200 REMARK 290 SMTRY1 21 0.000000 1.000000 0.000000 73.34200 REMARK 290 SMTRY2 21 0.000000 0.000000 1.000000 73.34200 REMARK 290 SMTRY3 21 1.000000 0.000000 0.000000 73.34200 REMARK 290 SMTRY1 22 0.000000 -1.000000 0.000000 73.34200 REMARK 290 SMTRY2 22 0.000000 0.000000 1.000000 73.34200 REMARK 290 SMTRY3 22 -1.000000 0.000000 0.000000 73.34200 REMARK 290 SMTRY1 23 0.000000 1.000000 0.000000 73.34200 REMARK 290 SMTRY2 23 0.000000 0.000000 -1.000000 73.34200 REMARK 290 SMTRY3 23 -1.000000 0.000000 0.000000 73.34200 REMARK 290 SMTRY1 24 0.000000 -1.000000 0.000000 73.34200 REMARK 290 SMTRY2 24 0.000000 0.000000 -1.000000 73.34200 REMARK 290 SMTRY3 24 1.000000 0.000000 0.000000 73.34200 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 GENERATING THE BIOMOLECULE 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: PQS REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B 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 0.000000 0.000000 -1.000000 146.68400 REMARK 350 BIOMT2 2 1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT3 2 0.000000 -1.000000 0.000000 146.68400 REMARK 350 BIOMT1 3 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT2 3 0.000000 0.000000 -1.000000 146.68400 REMARK 350 BIOMT3 3 -1.000000 0.000000 0.000000 146.68400 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; REMARK 480 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; REMARK 480 I=INSERTION CODE): REMARK 480 M RES CSSEQI ATOMS REMARK 480 LYS A 157 CG CD CE NZ REMARK 480 ILE A 175 CB CG1 CG2 REMARK 480 LYS B 151 CG CD CE NZ REMARK 480 LYS B 152 CG CD CE NZ REMARK 480 THR B 155 OG1 CG2 REMARK 480 LYS B 157 CG CD CE NZ REMARK 480 SER B 180 CB OG REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: COVALENT BOND ANGLES REMARK 500 REMARK 500 THE STEREOCHEMICAL PARAMETERS OF THE FOLLOWING RESIDUES REMARK 500 HAVE VALUES WHICH DEVIATE FROM EXPECTED VALUES BY MORE REMARK 500 THAN 6*RMSD (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 500 IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT: (10X,I3,1X,A3,1X,A1,I4,A1,3(1X,A4,2X),12X,F5.1) REMARK 500 REMARK 500 EXPECTED VALUES PROTEIN: ENGH AND HUBER, 1999 REMARK 500 EXPECTED VALUES NUCLEIC ACID: CLOWNEY ET AL 1996 REMARK 500 REMARK 500 M RES CSSEQI ATM1 ATM2 ATM3 REMARK 500 PRO B 17 C - N - CA ANGL. DEV. = 11.5 DEGREES 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 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 GLU A 15 -67.53 -122.41 REMARK 500 ASP A 35 35.42 -141.97 REMARK 500 LEU A 84 5.31 -69.13 REMARK 500 THR A 114 -92.83 -99.19 REMARK 500 LYS A 152 -84.00 -155.88 REMARK 500 ILE A 170 -70.30 -40.06 REMARK 500 SER A 182 -174.94 167.34 REMARK 500 ASP A 217 51.06 -65.06 REMARK 500 GLU A 224 145.38 179.38 REMARK 500 ASP B 6 75.56 -108.10 REMARK 500 PRO B 14 -93.24 -39.33 REMARK 500 ASN B 16 100.48 -168.01 REMARK 500 PRO B 17 133.19 -13.68 REMARK 500 PHE B 58 30.07 -93.82 REMARK 500 ARG B 85 -125.00 48.92 REMARK 500 LEU B 105 9.83 -66.24 REMARK 500 ASP B 149 108.77 -46.56 REMARK 500 LYS B 152 -70.83 -102.64 REMARK 500 PRO B 154 -4.28 -54.20 REMARK 500 MSE B 162 176.15 171.19 REMARK 500 ILE B 175 18.71 -55.16 REMARK 500 SER B 181 -80.23 -93.54 REMARK 500 SER B 182 178.03 57.68 REMARK 500 REMARK 500 REMARK: NULL REMARK 525 REMARK 525 SOLVENT REMARK 525 REMARK 525 THE SOLVENT MOLECULES HAVE CHAIN IDENTIFIERS THAT REMARK 525 INDICATE THE POLYMER CHAIN WITH WHICH THEY ARE MOST REMARK 525 CLOSELY ASSOCIATED. THE REMARK LISTS ALL THE SOLVENT REMARK 525 MOLECULES WHICH ARE MORE THAN 5A AWAY FROM THE REMARK 525 NEAREST POLYMER CHAIN (M = MODEL NUMBER; REMARK 525 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE REMARK 525 NUMBER; I=INSERTION CODE): REMARK 620 REMARK 620 METAL COORDINATION REMARK 620 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 620 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE): REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MG A1227 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP A 121 OD2 REMARK 620 2 ASP A 121 OD1 43.5 REMARK 620 3 ANP A1226 O1B 161.7 122.5 REMARK 620 N 1 2 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MG B1227 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ANP B1226 O1B REMARK 620 2 ANP B1226 O2A 67.2 REMARK 620 3 SER B 182 O 111.6 62.4 REMARK 620 4 ASP B 121 OD2 132.2 160.3 101.7 REMARK 620 N 1 2 3 REMARK 650 REMARK 650 HELIX REMARK 650 DETERMINATION METHOD: AUTHOR PROVIDED. REMARK 700 REMARK 700 SHEET REMARK 700 DETERMINATION METHOD: AUTHOR PROVIDED. REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MG A1227 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MG B1227 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ANP A1226 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ANP B1226 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 2BMU RELATED DB: PDB REMARK 900 UMP KINASE FROM PYROCOCCUS FURIOSUS COMPLEXED REMARK 900 WITH ITS SUBSTRATE UMP AND ITS SUBSTRATE REMARK 900 ANALOG AMPPNP DBREF 2BRI A 1 225 UNP Q8U122 PYRH_PYRFU 1 225 DBREF 2BRI B 1 225 UNP Q8U122 PYRH_PYRFU 1 225 SEQRES 1 A 225 MSE ARG ILE VAL PHE ASP ILE GLY GLY SER VAL LEU VAL SEQRES 2 A 225 PRO GLU ASN PRO ASP ILE ASP PHE ILE LYS GLU ILE ALA SEQRES 3 A 225 TYR GLN LEU THR LYS VAL SER GLU ASP HIS GLU VAL ALA SEQRES 4 A 225 VAL VAL VAL GLY GLY GLY LYS LEU ALA ARG LYS TYR ILE SEQRES 5 A 225 GLU VAL ALA GLU LYS PHE ASN SER SER GLU THR PHE LYS SEQRES 6 A 225 ASP PHE ILE GLY ILE GLN ILE THR ARG ALA ASN ALA MSE SEQRES 7 A 225 LEU LEU ILE ALA ALA LEU ARG GLU LYS ALA TYR PRO VAL SEQRES 8 A 225 VAL VAL GLU ASP PHE TRP GLU ALA TRP LYS ALA VAL GLN SEQRES 9 A 225 LEU LYS LYS ILE PRO VAL MSE GLY GLY THR HIS PRO GLY SEQRES 10 A 225 HIS THR THR ASP ALA VAL ALA ALA LEU LEU ALA GLU PHE SEQRES 11 A 225 LEU LYS ALA ASP LEU LEU VAL VAL ILE THR ASN VAL ASP SEQRES 12 A 225 GLY VAL TYR THR ALA ASP PRO LYS LYS ASP PRO THR ALA SEQRES 13 A 225 LYS LYS ILE LYS LYS MSE LYS PRO GLU GLU LEU LEU GLU SEQRES 14 A 225 ILE VAL GLY LYS GLY ILE GLU LYS ALA GLY SER SER SER SEQRES 15 A 225 VAL ILE ASP PRO LEU ALA ALA LYS ILE ILE ALA ARG SER SEQRES 16 A 225 GLY ILE LYS THR ILE VAL ILE GLY LYS GLU ASP ALA LYS SEQRES 17 A 225 ASP LEU PHE ARG VAL ILE LYS GLY ASP HIS ASN GLY THR SEQRES 18 A 225 THR ILE GLU PRO SEQRES 1 B 225 MSE ARG ILE VAL PHE ASP ILE GLY GLY SER VAL LEU VAL SEQRES 2 B 225 PRO GLU ASN PRO ASP ILE ASP PHE ILE LYS GLU ILE ALA SEQRES 3 B 225 TYR GLN LEU THR LYS VAL SER GLU ASP HIS GLU VAL ALA SEQRES 4 B 225 VAL VAL VAL GLY GLY GLY LYS LEU ALA ARG LYS TYR ILE SEQRES 5 B 225 GLU VAL ALA GLU LYS PHE ASN SER SER GLU THR PHE LYS SEQRES 6 B 225 ASP PHE ILE GLY ILE GLN ILE THR ARG ALA ASN ALA MSE SEQRES 7 B 225 LEU LEU ILE ALA ALA LEU ARG GLU LYS ALA TYR PRO VAL SEQRES 8 B 225 VAL VAL GLU ASP PHE TRP GLU ALA TRP LYS ALA VAL GLN SEQRES 9 B 225 LEU LYS LYS ILE PRO VAL MSE GLY GLY THR HIS PRO GLY SEQRES 10 B 225 HIS THR THR ASP ALA VAL ALA ALA LEU LEU ALA GLU PHE SEQRES 11 B 225 LEU LYS ALA ASP LEU LEU VAL VAL ILE THR ASN VAL ASP SEQRES 12 B 225 GLY VAL TYR THR ALA ASP PRO LYS LYS ASP PRO THR ALA SEQRES 13 B 225 LYS LYS ILE LYS LYS MSE LYS PRO GLU GLU LEU LEU GLU SEQRES 14 B 225 ILE VAL GLY LYS GLY ILE GLU LYS ALA GLY SER SER SER SEQRES 15 B 225 VAL ILE ASP PRO LEU ALA ALA LYS ILE ILE ALA ARG SER SEQRES 16 B 225 GLY ILE LYS THR ILE VAL ILE GLY LYS GLU ASP ALA LYS SEQRES 17 B 225 ASP LEU PHE ARG VAL ILE LYS GLY ASP HIS ASN GLY THR SEQRES 18 B 225 THR ILE GLU PRO MODRES 2BRI MSE A 1 MET SELENOMETHIONINE MODRES 2BRI MSE A 78 MET SELENOMETHIONINE MODRES 2BRI MSE A 111 MET SELENOMETHIONINE MODRES 2BRI MSE A 162 MET SELENOMETHIONINE MODRES 2BRI MSE B 1 MET SELENOMETHIONINE MODRES 2BRI MSE B 78 MET SELENOMETHIONINE MODRES 2BRI MSE B 111 MET SELENOMETHIONINE MODRES 2BRI MSE B 162 MET SELENOMETHIONINE HET MSE A 1 8 HET MSE A 78 8 HET MSE A 111 8 HET MSE A 162 8 HET MSE B 1 8 HET MSE B 78 8 HET MSE B 111 8 HET MSE B 162 8 HET MG A1227 1 HET MG B1227 1 HET ANP A1226 31 HET ANP B1226 31 HETNAM MSE SELENOMETHIONINE HETNAM MG MAGNESIUM ION HETNAM ANP PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER FORMUL 1 MSE 8(C5 H11 N O2 SE) FORMUL 3 MG 2(MG 2+) FORMUL 5 ANP 2(C10 H17 N6 O12 P3) FORMUL 7 HOH *14(H2 O1) HELIX 1 1 GLY A 8 VAL A 13 1 6 HELIX 2 2 ASP A 18 SER A 33 1 16 HELIX 3 3 GLY A 45 LYS A 57 1 13 HELIX 4 4 SER A 61 LEU A 84 1 24 HELIX 5 5 PHE A 96 LEU A 105 1 10 HELIX 6 6 THR A 119 LEU A 131 1 13 HELIX 7 7 LYS A 163 VAL A 171 1 9 HELIX 8 8 ASP A 185 SER A 195 1 11 HELIX 9 9 GLY A 203 LYS A 208 1 6 HELIX 10 10 ASP A 209 LYS A 215 1 7 HELIX 11 11 ASP B 18 GLU B 34 1 17 HELIX 12 12 GLY B 45 LYS B 57 1 13 HELIX 13 13 SER B 61 ARG B 85 1 25 HELIX 14 14 PHE B 96 LEU B 105 1 10 HELIX 15 15 THR B 119 LYS B 132 1 14 HELIX 16 16 LYS B 163 VAL B 171 1 9 HELIX 17 17 ASP B 185 SER B 195 1 11 HELIX 18 18 GLY B 203 LYS B 208 1 6 HELIX 19 19 ASP B 209 ILE B 214 1 6 SHEET 1 AA 8 VAL A 92 VAL A 93 0 SHEET 2 AA 8 PRO A 109 MSE A 111 1 O VAL A 110 N VAL A 93 SHEET 3 AA 8 GLU A 37 VAL A 42 1 N VAL A 40 O PRO A 109 SHEET 4 AA 8 MSE A 1 GLY A 8 1 O MSE A 1 N GLU A 37 SHEET 5 AA 8 LEU A 135 THR A 140 1 O LEU A 135 N VAL A 4 SHEET 6 AA 8 LYS A 198 ILE A 202 1 O LYS A 198 N LEU A 136 SHEET 7 AA 8 THR A 221 ILE A 223 -1 O THR A 221 N VAL A 201 SHEET 8 AA 8 LYS A 160 MSE A 162 1 O LYS A 160 N THR A 222 SHEET 1 AB 2 VAL A 145 THR A 147 0 SHEET 2 AB 2 LYS A 157 ILE A 159 -1 N ILE A 159 O VAL A 145 SHEET 1 BA 8 VAL B 92 VAL B 93 0 SHEET 2 BA 8 PRO B 109 MSE B 111 1 O VAL B 110 N VAL B 93 SHEET 3 BA 8 GLU B 37 VAL B 42 1 N VAL B 42 O MSE B 111 SHEET 4 BA 8 MSE B 1 ILE B 7 1 O MSE B 1 N GLU B 37 SHEET 5 BA 8 LEU B 135 ILE B 139 1 O LEU B 135 N VAL B 4 SHEET 6 BA 8 LYS B 198 ILE B 202 1 O LYS B 198 N LEU B 136 SHEET 7 BA 8 THR B 221 ILE B 223 -1 N THR B 221 O VAL B 201 SHEET 8 BA 8 LYS B 160 MSE B 162 1 O LYS B 160 N THR B 222 SHEET 1 BB 2 VAL B 145 TYR B 146 0 SHEET 2 BB 2 LYS B 157 ILE B 159 -1 N ILE B 159 O VAL B 145 LINK C MSE A 1 N ARG A 2 1555 1555 1.33 LINK C ALA A 77 N MSE A 78 1555 1555 1.33 LINK C MSE A 78 N LEU A 79 1555 1555 1.33 LINK C VAL A 110 N MSE A 111 1555 1555 1.32 LINK C MSE A 111 N GLY A 112 1555 1555 1.33 LINK C LYS A 161 N MSE A 162 1555 1555 1.33 LINK C MSE A 162 N LYS A 163 1555 1555 1.33 LINK MG MG A1227 OD2 ASP A 121 1555 1555 2.96 LINK MG MG A1227 O1B ANP A1226 1555 1555 2.34 LINK MG MG A1227 OD1 ASP A 121 1555 1555 2.99 LINK C MSE B 1 N ARG B 2 1555 1555 1.33 LINK C ALA B 77 N MSE B 78 1555 1555 1.33 LINK C MSE B 78 N LEU B 79 1555 1555 1.32 LINK C VAL B 110 N MSE B 111 1555 1555 1.33 LINK C MSE B 111 N GLY B 112 1555 1555 1.33 LINK C LYS B 161 N MSE B 162 1555 1555 1.33 LINK C MSE B 162 N LYS B 163 1555 1555 1.33 LINK MG MG B1227 O2A ANP B1226 1555 1555 2.98 LINK MG MG B1227 O SER B 182 1555 1555 2.93 LINK MG MG B1227 OD2 ASP B 121 1555 1555 3.13 LINK MG MG B1227 O1B ANP B1226 1555 1555 2.59 SITE 1 AC1 4 ASP A 121 SER A 182 VAL A 183 ANP A1226 SITE 1 AC2 5 ASP B 121 SER B 181 SER B 182 ASP B 185 SITE 2 AC2 5 ANP B1226 SITE 1 AC3 19 GLY A 8 GLY A 9 SER A 10 GLY A 43 SITE 2 AC3 19 GLY A 45 THR A 120 THR A 140 ASN A 141 SITE 3 AC3 19 VAL A 142 GLY A 144 TYR A 146 ALA A 148 SITE 4 AC3 19 ASP A 149 PRO A 150 LYS A 151 SER A 181 SITE 5 AC3 19 SER A 182 VAL A 183 MG A1227 SITE 1 AC4 19 GLY B 8 GLY B 9 SER B 10 GLY B 43 SITE 2 AC4 19 GLY B 44 GLY B 45 THR B 140 ASN B 141 SITE 3 AC4 19 GLY B 144 TYR B 146 ALA B 148 ASP B 149 SITE 4 AC4 19 ILE B 170 SER B 181 SER B 182 VAL B 183 SITE 5 AC4 19 MG B1227 HOH B2005 HOH B2006 CRYST1 146.684 146.684 146.684 90.00 90.00 90.00 I 2 3 48 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 0.006817 0.000000 0.000000 0.00000 SCALE2 0.000000 0.006817 0.000000 0.00000 SCALE3 0.000000 0.000000 0.006817 0.00000 MTRIX1 1 0.310930 -0.812820 0.492600 125.57504 1 MTRIX2 1 -0.840320 -0.477250 -0.257080 241.52122 1 MTRIX3 1 0.444050 -0.334010 -0.831420 77.02380 1 HETATM 1 N MSE A 1 71.111 79.994 51.243 1.00 66.28 N HETATM 2 CA MSE A 1 71.522 80.309 49.846 1.00 65.91 C HETATM 3 C MSE A 1 72.387 81.564 49.770 1.00 62.53 C HETATM 4 O MSE A 1 72.189 82.523 50.523 1.00 62.61 O HETATM 5 CB MSE A 1 70.292 80.510 48.955 1.00 71.72 C HETATM 6 CG MSE A 1 69.378 79.304 48.832 1.00 79.47 C HETATM 7 SE MSE A 1 67.889 79.669 47.652 1.00 92.09 SE HETATM 8 CE MSE A 1 66.570 80.251 48.959 1.00 85.47 C