HEADER NUCLEOTIDE MONOPHOSPHATE KINASE 19-MAY-96 1UKD OBSLTE 29-APR-98 1UKD 1UKE TITLE UMP/CMP KINASE FROM SLIME MOLD COMPND MOL_ID: 1; COMPND 2 MOLECULE: URIDYLMONOPHOSPHATE/CYTIDYLMONOPHOSPHATE KINASE; COMPND 3 CHAIN: NULL; COMPND 4 SYNONYM: UMP/CMP KINASE; COMPND 5 EC: 2.7.4.14; COMPND 6 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: DICTYOSTELIUM DISCOIDEUM; SOURCE 3 ORGANISM_COMMON: SLIME MOLD; SOURCE 4 STRAIN: AX2-214; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 6 EXPRESSION_SYSTEM_PLASMID: PIMS5-CDUK-1; SOURCE 7 EXPRESSION_SYSTEM_GENE: KCY_DICDI KEYWDS NMP KINASE, NUCLEOTIDE SPECIFICITY, PHOSPHORYL TRANSFER, KEYWDS 2 BISUBSTRATE INHIBITOR, NUCLEOTIDE MONOPHOSPHATE KINASE EXPDTA X-RAY DIFFRACTION AUTHOR K.SCHEFFZEK,W.KLICHE,L.WIESMUELLER,J.REINSTEIN REVDAT 1 12-FEB-97 1UKD 0 JRNL AUTH K.SCHEFFZEK,W.KLICHE,L.WIESMULLER,J.REINSTEIN JRNL TITL CRYSTAL STRUCTURE OF THE COMPLEX OF UMP/CMP KINASE JRNL TITL 2 FROM DICTYOSTELIUM DISCOIDEUM AND THE BISUBSTRATE JRNL TITL 3 INHIBITOR P1-(5'-ADENOSYL) P5-(5'-URIDYL) JRNL TITL 4 PENTAPHOSPHATE (UP5A) AND MG2+ AT 2.2 A: JRNL TITL 5 IMPLICATIONS FOR WATER-MEDIATED SPECIFICITY JRNL REF BIOCHEMISTRY V. 35 9716 1996 JRNL REFN ASTM BICHAW US ISSN 0006-2960 REMARK 1 REMARK 1 REFERENCE 1 REMARK 1 AUTH U.ABELE,G.E.SCHULZ REMARK 1 TITL HIGH-RESOLUTION STRUCTURES OF ADENYLATE KINASE REMARK 1 TITL 2 FROM YEAST LIGATED WITH INHIBITOR AP5A, SHOWING REMARK 1 TITL 3 THE PATHWAY OF PHOSPHORYL TRANSFER REMARK 1 REF PROTEIN SCI. V. 4 1262 1995 REMARK 1 REFN ASTM PRCIEI US ISSN 0961-8368 REMARK 1 REFERENCE 2 REMARK 1 AUTH C.VONRHEIN,G.J.SCHLAUDERER,G.E.SCHULZ REMARK 1 TITL MOVIE OF THE STRUCTURAL CHANGES DURING A CATALYTIC REMARK 1 TITL 2 CYCLE OF NUCLEOSIDE MONOPHOSPHATE KINASES REMARK 1 REF STRUCTURE (LONDON) V. 3 483 1995 REMARK 1 REFN ASTM STRUE6 UK ISSN 0969-2126 REMARK 1 REFERENCE 3 REMARK 1 AUTH H.J.MULLER-DIECKMANN,G.E.SCHULZ REMARK 1 TITL SUBSTRATE SPECIFICITY AND ASSEMBLY OF THE REMARK 1 TITL 2 CATALYTIC CENTER DERIVED FROM TWO STRUCTURES OF REMARK 1 TITL 3 LIGATED URIDYLATE KINASE REMARK 1 REF J.MOL.BIOL. V. 246 522 1995 REMARK 1 REFN ASTM JMOBAK UK ISSN 0022-2836 REMARK 1 REFERENCE 4 REMARK 1 AUTH L.WIESMULLER,K.SCHEFFZEK,W.KLICHE,R.S.GOODY, REMARK 1 AUTH 2 A.WITTINGHOFER,J.REINSTEIN REMARK 1 TITL CRYSTALLIZATION AND PRELIMINARY X-RAY ANALYSIS OF REMARK 1 TITL 2 UMP/CMP-KINASE FROM DICTYOSTELIUM DISCOIDEUM WITH REMARK 1 TITL 3 THE SPECIFIC BISUBSTRATE INHIBITOR P1-(ADENOSINE REMARK 1 TITL 4 5')-P5-(URIDINE 5')-PENTAPHOSPHATE (UP5A) REMARK 1 REF FEBS LETT. V. 363 22 1995 REMARK 1 REFN ASTM FEBLAL NE ISSN 0014-5793 REMARK 1 REFERENCE 5 REMARK 1 AUTH L.WIESMULLER,A.A.NOEGEL,O.BARZU,G.GERISCH, REMARK 1 AUTH 2 M.SCHLEICHER REMARK 1 TITL CDNA-DERIVED SEQUENCE OF UMP-CMP KINASE FROM REMARK 1 TITL 2 DICTYOSTELIUM DISCOIDEUM AND EXPRESSION OF THE REMARK 1 TITL 3 ENZYME IN ESCHERICHIA COLI REMARK 1 REF J.BIOL.CHEM. V. 265 6339 1990 REMARK 1 REFN ASTM JBCHA3 US ISSN 0021-9258 REMARK 2 REMARK 2 RESOLUTION. 2.20 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : X-PLOR 3.1 REMARK 3 AUTHORS : BRUNGER REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.20 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 8.00 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) (%) : 99.7 REMARK 3 NUMBER OF REFLECTIONS : 15781 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 CROSS-VALIDATION METHOD : NULL REMARK 3 FREE R VALUE TEST SET SELECTION : NULL REMARK 3 R VALUE (WORKING SET) : 0.215 REMARK 3 FREE R VALUE : 0.276 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 10.000 REMARK 3 FREE R VALUE TEST SET COUNT : NULL 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 : 1896 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 76 REMARK 3 SOLVENT ATOMS : 129 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 28.00 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 ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM LUZZATI PLOT (A) : 0.27 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) : 0.009 REMARK 3 BOND ANGLES (DEGREES) : 1.20 REMARK 3 DIHEDRAL ANGLES (DEGREES) : 24.30 REMARK 3 IMPROPER ANGLES (DEGREES) : 2.30 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 ; 1.500 REMARK 3 MAIN-CHAIN ANGLE (A**2) : NULL ; 2.000 REMARK 3 SIDE-CHAIN BOND (A**2) : NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE (A**2) : NULL ; 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: ESTIMATED COORD. ERROR 0.3 ANGSTROMS REMARK 3 FINAL RMS COORD. SHIFT 0.17 ANGSTROMS REMARK 4 REMARK 4 1UKD COMPLIES WITH FORMAT V. 2.3, 09-JULY-1998 REMARK 6 REMARK 6 SIDE CHAINS OF THE FOLLOWING RESIDUES ARE NOT ENTIRELY REMARK 6 WELL DEFINED IN THE DENSITY AND WERE MODELLED BY REMARK 6 STEREOCHEMISTRY: LYS 2, GLU 3, LYS 5, LYS 50, GLU 53, REMARK 6 LYS 60, LYS 72, GLN 82, LYS 106, PHE 108, SER 135, ARG 137, REMARK 6 LYS146. IN THE CASE OF ARG 137 DENSITY FOR MAIN CHAIN REMARK 6 ATOMS IS DISCONNECTIVE. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 09-MAR-1993 REMARK 200 TEMPERATURE (KELVIN) : 277.0 REMARK 200 PH : 8.00 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 : ELLIOTT/ENRAF-NONIUS REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.5419 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NICKEL COATED FRANKS DOUBLE REMARK 200 MIRRORS REMARK 200 REMARK 200 DETECTOR TYPE : XENTRONICS REMARK 200 DETECTOR MANUFACTURER : SIEMENS REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : XSCALE REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 119529 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.200 REMARK 200 RESOLUTION RANGE LOW (A) : 40.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 0.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.6 REMARK 200 DATA REDUNDANCY : 7.200 REMARK 200 R MERGE (I) : 0.07500 REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 22.1000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.20 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.70 REMARK 200 COMPLETENESS FOR SHELL (%) : 98.7 REMARK 200 DATA REDUNDANCY IN SHELL : 3.70 REMARK 200 R MERGE FOR SHELL (I) : 0.05200 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 <I/SIGMA(I)> FOR SHELL : 2.700 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: NULL REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MULTIPLE ISOMORPHOUS REMARK 200 REPLACEMENT (MIR) REMARK 200 SOFTWARE USED: PROGRAM SUITE BY W.KABSCH, X-PLOR3.1, 'O' (A. REMARK 200 JONES) REMARK 200 STARTING MODEL: ADENYLATE KINASE (PORCINE), 1ADK3 REMARK 200 REMARK 200 REMARK: NUMBER OF MEASURED REFLECTIONS : 119529 REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 65.00 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 3.56 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: PH 8. REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 41 21 2 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,-Y,1/2+Z REMARK 290 3555 1/2-Y,1/2+X,1/4+Z REMARK 290 4555 1/2+Y,1/2-X,3/4+Z REMARK 290 5555 1/2-X,1/2+Y,1/4-Z REMARK 290 6555 1/2+X,1/2-Y,3/4-Z REMARK 290 7555 Y,X,-Z REMARK 290 8555 -Y,-X,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 0.00000 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 50.75000 REMARK 290 SMTRY1 3 0.000000 -1.000000 0.000000 39.25000 REMARK 290 SMTRY2 3 1.000000 0.000000 0.000000 39.25000 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 25.37500 REMARK 290 SMTRY1 4 0.000000 1.000000 0.000000 39.25000 REMARK 290 SMTRY2 4 -1.000000 0.000000 0.000000 39.25000 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 76.12500 REMARK 290 SMTRY1 5 -1.000000 0.000000 0.000000 39.25000 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 39.25000 REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 25.37500 REMARK 290 SMTRY1 6 1.000000 0.000000 0.000000 39.25000 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 39.25000 REMARK 290 SMTRY3 6 0.000000 0.000000 -1.000000 76.12500 REMARK 290 SMTRY1 7 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY2 7 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 8 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY2 8 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 8 0.000000 0.000000 -1.000000 50.75000 REMARK 290 REMARK 290 REMARK: NULL REMARK 300 REMARK 300 BIOMOLECULE: 1 REMARK 300 THIS ENTRY CONTAINS THE CRYSTALLOGRAPHIC ASYMMETRIC UNIT REMARK 300 WHICH CONSISTS OF 1 CHAIN(S). SEE REMARK 350 FOR REMARK 300 INFORMATION ON GENERATING THE BIOLOGICAL MOLECULE(S). 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 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 1 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 M RES CSSEQI PSI PHI REMARK 500 GLU 53 -43.43 81.97 REMARK 850 REMARK 850 CORRECTION BEFORE RELEASE REMARK 850 ORIGINAL DEPOSITION REVISED PRIOR TO RELEASE REMARK 850 DATE REVISED: 17-OCT-1996 TRACKING NUMBER: T8750 REMARK 999 REMARK 999 SEQUENCE REMARK 999 1UKD SWS P20425 1 - 1 NOT IN ATOMS LIST DBREF 1UKD 2 194 UNP P20425 KCY_DICDI 2 194 SEQRES 1 194 MET GLU LYS SER LYS PRO ASN VAL VAL PHE VAL LEU GLY SEQRES 2 194 GLY PRO GLY SER GLY LYS GLY THR GLN CYS ALA ASN ILE SEQRES 3 194 VAL ARG ASP PHE GLY TRP VAL HIS LEU SER ALA GLY ASP SEQRES 4 194 LEU LEU ARG GLN GLU GLN GLN SER GLY SER LYS ASP GLY SEQRES 5 194 GLU MET ILE ALA THR MET ILE LYS ASN GLY GLU ILE VAL SEQRES 6 194 PRO SER ILE VAL THR VAL LYS LEU LEU LYS ASN ALA ILE SEQRES 7 194 ASP ALA ASN GLN GLY LYS ASN PHE LEU VAL ASP GLY PHE SEQRES 8 194 PRO ARG ASN GLU GLU ASN ASN ASN SER TRP GLU GLU ASN SEQRES 9 194 MET LYS ASP PHE VAL ASP THR LYS PHE VAL LEU PHE PHE SEQRES 10 194 ASP CYS PRO GLU GLU VAL MET THR GLN ARG LEU LEU LYS SEQRES 11 194 ARG GLY GLU SER SER GLY ARG SER ASP ASP ASN ILE GLU SEQRES 12 194 SER ILE LYS LYS ARG PHE ASN THR PHE ASN VAL GLN THR SEQRES 13 194 LYS LEU VAL ILE ASP HIS TYR ASN LYS PHE ASP LYS VAL SEQRES 14 194 LYS ILE ILE PRO ALA ASN ARG ASP VAL ASN GLU VAL TYR SEQRES 15 194 ASN ASP VAL GLU ASN LEU PHE LYS SER MET GLY PHE HET UP5 195 76 HETNAM UP5 P1-(ADENOSINE-5'-P5-(URIDINE-5')PENTAPHOSPHATE FORMUL 2 UP5 C19 H28 N7 O24 P5 FORMUL 3 HOH *43(H2 O1) HELIX 1 1 LYS 19 PHE 30 1 12 HELIX 2 2 ALA 37 GLN 46 1 10 HELIX 3 3 MET 54 ASN 61 1 8 HELIX 4 4 SER 67 ASN 81 1 15 HELIX 5 5 GLU 95 ASN 104 1 10 HELIX 6 6 GLU 121 GLU 133 1 13 HELIX 7 7 ILE 142 LYS 165 1 24 HELIX 8 8 VAL 178 SER 191 1 14 SHEET 1 A 5 VAL 33 SER 36 0 SHEET 2 A 5 PHE 86 ASP 89 1 N LEU 87 O VAL 33 SHEET 3 A 5 PRO 6 GLY 13 1 N VAL 9 O PHE 86 SHEET 4 A 5 VAL 109 ASP 118 1 N ASP 110 O PRO 6 SHEET 5 A 5 VAL 169 PRO 173 1 N LYS 170 O VAL 114 CISPEP 1 PHE 91 PRO 92 0 2.02 CRYST1 78.500 78.500 101.500 90.00 90.00 90.00 P 41 21 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 0.012739 0.000000 0.000000 0.00000 SCALE2 0.000000 0.012739 0.000000 0.00000 SCALE3 0.000000 0.000000 0.009852 0.00000