HEADER PHOSPHOTRANSFERASE(PO4 AS ACCEPTOR) 15-NOV-93 2NCK TITLE CRYSTAL STRUCTURE OF MYXOCOCCUS XANTHUS NUCLEOSIDE DIPHOSPHATE KINASE TITLE 2 AND ITS INTERACTION WITH A NUCLEOTIDE SUBSTRATE AT 2.0 ANGSTROMS TITLE 3 RESOLUTION COMPND MOL_ID: 1; COMPND 2 MOLECULE: NUCLEOSIDE DIPHOSPHATE KINASE; COMPND 3 CHAIN: R, L; COMPND 4 EC: 2.7.4.6; COMPND 5 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: MYXOCOCCUS XANTHUS; SOURCE 3 ORGANISM_TAXID: 34 KEYWDS PHOSPHOTRANSFERASE(PO4 AS ACCEPTOR) EXPDTA X-RAY DIFFRACTION AUTHOR R.L.WILLIAMS,D.A.OREN,E.ARNOLD REVDAT 6 21-FEB-24 2NCK 1 REMARK REVDAT 5 14-AUG-19 2NCK 1 REMARK REVDAT 4 17-JUL-19 2NCK 1 REMARK REVDAT 3 29-NOV-17 2NCK 1 HELIX REVDAT 2 24-FEB-09 2NCK 1 VERSN REVDAT 1 31-JAN-94 2NCK 0 JRNL AUTH R.L.WILLIAMS,D.A.OREN,J.MUNOZ-DORADO,S.INOUYE,M.INOUYE, JRNL AUTH 2 E.ARNOLD JRNL TITL CRYSTAL STRUCTURE OF MYXOCOCCUS XANTHUS NUCLEOSIDE JRNL TITL 2 DIPHOSPHATE KINASE AND ITS INTERACTION WITH A NUCLEOTIDE JRNL TITL 3 SUBSTRATE AT 2.0 A RESOLUTION. JRNL REF J.MOL.BIOL. V. 234 1230 1993 JRNL REFN ISSN 0022-2836 JRNL PMID 8263923 JRNL DOI 10.1006/JMBI.1993.1673 REMARK 1 REMARK 1 REFERENCE 1 REMARK 1 AUTH R.L.WILLIAMS,J.MUNOZ-DORADO,A.JACOBO-MOLINA,S.INOUYE, REMARK 1 AUTH 2 M.INOUYE,E.ARNOLD REMARK 1 TITL CRYSTALLIZATION AND PRELIMINARY X-RAY DIFFRACTION ANALYSIS REMARK 1 TITL 2 OF NUCLEOSIDE DIPHOSPHATE KINASE FROM MYXOCOCCUS XANTHUS REMARK 1 REF J.MOL.BIOL. V. 220 5 1991 REMARK 1 REFN ISSN 0022-2836 REMARK 2 REMARK 2 RESOLUTION. 2.00 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PROLSQ REMARK 3 AUTHORS : KONNERT,HENDRICKSON REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.00 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : NULL REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : NULL REMARK 3 NUMBER OF REFLECTIONS : NULL 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 + TEST SET) : 0.170 REMARK 3 R VALUE (WORKING SET) : 0.170 REMARK 3 FREE R VALUE : NULL REMARK 3 FREE R VALUE TEST SET SIZE (%) : NULL REMARK 3 FREE R VALUE TEST SET COUNT : NULL REMARK 3 REMARK 3 FIT/AGREEMENT OF MODEL WITH ALL DATA. REMARK 3 R VALUE (WORKING + TEST SET, NO CUTOFF) : NULL REMARK 3 R VALUE (WORKING SET, NO CUTOFF) : NULL REMARK 3 FREE R VALUE (NO CUTOFF) : NULL REMARK 3 FREE R VALUE TEST SET SIZE (%, NO CUTOFF) : NULL REMARK 3 FREE R VALUE TEST SET COUNT (NO CUTOFF) : NULL REMARK 3 TOTAL NUMBER OF REFLECTIONS (NO CUTOFF) : NULL REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 2247 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 0 REMARK 3 SOLVENT ATOMS : 205 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) : 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) : NULL REMARK 3 ESD FROM SIGMAA (A) : NULL REMARK 3 LOW RESOLUTION CUTOFF (A) : NULL REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 DISTANCE RESTRAINTS. RMS SIGMA REMARK 3 BOND LENGTH (A) : NULL ; NULL REMARK 3 ANGLE DISTANCE (A) : NULL ; NULL REMARK 3 INTRAPLANAR 1-4 DISTANCE (A) : NULL ; NULL REMARK 3 H-BOND OR METAL COORDINATION (A) : NULL ; NULL REMARK 3 REMARK 3 PLANE RESTRAINT (A) : NULL ; NULL REMARK 3 CHIRAL-CENTER RESTRAINT (A**3) : NULL ; NULL REMARK 3 REMARK 3 NON-BONDED CONTACT RESTRAINTS. REMARK 3 SINGLE TORSION (A) : NULL ; NULL REMARK 3 MULTIPLE TORSION (A) : NULL ; NULL REMARK 3 H-BOND (X...Y) (A) : NULL ; NULL REMARK 3 H-BOND (X-H...Y) (A) : NULL ; NULL REMARK 3 REMARK 3 CONFORMATIONAL TORSION ANGLE RESTRAINTS. REMARK 3 SPECIFIED (DEGREES) : NULL ; NULL REMARK 3 PLANAR (DEGREES) : NULL ; NULL REMARK 3 STAGGERED (DEGREES) : NULL ; NULL REMARK 3 TRANSVERSE (DEGREES) : NULL ; 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 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 2NCK COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY BNL. REMARK 100 THE DEPOSITION ID IS D_1000178398. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : NULL REMARK 200 TEMPERATURE (KELVIN) : NULL REMARK 200 PH : NULL REMARK 200 NUMBER OF CRYSTALS USED : NULL REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : NULL REMARK 200 RADIATION SOURCE : NULL REMARK 200 BEAMLINE : NULL REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : NULL REMARK 200 WAVELENGTH OR RANGE (A) : NULL REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : NULL REMARK 200 DETECTOR MANUFACTURER : NULL REMARK 200 INTENSITY-INTEGRATION SOFTWARE : NULL REMARK 200 DATA SCALING SOFTWARE : NULL REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : NULL REMARK 200 RESOLUTION RANGE HIGH (A) : NULL REMARK 200 RESOLUTION RANGE LOW (A) : NULL REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : NULL REMARK 200 DATA REDUNDANCY : NULL REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : NULL REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : NULL REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : NULL REMARK 200 COMPLETENESS FOR SHELL (%) : NULL 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 FOR SHELL : NULL REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: NULL REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: NULL REMARK 200 SOFTWARE USED: X-PLOR REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 50.48 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.48 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: NULL REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 43 21 2 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,-Y,Z+1/2 REMARK 290 3555 -Y+1/2,X+1/2,Z+3/4 REMARK 290 4555 Y+1/2,-X+1/2,Z+1/4 REMARK 290 5555 -X+1/2,Y+1/2,-Z+3/4 REMARK 290 6555 X+1/2,-Y+1/2,-Z+1/4 REMARK 290 7555 Y,X,-Z REMARK 290 8555 -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 -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 79.00000 REMARK 290 SMTRY1 3 0.000000 -1.000000 0.000000 31.75000 REMARK 290 SMTRY2 3 1.000000 0.000000 0.000000 31.75000 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 118.50000 REMARK 290 SMTRY1 4 0.000000 1.000000 0.000000 31.75000 REMARK 290 SMTRY2 4 -1.000000 0.000000 0.000000 31.75000 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 39.50000 REMARK 290 SMTRY1 5 -1.000000 0.000000 0.000000 31.75000 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 31.75000 REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 118.50000 REMARK 290 SMTRY1 6 1.000000 0.000000 0.000000 31.75000 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 31.75000 REMARK 290 SMTRY3 6 0.000000 0.000000 -1.000000 39.50000 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 79.00000 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: TETRAMERIC REMARK 350 APPLY THE FOLLOWING TO CHAINS: R, L 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 1.000000 0.000000 0.00000 REMARK 350 BIOMT2 2 1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT3 2 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 L 145 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 VAL R 53 -9.55 -59.81 REMARK 500 LYS R 113 70.56 -112.56 REMARK 500 ASN R 114 31.05 -97.68 REMARK 500 THR R 115 -38.19 58.35 REMARK 500 THR L 115 -39.56 62.75 REMARK 500 REMARK 500 REMARK: NULL REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: EPR REMARK 800 EVIDENCE_CODE: AUTHOR REMARK 800 SITE_DESCRIPTION: THE CATALYTIC HIS 117 THAT IS PHOSPHORYLATED IN REMARK 800 THE PHOSPHOENZYME INTERMEDIATE OF THE ENZYMATIC REACTION. REMARK 800 REMARK 800 SITE_IDENTIFIER: EPL REMARK 800 EVIDENCE_CODE: AUTHOR REMARK 800 SITE_DESCRIPTION: THE CATALYTIC HIS 117 THAT IS PHOSPHORYLATED IN REMARK 800 THE PHOSPHOENZYME INTERMEDIATE OF THE ENZYMATIC REACTION. DBREF 2NCK R 2 145 UNP P15266 NDK_MYXXA 1 144 DBREF 2NCK L 2 145 UNP P15266 NDK_MYXXA 1 144 SEQRES 1 R 144 ALA ILE GLU ARG THR LEU SER ILE ILE LYS PRO ASP GLY SEQRES 2 R 144 LEU GLU LYS GLY VAL ILE GLY LYS ILE ILE SER ARG PHE SEQRES 3 R 144 GLU GLU LYS GLY LEU LYS PRO VAL ALA ILE ARG LEU GLN SEQRES 4 R 144 HIS LEU SER GLN ALA GLN ALA GLU GLY PHE TYR ALA VAL SEQRES 5 R 144 HIS LYS ALA ARG PRO PHE PHE LYS ASP LEU VAL GLN PHE SEQRES 6 R 144 MET ILE SER GLY PRO VAL VAL LEU MET VAL LEU GLU GLY SEQRES 7 R 144 GLU ASN ALA VAL LEU ALA ASN ARG ASP ILE MET GLY ALA SEQRES 8 R 144 THR ASN PRO ALA GLN ALA ALA GLU GLY THR ILE ARG LYS SEQRES 9 R 144 ASP PHE ALA THR SER ILE ASP LYS ASN THR VAL HIS GLY SEQRES 10 R 144 SER ASP SER LEU GLU ASN ALA LYS ILE GLU ILE ALA TYR SEQRES 11 R 144 PHE PHE ARG GLU THR GLU ILE HIS SER TYR PRO TYR GLN SEQRES 12 R 144 LYS SEQRES 1 L 144 ALA ILE GLU ARG THR LEU SER ILE ILE LYS PRO ASP GLY SEQRES 2 L 144 LEU GLU LYS GLY VAL ILE GLY LYS ILE ILE SER ARG PHE SEQRES 3 L 144 GLU GLU LYS GLY LEU LYS PRO VAL ALA ILE ARG LEU GLN SEQRES 4 L 144 HIS LEU SER GLN ALA GLN ALA GLU GLY PHE TYR ALA VAL SEQRES 5 L 144 HIS LYS ALA ARG PRO PHE PHE LYS ASP LEU VAL GLN PHE SEQRES 6 L 144 MET ILE SER GLY PRO VAL VAL LEU MET VAL LEU GLU GLY SEQRES 7 L 144 GLU ASN ALA VAL LEU ALA ASN ARG ASP ILE MET GLY ALA SEQRES 8 L 144 THR ASN PRO ALA GLN ALA ALA GLU GLY THR ILE ARG LYS SEQRES 9 L 144 ASP PHE ALA THR SER ILE ASP LYS ASN THR VAL HIS GLY SEQRES 10 L 144 SER ASP SER LEU GLU ASN ALA LYS ILE GLU ILE ALA TYR SEQRES 11 L 144 PHE PHE ARG GLU THR GLU ILE HIS SER TYR PRO TYR GLN SEQRES 12 L 144 LYS FORMUL 3 HOH *205(H2 O) HELIX 1 A1R VAL R 19 PHE R 27 1 9 HELIX 2 A2R PHE R 59 PHE R 66 1 8 HELIX 3 A3R ALA R 82 MET R 90 1 9 HELIX 4 A4R THR R 102 ALA R 108 1 7 HELIX 5 A5R LEU R 122 PHE R 132 1 11 HELIX 6 A1L VAL L 19 PHE L 27 1 9 HELIX 7 A2L PHE L 59 PHE L 66 1 8 HELIX 8 A3L ALA L 82 MET L 90 1 9 HELIX 9 A4L THR L 102 ALA L 108 1 7 HELIX 10 A5L LEU L 122 PHE L 132 1 11 SHEET 1 BR 4 LYS R 33 GLN R 40 0 SHEET 2 BR 4 VAL R 72 GLY R 79 -1 O VAL R 72 N GLN R 40 SHEET 3 BR 4 GLU R 4 ILE R 10 -1 O ILE R 10 N VAL R 73 SHEET 4 BR 4 VAL R 116 SER R 119 -1 N HIS R 117 O ILE R 9 SHEET 1 BL 4 LYS L 33 GLN L 40 0 SHEET 2 BL 4 VAL L 72 GLY L 79 -1 O VAL L 72 N GLN L 40 SHEET 3 BL 4 GLU L 4 ILE L 10 -1 O ILE L 10 N VAL L 73 SHEET 4 BL 4 VAL L 116 SER L 119 -1 N HIS L 117 O ILE L 9 SITE 1 EPR 1 HIS R 117 SITE 1 EPL 1 HIS L 117 CRYST1 63.500 63.500 158.000 90.00 90.00 90.00 P 43 21 2 16 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 0.015748 0.000000 0.000000 0.00000 SCALE2 0.000000 0.015748 0.000000 0.00000 SCALE3 0.000000 0.000000 0.006329 0.00000 MTRIX1 1 -0.004700 -0.987600 0.157000 66.70100 1 MTRIX2 1 -0.988700 -0.019000 -0.148700 67.15600 1 MTRIX3 1 0.149840 -0.156000 -0.976300 -0.39000 1