HEADER HYDROLASE 23-JAN-03 1NQZ TITLE THE STRUCTURE OF A COA PYROPHOSPHATASE FROM D. RADIODURANS COMPLEXED TITLE 2 WITH A MAGNESIUM ION COMPND MOL_ID: 1; COMPND 2 MOLECULE: COA PYROPHOSPHATASE (MUTT/NUDIX FAMILY PROTEIN); COMPND 3 CHAIN: A; COMPND 4 EC: 3.6.1.9; COMPND 5 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: DEINOCOCCUS RADIODURANS; SOURCE 3 ORGANISM_TAXID: 1299; SOURCE 4 GENE: DR1184; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS NUDIX, MUTT, PYROPHOSPHATASE, COA, D.RADIODURANS, HYDROLASE EXPDTA X-RAY DIFFRACTION AUTHOR L.W.KANG,S.B.GABELLI,M.A.BIANCHET,W.L.XU,M.J.BESSMAN,L.M.AMZEL REVDAT 4 16-AUG-23 1NQZ 1 REMARK LINK REVDAT 3 24-FEB-09 1NQZ 1 VERSN REVDAT 2 09-SEP-03 1NQZ 1 JRNL REVDAT 1 13-MAY-03 1NQZ 0 JRNL AUTH L.W.KANG,S.B.GABELLI,M.A.BIANCHET,W.L.XU,M.J.BESSMAN, JRNL AUTH 2 L.M.AMZEL JRNL TITL STRUCTURE OF A COENZYME A PYROPHOSPHATASE FROM DEINOCOCCUS JRNL TITL 2 RADIODURANS: A MEMBER OF THE NUDIX FAMILY. JRNL REF J.BACTERIOL. V. 185 4110 2003 JRNL REFN ISSN 0021-9193 JRNL PMID 12837785 JRNL DOI 10.1128/JB.185.14.4110-4118.2003 REMARK 2 REMARK 2 RESOLUTION. 1.70 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 : ENGH & HUBER REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.70 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 30.00 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 : 19112 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 CROSS-VALIDATION METHOD : NULL REMARK 3 FREE R VALUE TEST SET SELECTION : RANDOM REMARK 3 R VALUE (WORKING SET) : 0.216 REMARK 3 FREE R VALUE : 0.258 REMARK 3 FREE R VALUE TEST SET SIZE (%) : NULL 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 : 1326 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 1 REMARK 3 SOLVENT ATOMS : 123 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 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) : 0.012 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) : 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 1NQZ COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 20-FEB-03. REMARK 100 THE DEPOSITION ID IS D_1000018129. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 20-OCT-02 REMARK 200 TEMPERATURE (KELVIN) : 90 REMARK 200 PH : 6.0 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : NSLS REMARK 200 BEAMLINE : X25 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.009 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 4 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : DENZO REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 19112 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.700 REMARK 200 RESOLUTION RANGE LOW (A) : 30.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 0.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.6 REMARK 200 DATA REDUNDANCY : NULL REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : 0.06200 REMARK 200 FOR THE DATA SET : 15.4000 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: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: CNS REMARK 200 STARTING MODEL: 1NQY REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 37.21 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 1.96 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: PEG1500, MES BUFFER, PH 6.0, VAPOR REMARK 280 DIFFUSION, HANGING DROP, TEMPERATURE 293K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 21 21 2 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+1/2,Y+1/2,-Z REMARK 290 4555 X+1/2,-Y+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 0.00000 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 20.30900 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 47.03300 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 20.30900 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 47.03300 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000 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: 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 375 REMARK 375 SPECIAL POSITION REMARK 375 THE FOLLOWING ATOMS ARE FOUND TO BE WITHIN 0.15 ANGSTROMS REMARK 375 OF A SYMMETRY RELATED ATOM AND ARE ASSUMED TO BE ON SPECIAL REMARK 375 POSITIONS. REMARK 375 REMARK 375 ATOM RES CSSEQI REMARK 375 HOH A 316 LIES ON A SPECIAL POSITION. 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 ALA A 3 REMARK 465 ARG A 23 REMARK 465 THR A 24 REMARK 465 ARG A 25 REMARK 465 THR A 26 REMARK 465 ALA A 27 REMARK 465 LEU A 28 REMARK 465 GLU A 29 REMARK 465 LEU A 30 REMARK 465 PRO A 31 REMARK 465 HIS A 32 REMARK 465 SER A 57 REMARK 465 GLU A 58 REMARK 465 LEU A 59 REMARK 465 PRO A 60 REMARK 465 THR A 61 REMARK 465 HIS A 62 REMARK 465 GLN A 191 REMARK 465 GLY A 192 REMARK 465 PRO A 193 REMARK 465 GLY A 194 REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS IN SAME ASYMMETRIC UNIT REMARK 500 REMARK 500 THE FOLLOWING ATOMS ARE IN CLOSE CONTACT. REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI DISTANCE REMARK 500 OD1 ASP A 47 O HOH A 318 2.12 REMARK 500 REMARK 500 REMARK: NULL 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 A 201 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 GLU A 86 OE2 REMARK 620 2 HOH A 217 O 98.2 REMARK 620 3 HOH A 233 O 91.1 85.1 REMARK 620 4 HOH A 258 O 79.4 167.2 107.4 REMARK 620 5 HOH A 262 O 90.0 87.8 172.9 79.7 REMARK 620 6 HOH A 269 O 170.2 76.0 80.6 108.0 97.6 REMARK 620 N 1 2 3 4 5 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MG A 201 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 1NQY RELATED DB: PDB REMARK 900 APO-ENZYME DBREF 1NQZ A 1 194 UNP Q9RV46 Q9RV46_DEIRA 1 194 SEQRES 1 A 194 MET THR ALA PRO HIS ASP PRO LEU ASP ASP ILE GLN ALA SEQRES 2 A 194 ASP PRO TRP ALA LEU TRP LEU SER GLY ARG THR ARG THR SEQRES 3 A 194 ALA LEU GLU LEU PRO HIS TYR ARG ARG ALA ALA VAL LEU SEQRES 4 A 194 VAL ALA LEU THR ARG GLU ALA ASP PRO ARG VAL LEU LEU SEQRES 5 A 194 THR VAL ARG SER SER GLU LEU PRO THR HIS LYS GLY GLN SEQRES 6 A 194 ILE ALA PHE PRO GLY GLY SER LEU ASP ALA GLY GLU THR SEQRES 7 A 194 PRO THR GLN ALA ALA LEU ARG GLU ALA GLN GLU GLU VAL SEQRES 8 A 194 ALA LEU ASP PRO ALA ALA VAL THR LEU LEU GLY GLU LEU SEQRES 9 A 194 ASP ASP VAL PHE THR PRO VAL GLY PHE HIS VAL THR PRO SEQRES 10 A 194 VAL LEU GLY ARG ILE ALA PRO GLU ALA LEU ASP THR LEU SEQRES 11 A 194 ARG VAL THR PRO GLU VAL ALA GLN ILE ILE THR PRO THR SEQRES 12 A 194 LEU ALA GLU LEU ARG ALA VAL PRO LEU VAL ARG GLU ARG SEQRES 13 A 194 ARG THR LEU PRO ASP GLY THR GLU VAL PRO LEU TYR ARG SEQRES 14 A 194 TYR PRO TRP ARG GLY LEU ASP ILE TRP GLY MET THR ALA SEQRES 15 A 194 ARG VAL LEU HIS ASP LEU LEU GLU GLN GLY PRO GLY HET MG A 201 1 HETNAM MG MAGNESIUM ION FORMUL 2 MG MG 2+ FORMUL 3 HOH *123(H2 O) HELIX 1 1 ASP A 6 ALA A 13 1 8 HELIX 2 2 THR A 78 ALA A 92 1 15 HELIX 3 3 ASP A 94 VAL A 98 5 5 HELIX 4 4 ALA A 123 LEU A 130 5 8 HELIX 5 5 THR A 143 VAL A 150 1 8 HELIX 6 6 GLY A 179 GLU A 190 1 12 SHEET 1 A 4 GLY A 70 SER A 72 0 SHEET 2 A 4 ARG A 34 THR A 43 -1 N ALA A 37 O GLY A 71 SHEET 3 A 4 PHE A 113 ILE A 122 1 O HIS A 114 N ARG A 34 SHEET 4 A 4 THR A 99 GLU A 103 -1 N GLY A 102 O LEU A 119 SHEET 1 B 4 GLY A 70 SER A 72 0 SHEET 2 B 4 ARG A 34 THR A 43 -1 N ALA A 37 O GLY A 71 SHEET 3 B 4 PHE A 113 ILE A 122 1 O HIS A 114 N ARG A 34 SHEET 4 B 4 VAL A 107 THR A 109 -1 N VAL A 107 O VAL A 115 SHEET 1 C 3 ILE A 66 ALA A 67 0 SHEET 2 C 3 LEU A 52 ARG A 55 -1 N THR A 53 O ALA A 67 SHEET 3 C 3 VAL A 136 ILE A 140 -1 O ALA A 137 N VAL A 54 SHEET 1 D 3 VAL A 153 THR A 158 0 SHEET 2 D 3 GLU A 164 TRP A 172 -1 O LEU A 167 N GLU A 155 SHEET 3 D 3 LEU A 175 TRP A 178 -1 O ILE A 177 N TYR A 170 LINK OE2 GLU A 86 MG MG A 201 1555 1555 2.19 LINK MG MG A 201 O HOH A 217 1555 1555 2.05 LINK MG MG A 201 O HOH A 233 1555 1555 2.23 LINK MG MG A 201 O HOH A 258 1555 1555 2.03 LINK MG MG A 201 O HOH A 262 1555 1555 2.13 LINK MG MG A 201 O HOH A 269 1555 1555 2.16 SITE 1 AC1 6 GLU A 86 HOH A 217 HOH A 233 HOH A 258 SITE 2 AC1 6 HOH A 262 HOH A 269 CRYST1 40.618 94.066 43.664 90.00 90.00 90.00 P 21 21 2 4 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 0.024620 0.000000 0.000000 0.00000 SCALE2 0.000000 0.010631 0.000000 0.00000 SCALE3 0.000000 0.000000 0.022902 0.00000