HEADER HYDROLASE 04-MAR-04 1SJY TITLE CRYSTAL STRUCTURE OF NUDIX HYDROLASE DR1025 FROM DEINOCOCCUS TITLE 2 RADIODURANS COMPND MOL_ID: 1; COMPND 2 MOLECULE: MUTT/NUDIX FAMILY PROTEIN; COMPND 3 CHAIN: A; COMPND 4 EC: 3.6.1.-; COMPND 5 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: DEINOCOCCUS RADIODURANS; SOURCE 3 ORGANISM_TAXID: 1299; SOURCE 4 GENE: DR1025; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 7 EXPRESSION_SYSTEM_STRAIN: BL21TUNER; SOURCE 8 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 9 EXPRESSION_SYSTEM_PLASMID: PET24A KEYWDS NUDIX FOLD, ALPHA-BETA-ALPHA SANDWICH, STRUCTURAL GENOMICS, BSGC KEYWDS 2 STRUCTURE FUNDED BY NIH, PROTEIN STRUCTURE INITIATIVE, PSI, BERKELEY KEYWDS 3 STRUCTURAL GENOMICS CENTER, HYDROLASE EXPDTA X-RAY DIFFRACTION AUTHOR W.RANATUNGA,E.E.HILL,J.L.MOOSTER,E.L.HOLBROOK,U.SCHULZE-GAHMEN,W.XU, AUTHOR 2 M.J.BESSMAN,S.E.BRENNER,S.R.HOLBROOK,BERKELEY STRUCTURAL GENOMICS AUTHOR 3 CENTER (BSGC) REVDAT 5 14-FEB-24 1SJY 1 REMARK REVDAT 4 24-FEB-09 1SJY 1 VERSN REVDAT 3 08-MAR-05 1SJY 1 AUTHOR KEYWDS REMARK REVDAT 2 24-AUG-04 1SJY 1 KEYWDS REVDAT 1 11-MAY-04 1SJY 0 JRNL AUTH W.RANATUNGA,E.E.HILL,J.L.MOOSTER,E.L.HOLBROOK, JRNL AUTH 2 U.SCHULZE-GAHMEN,W.XU,M.J.BESSMAN,S.E.BRENNER,S.R.HOLBROOK JRNL TITL STRUCTURAL STUDIES OF THE NUDIX HYDROLASE DR1025 FROM JRNL TITL 2 DEINOCOCCUS RADIODURANS AND ITS LIGAND COMPLEXES. JRNL REF J.MOL.BIOL. V. 339 103 2004 JRNL REFN ISSN 0022-2836 JRNL PMID 15123424 JRNL DOI 10.1016/J.JMB.2004.01.065 REMARK 2 REMARK 2 RESOLUTION. 1.39 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) : 1.39 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 100.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 DATA CUTOFF HIGH (ABS(F)) : 1092.600 REMARK 3 DATA CUTOFF LOW (ABS(F)) : 4.3000 REMARK 3 COMPLETENESS (WORKING+TEST) (%) : 98.4 REMARK 3 NUMBER OF REFLECTIONS : 35334 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) : 0.228 REMARK 3 FREE R VALUE : 0.242 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 9.900 REMARK 3 FREE R VALUE TEST SET COUNT : 3520 REMARK 3 ESTIMATED ERROR OF FREE R VALUE : 0.004 REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : 10 REMARK 3 BIN RESOLUTION RANGE HIGH (A) : 1.39 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.44 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 89.50 REMARK 3 REFLECTIONS IN BIN (WORKING SET) : 3 REMARK 3 BIN R VALUE (WORKING SET) : 0.2810 REMARK 3 BIN FREE R VALUE : 0.3260 REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : 10.00 REMARK 3 BIN FREE R VALUE TEST SET COUNT : 386 REMARK 3 ESTIMATED ERROR OF BIN FREE R VALUE : 0.000 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 1205 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 0 REMARK 3 SOLVENT ATOMS : 102 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 17.75 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -0.82200 REMARK 3 B22 (A**2) : -0.82200 REMARK 3 B33 (A**2) : 1.64500 REMARK 3 B12 (A**2) : 0.00000 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) : 0.18 REMARK 3 ESD FROM SIGMAA (A) : 0.03 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) : 0.19 REMARK 3 ESD FROM C-V SIGMAA (A) : 0.06 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 BOND LENGTHS (A) : 0.004 REMARK 3 BOND ANGLES (DEGREES) : 1.278 REMARK 3 DIHEDRAL ANGLES (DEGREES) : 23.47 REMARK 3 IMPROPER ANGLES (DEGREES) : 0.750 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) : 1.115 ; NULL REMARK 3 MAIN-CHAIN ANGLE (A**2) : 1.790 ; NULL REMARK 3 SIDE-CHAIN BOND (A**2) : 1.846 ; NULL REMARK 3 SIDE-CHAIN ANGLE (A**2) : 2.654 ; NULL REMARK 3 REMARK 3 BULK SOLVENT MODELING. REMARK 3 METHOD USED : FLAT MODEL REMARK 3 KSOL : 0.47 REMARK 3 BSOL : 50.80 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 : WATER_REP.PARAM REMARK 3 PARAMETER FILE 3 : NULL REMARK 3 TOPOLOGY FILE 1 : PROTEIN.TOP REMARK 3 TOPOLOGY FILE 2 : NULL REMARK 3 TOPOLOGY FILE 3 : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 1SJY COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 05-MAR-04. REMARK 100 THE DEPOSITION ID IS D_1000021774. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 01-JUL-02 REMARK 200 TEMPERATURE (KELVIN) : 100.0 REMARK 200 PH : 4.5 REMARK 200 NUMBER OF CRYSTALS USED : 2 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) : 1.0 REMARK 200 MONOCHROMATOR : SI(220), CYLINDRICALLY BENT REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 4 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 35334 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.390 REMARK 200 RESOLUTION RANGE LOW (A) : 100.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 1.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 98.4 REMARK 200 DATA REDUNDANCY : 10.60 REMARK 200 R MERGE (I) : 0.05800 REMARK 200 R SYM (I) : 0.05800 REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 56.1000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.39 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.44 REMARK 200 COMPLETENESS FOR SHELL (%) : 89.5 REMARK 200 DATA REDUNDANCY IN SHELL : 3.80 REMARK 200 R MERGE FOR SHELL (I) : 0.34400 REMARK 200 R SYM FOR SHELL (I) : 0.05800 REMARK 200 <I/SIGMA(I)> FOR SHELL : 4.400 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: SAD REMARK 200 SOFTWARE USED: SOLVE, CNS 1.1 REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 50.07 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.45 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: SODIUM ACETATE, SODIUM FORMATE, PH REMARK 280 4.5, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 295K 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,Z+1/2 REMARK 290 3555 -Y+1/2,X+1/2,Z+1/4 REMARK 290 4555 Y+1/2,-X+1/2,Z+3/4 REMARK 290 5555 -X+1/2,Y+1/2,-Z+1/4 REMARK 290 6555 X+1/2,-Y+1/2,-Z+3/4 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 61.25800 REMARK 290 SMTRY1 3 0.000000 -1.000000 0.000000 26.60500 REMARK 290 SMTRY2 3 1.000000 0.000000 0.000000 26.60500 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 30.62900 REMARK 290 SMTRY1 4 0.000000 1.000000 0.000000 26.60500 REMARK 290 SMTRY2 4 -1.000000 0.000000 0.000000 26.60500 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 91.88700 REMARK 290 SMTRY1 5 -1.000000 0.000000 0.000000 26.60500 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 26.60500 REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 30.62900 REMARK 290 SMTRY1 6 1.000000 0.000000 0.000000 26.60500 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 26.60500 REMARK 290 SMTRY3 6 0.000000 0.000000 -1.000000 91.88700 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 61.25800 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 ASYMMETRIC UNIT OF A CRYSTAL STRUCTURE CONTAINS ONE REMARK 300 BIOLOGICAL UNIT 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: DIMERIC 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 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 61.25800 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 PRO A 36 REMARK 465 GLY A 37 REMARK 465 HIS A 38 REMARK 465 PRO A 39 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 GLU A 118 -179.39 -178.21 REMARK 500 PRO A 158 91.94 -40.26 REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: BSGCAIR30561 RELATED DB: TARGETDB DBREF 1SJY A 1 159 UNP Q9RVK2 Q9RVK2_DEIRA 1 159 SEQRES 1 A 159 MET GLU HIS ASP GLU ARG THR HIS VAL PRO VAL GLU LEU SEQRES 2 A 159 ARG ALA ALA GLY VAL VAL LEU LEU ASN GLU ARG GLY ASP SEQRES 3 A 159 ILE LEU LEU VAL GLN GLU LYS GLY ILE PRO GLY HIS PRO SEQRES 4 A 159 GLU LYS ALA GLY LEU TRP HIS ILE PRO SER GLY ALA VAL SEQRES 5 A 159 GLU ASP GLY GLU ASN PRO GLN ASP ALA ALA VAL ARG GLU SEQRES 6 A 159 ALA CYS GLU GLU THR GLY LEU ARG VAL ARG PRO VAL LYS SEQRES 7 A 159 PHE LEU GLY ALA TYR LEU GLY ARG PHE PRO ASP GLY VAL SEQRES 8 A 159 LEU ILE LEU ARG HIS VAL TRP LEU ALA GLU PRO GLU PRO SEQRES 9 A 159 GLY GLN THR LEU ALA PRO ALA PHE THR ASP GLU ILE ALA SEQRES 10 A 159 GLU ALA SER PHE VAL SER ARG GLU ASP PHE ALA GLN LEU SEQRES 11 A 159 TYR ALA ALA GLY GLN ILE ARG MET TYR GLN THR LYS LEU SEQRES 12 A 159 PHE TYR ALA ASP ALA LEU ARG GLU LYS GLY PHE PRO ALA SEQRES 13 A 159 LEU PRO VAL FORMUL 2 HOH *102(H2 O) HELIX 1 1 ASN A 57 GLY A 71 1 15 HELIX 2 2 SER A 123 ALA A 133 1 11 HELIX 3 3 TYR A 139 GLY A 153 1 15 SHEET 1 A 4 SER A 49 ALA A 51 0 SHEET 2 A 4 LEU A 13 LEU A 20 -1 N ALA A 16 O GLY A 50 SHEET 3 A 4 LEU A 92 PRO A 102 1 O TRP A 98 N VAL A 19 SHEET 4 A 4 VAL A 74 ARG A 86 -1 N LYS A 78 O LEU A 99 SHEET 1 B 3 TRP A 45 HIS A 46 0 SHEET 2 B 3 ILE A 27 GLU A 32 -1 N VAL A 30 O HIS A 46 SHEET 3 B 3 ILE A 116 VAL A 122 -1 O GLU A 118 N GLN A 31 CRYST1 53.210 53.210 122.516 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 0.018793 0.000000 0.000000 0.00000 SCALE2 0.000000 0.018793 0.000000 0.00000 SCALE3 0.000000 0.000000 0.008162 0.00000