HEADER HYDROLASE 13-APR-07 2YVN TITLE CRYSTAL STRUCTURE OF NDX2 FROM THERMUS THERMOPHILUS HB8 COMPND MOL_ID: 1; COMPND 2 MOLECULE: MUTT/NUDIX FAMILY PROTEIN; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: NDX2; COMPND 5 EC: 3.6.1.-; COMPND 6 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: THERMUS THERMOPHILUS; SOURCE 3 ORGANISM_TAXID: 300852; SOURCE 4 STRAIN: HB8; SOURCE 5 GENE: NDX2; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3); SOURCE 7 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: BL21(DE3); SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 10 EXPRESSION_SYSTEM_PLASMID: PET11A KEYWDS NUDIX PROTEIN, ADP-RIBOSE, FAD, THERMUS THERMOPHILUS, HYDROLAS, KEYWDS 2 STRUCTURAL GENOMICS, NPPSFA, NATIONAL PROJECT ON PROTEIN STRUCTURAL KEYWDS 3 AND FUNCTIONAL ANALYSES, RIKEN STRUCTURAL GENOMICS/PROTEOMICS KEYWDS 4 INITIATIVE, RSGI, HYDROLASE EXPDTA X-RAY DIFFRACTION AUTHOR T.WAKAMATSU,N.NAKAGAWA,S.KURAMITSU,S.YOKOYAMA,R.MASUI,RIKEN AUTHOR 2 STRUCTURAL GENOMICS/PROTEOMICS INITIATIVE (RSGI) REVDAT 4 25-OCT-23 2YVN 1 REMARK REVDAT 3 13-JUL-11 2YVN 1 VERSN REVDAT 2 24-FEB-09 2YVN 1 VERSN REVDAT 1 26-FEB-08 2YVN 0 JRNL AUTH T.WAKAMATSU,N.NAKAGAWA,S.KURAMITSU,R.MASUI JRNL TITL STRUCTURAL BASIS FOR DIFFERENT SUBSTRATE SPECIFICITIES OF JRNL TITL 2 TWO ADP-RIBOSE PYROPHOSPHATASES FROM THERMUS THERMOPHILUS JRNL TITL 3 HB8 JRNL REF J.BACTERIOL. V. 190 1108 2008 JRNL REFN ISSN 0021-9193 JRNL PMID 18039767 JRNL DOI 10.1128/JB.01522-07 REMARK 2 REMARK 2 RESOLUTION. 1.84 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) : 1.84 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 27.36 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) (%) : 98.3 REMARK 3 NUMBER OF REFLECTIONS : 17840 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) : 0.224 REMARK 3 FREE R VALUE : 0.255 REMARK 3 FREE R VALUE TEST SET SIZE (%) : NULL REMARK 3 FREE R VALUE TEST SET COUNT : 1757 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) : 1.84 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.96 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 95.20 REMARK 3 REFLECTIONS IN BIN (WORKING SET) : NULL REMARK 3 BIN R VALUE (WORKING SET) : 0.2490 REMARK 3 BIN FREE R VALUE : 0.2880 REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : NULL REMARK 3 BIN FREE R VALUE TEST SET COUNT : 289 REMARK 3 ESTIMATED ERROR OF BIN FREE R VALUE : 0.017 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 1437 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 0 REMARK 3 SOLVENT ATOMS : 101 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 9.60 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 20.70 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 6.46000 REMARK 3 B22 (A**2) : -4.43000 REMARK 3 B33 (A**2) : -2.03000 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) : 0.23 REMARK 3 ESD FROM SIGMAA (A) : 0.13 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) : 0.27 REMARK 3 ESD FROM C-V SIGMAA (A) : 0.20 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 BOND LENGTHS (A) : 0.008 REMARK 3 BOND ANGLES (DEGREES) : 1.500 REMARK 3 DIHEDRAL ANGLES (DEGREES) : 24.50 REMARK 3 IMPROPER ANGLES (DEGREES) : 1.010 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) : 1.050 ; NULL REMARK 3 MAIN-CHAIN ANGLE (A**2) : 1.720 ; NULL REMARK 3 SIDE-CHAIN BOND (A**2) : 1.460 ; NULL REMARK 3 SIDE-CHAIN ANGLE (A**2) : 2.240 ; 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 2YVN COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 02-JUL-07. REMARK 100 THE DEPOSITION ID IS D_1000027191. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 29-JUL-05 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 6.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : SPRING-8 REMARK 200 BEAMLINE : BL44B2 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.0000 REMARK 200 MONOCHROMATOR : TRANSPARENT DIAMOND DOUBLE REMARK 200 CRYSTAL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 210 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 19698 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.790 REMARK 200 RESOLUTION RANGE LOW (A) : 50.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : -3.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.8 REMARK 200 DATA REDUNDANCY : 5.900 REMARK 200 R MERGE (I) : 0.04500 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 37.2000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.79 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.85 REMARK 200 COMPLETENESS FOR SHELL (%) : 98.9 REMARK 200 DATA REDUNDANCY IN SHELL : 5.50 REMARK 200 R MERGE FOR SHELL (I) : 0.24800 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 5.800 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: MLPHARE REMARK 200 STARTING MODEL: PDB ENTRY 2YVM REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 50.73 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.50 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.05M MES (PH 6.5), 0.08M SODIUM REMARK 280 ACETATE, 7%(W/V) PEG 8000, 10%(W/V) GLYCEROL, VAPOR DIFFUSION, REMARK 280 HANGING DROP, TEMPERATURE 293K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: C 2 2 21 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 -X,Y,-Z+1/2 REMARK 290 4555 X,-Y,-Z REMARK 290 5555 X+1/2,Y+1/2,Z REMARK 290 6555 -X+1/2,-Y+1/2,Z+1/2 REMARK 290 7555 -X+1/2,Y+1/2,-Z+1/2 REMARK 290 8555 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 48.77950 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 48.77950 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 1.000000 0.000000 0.000000 20.58750 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 50.60050 REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 6 -1.000000 0.000000 0.000000 20.58750 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 50.60050 REMARK 290 SMTRY3 6 0.000000 0.000000 1.000000 48.77950 REMARK 290 SMTRY1 7 -1.000000 0.000000 0.000000 20.58750 REMARK 290 SMTRY2 7 0.000000 1.000000 0.000000 50.60050 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 48.77950 REMARK 290 SMTRY1 8 1.000000 0.000000 0.000000 20.58750 REMARK 290 SMTRY2 8 0.000000 -1.000000 0.000000 50.60050 REMARK 290 SMTRY3 8 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: DIMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA,PQS REMARK 350 TOTAL BURIED SURFACE AREA: 4640 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 16190 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -35.0 KCAL/MOL 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 -1.000000 0.000000 0.000000 41.17500 REMARK 350 BIOMT2 2 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT3 2 0.000000 0.000000 -1.000000 146.33850 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 100 -96.84 -92.16 REMARK 500 GLN A 111 77.26 -156.56 REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 2YVM RELATED DB: PDB REMARK 900 RELATED ID: 2YVO RELATED DB: PDB REMARK 900 RELATED ID: 2YVP RELATED DB: PDB REMARK 900 RELATED ID: TTK003001256.3 RELATED DB: TARGETDB DBREF 2YVN A 1 182 UNP Q5SJY9 Q5SJY9_THET8 1 182 SEQRES 1 A 182 MET SER PRO TRP GLU ARG ILE LEU LEU GLU GLU ILE LEU SEQRES 2 A 182 SER GLU PRO VAL ARG LEU VAL LYS GLU ARG VAL ARG THR SEQRES 3 A 182 HIS THR GLY ARG GLU LEU THR TYR VAL TYR ARG PRO GLY SEQRES 4 A 182 PRO VAL ALA ALA SER PHE VAL LEU PRO VAL THR GLU ARG SEQRES 5 A 182 GLY THR ALA LEU LEU VAL ARG GLN TYR ARG HIS PRO THR SEQRES 6 A 182 GLY LYS PHE LEU LEU GLU VAL PRO ALA GLY LYS VAL ASP SEQRES 7 A 182 GLU GLY GLU THR PRO GLU ALA ALA ALA ARG ARG GLU LEU SEQRES 8 A 182 ARG GLU GLU VAL GLY ALA GLU ALA GLU THR LEU ILE PRO SEQRES 9 A 182 LEU PRO SER PHE HIS PRO GLN PRO SER PHE THR ALA VAL SEQRES 10 A 182 VAL PHE HIS PRO PHE LEU ALA LEU LYS ALA ARG VAL VAL SEQRES 11 A 182 THR PRO PRO THR LEU GLU GLU GLY GLU LEU LEU GLU SER SEQRES 12 A 182 LEU GLU LEU PRO LEU THR GLU VAL TYR ALA LEU LEU ALA SEQRES 13 A 182 LYS GLY GLU ILE GLN ASP ALA SER THR ALA LEU THR LEU SEQRES 14 A 182 PHE TYR ALA GLU PRO HIS LEU LYS ARG LEU GLY LEU LEU FORMUL 2 HOH *101(H2 O) HELIX 1 1 HIS A 63 GLY A 66 5 4 HELIX 2 2 THR A 82 GLY A 96 1 15 HELIX 3 3 LEU A 148 LYS A 157 1 10 HELIX 4 4 ASP A 162 LEU A 179 1 18 SHEET 1 A 3 GLU A 5 LEU A 13 0 SHEET 2 A 3 LEU A 19 ARG A 25 -1 O LEU A 19 N ILE A 12 SHEET 3 A 3 GLU A 31 TYR A 36 -1 O TYR A 34 N GLU A 22 SHEET 1 B 4 ALA A 74 LYS A 76 0 SHEET 2 B 4 ALA A 42 PRO A 48 -1 N SER A 44 O GLY A 75 SHEET 3 B 4 VAL A 118 ALA A 124 1 O ALA A 124 N LEU A 47 SHEET 4 B 4 LEU A 102 PRO A 104 -1 N ILE A 103 O LEU A 123 SHEET 1 C 3 LYS A 67 GLU A 71 0 SHEET 2 C 3 THR A 54 ARG A 62 -1 N VAL A 58 O GLU A 71 SHEET 3 C 3 LEU A 141 PRO A 147 -1 O LEU A 146 N ALA A 55 SHEET 1 D 2 ALA A 97 GLU A 98 0 SHEET 2 D 2 ARG A 128 VAL A 129 -1 O ARG A 128 N GLU A 98 CISPEP 1 GLU A 15 PRO A 16 0 0.17 CISPEP 2 GLY A 39 PRO A 40 0 -0.09 CRYST1 41.175 101.201 97.559 90.00 90.00 90.00 C 2 2 21 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 0.024287 0.000000 0.000000 0.00000 SCALE2 0.000000 0.009881 0.000000 0.00000 SCALE3 0.000000 0.000000 0.010250 0.00000