HEADER STRUCTURAL GENOMICS, UNKNOWN FUNCTION 27-JUN-11 3SMD TITLE CRYSTAL STRUCTURE OF A MUT/NUDIX FAMILY PROTEIN FROM BACILLUS TITLE 2 THURINGIENSIS COMPND MOL_ID: 1; COMPND 2 MOLECULE: MUTT/NUDIX FAMILY PROTEIN; COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: BACILLUS THURINGIENSIS; SOURCE 3 ORGANISM_TAXID: 412694; SOURCE 4 STRAIN: AL HAKAM; SOURCE 5 GENE: BALH_2480; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; 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: BC-PSGX3 (BC) KEYWDS STRUCTURAL GENOMICS, PSI-2, PROTEIN STRUCTURE INITIATIVE, NEW YORK KEYWDS 2 SGX RESEARCH CENTER FOR STRUCTURAL GENOMICS, NYSGXRC, MUT/NUDIX KEYWDS 3 PROTEIN, PROTEIN STRUCTURE INITIATIVE II(PSI II), 11181D, HYDROLASE, KEYWDS 4 UNKNOWN FUNCTION EXPDTA X-RAY DIFFRACTION AUTHOR K.PALANI,D.KUMARAN,S.K.BURLEY,S.SWAMINATHAN,NEW YORK SGX RESEARCH AUTHOR 2 CENTER FOR STRUCTURAL GENOMICS (NYSGXRC) REVDAT 2 10-FEB-21 3SMD 1 AUTHOR JRNL LINK REVDAT 1 20-JUL-11 3SMD 0 SPRSDE 20-JUL-11 3SMD 3EDS JRNL AUTH K.PALANI,D.KUMARAN,S.K.BURLEY,S.SWAMINATHAN JRNL TITL CRYSTAL STRUCTURE OF A MUT/NUDIX FAMILY PROTEIN FROM JRNL TITL 2 BACILLUS THURINGIENSIS JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. 1.76 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) : 1.76 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 40.40 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 DATA CUTOFF HIGH (ABS(F)) : 123240.090 REMARK 3 DATA CUTOFF LOW (ABS(F)) : 0.0000 REMARK 3 COMPLETENESS (WORKING+TEST) (%) : 97.1 REMARK 3 NUMBER OF REFLECTIONS : 13825 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) : 0.227 REMARK 3 FREE R VALUE : 0.259 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 696 REMARK 3 ESTIMATED ERROR OF FREE R VALUE : 0.010 REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : 6 REMARK 3 BIN RESOLUTION RANGE HIGH (A) : 1.76 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.87 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 91.00 REMARK 3 REFLECTIONS IN BIN (WORKING SET) : 2001 REMARK 3 BIN R VALUE (WORKING SET) : 0.2530 REMARK 3 BIN FREE R VALUE : 0.2940 REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : 4.80 REMARK 3 BIN FREE R VALUE TEST SET COUNT : 101 REMARK 3 ESTIMATED ERROR OF BIN FREE R VALUE : 0.029 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 1084 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 0 REMARK 3 SOLVENT ATOMS : 124 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 15.20 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 24.10 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 2.86000 REMARK 3 B22 (A**2) : 2.86000 REMARK 3 B33 (A**2) : -5.71000 REMARK 3 B12 (A**2) : 1.05000 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) : 0.12 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) : 0.26 REMARK 3 ESD FROM C-V SIGMAA (A) : 0.13 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 BOND LENGTHS (A) : 0.006 REMARK 3 BOND ANGLES (DEGREES) : 1.500 REMARK 3 DIHEDRAL ANGLES (DEGREES) : 24.30 REMARK 3 IMPROPER ANGLES (DEGREES) : 0.810 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) : 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 : FLAT MODEL REMARK 3 KSOL : 0.36 REMARK 3 BSOL : 46.87 REMARK 3 REMARK 3 NCS MODEL : NONE 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 : CARBOHYDRATE.PARAM REMARK 3 PARAMETER FILE 3 : WATER_REP.PARAM REMARK 3 PARAMETER FILE 4 : ION.PARAM REMARK 3 PARAMETER FILE 5 : NULL REMARK 3 TOPOLOGY FILE 1 : PROTEIN.TOP REMARK 3 TOPOLOGY FILE 2 : CARBOHYDRATE.TOP REMARK 3 TOPOLOGY FILE 3 : WATER.TOP REMARK 3 TOPOLOGY FILE 4 : ION.TOP REMARK 3 TOPOLOGY FILE 5 : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 3SMD COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 11-JUL-11. REMARK 100 THE DEPOSITION ID IS D_1000066380. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 17-AUG-08 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 7.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : NSLS REMARK 200 BEAMLINE : X12C REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.9205 REMARK 200 MONOCHROMATOR : SI(III) REMARK 200 OPTICS : MIRRORS 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 : HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 14215 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.760 REMARK 200 RESOLUTION RANGE LOW (A) : 50.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 0.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.5 REMARK 200 DATA REDUNDANCY : 21.10 REMARK 200 R MERGE (I) : 0.04200 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 28.0000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.76 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.82 REMARK 200 COMPLETENESS FOR SHELL (%) : 94.9 REMARK 200 DATA REDUNDANCY IN SHELL : 18.90 REMARK 200 R MERGE FOR SHELL (I) : 0.44700 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 4.000 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: SAD REMARK 200 SOFTWARE USED: SHELXD, SHARP REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 37.98 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 1.98 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.1M HEPES-NA, 10% ISOPROPANAL, 20% REMARK 280 PEG4000 , PH 7.5, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE REMARK 280 298.0K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 32 2 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -Y,X-Y,Z+2/3 REMARK 290 3555 -X+Y,-X,Z+1/3 REMARK 290 4555 Y,X,-Z REMARK 290 5555 X-Y,-Y,-Z+1/3 REMARK 290 6555 -X,-X+Y,-Z+2/3 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 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 2 0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 39.34000 REMARK 290 SMTRY1 3 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 3 -0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 19.67000 REMARK 290 SMTRY1 4 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 4 0.866025 0.500000 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 0.00000 REMARK 290 SMTRY2 5 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 19.67000 REMARK 290 SMTRY1 6 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 6 -0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 6 0.000000 0.000000 -1.000000 39.34000 REMARK 290 REMARK 290 REMARK: NULL REMARK 300 REMARK 300 BIOMOLECULE: 1, 2 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 350 REMARK 350 BIOMOLECULE: 2 REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 2030 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 13850 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -15.0 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 -0.500000 -0.866025 0.000000 96.00000 REMARK 350 BIOMT2 2 -0.866025 0.500000 0.000000 55.42563 REMARK 350 BIOMT3 2 0.000000 0.000000 -1.000000 -19.67000 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 MSE A 1 REMARK 465 SER A 2 REMARK 465 GLY A 41 REMARK 465 GLY A 42 REMARK 465 GLU A 43 REMARK 465 SER A 116 REMARK 465 ILE A 117 REMARK 465 ASP A 118 REMARK 465 GLY A 119 REMARK 465 GLU A 120 REMARK 465 SER A 121 REMARK 465 LEU A 122 REMARK 465 GLU A 146 REMARK 465 GLY A 147 REMARK 465 HIS A 148 REMARK 465 HIS A 149 REMARK 465 HIS A 150 REMARK 465 HIS A 151 REMARK 465 HIS A 152 REMARK 465 HIS A 153 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 11181D RELATED DB: TARGETDB REMARK 900 RELATED ID: NYSGXRC-11181D RELATED DB: TARGETDB DBREF 3SMD A 1 153 PDB 3SMD 3SMD 1 153 SEQRES 1 A 153 MSE SER LEU SER LEU TYR TYR LYS LYS ILE ARG GLU GLN SEQRES 2 A 153 LEU GLY HIS GLU LEU ILE PHE MSE PRO SER VAL ALA ALA SEQRES 3 A 153 VAL ILE LYS ASN GLU GLN GLY GLU LEU LEU PHE GLN TYR SEQRES 4 A 153 PRO GLY GLY GLU TYR TRP SER LEU PRO ALA GLY ALA ILE SEQRES 5 A 153 GLU PRO GLY GLU THR PRO GLU GLU ALA VAL ILE ARG GLU SEQRES 6 A 153 VAL TRP GLU GLU THR GLY LEU LYS VAL GLN VAL LYS LYS SEQRES 7 A 153 GLN LYS GLY VAL PHE GLY GLY LYS GLU PHE ARG TYR THR SEQRES 8 A 153 TYR ALA ASN GLY ASP LYS VAL GLU TYR ILE VAL VAL VAL SEQRES 9 A 153 PHE GLU CYS GLU ILE THR SER GLY LYS LEU LYS SER ILE SEQRES 10 A 153 ASP GLY GLU SER LEU LYS LEU GLN TYR PHE SER PHE SER SEQRES 11 A 153 GLU LYS PRO PRO LEU ALA LEU PRO TYR PRO ASP LYS ILE SEQRES 12 A 153 PHE LEU GLU GLY HIS HIS HIS HIS HIS HIS MODRES 3SMD MSE A 21 MET SELENOMETHIONINE HET MSE A 21 8 HETNAM MSE SELENOMETHIONINE FORMUL 1 MSE C5 H11 N O2 SE FORMUL 2 HOH *124(H2 O) HELIX 1 1 SER A 4 GLY A 15 1 12 HELIX 2 2 THR A 57 GLY A 71 1 15 HELIX 3 3 GLY A 85 GLU A 87 5 3 HELIX 4 4 SER A 128 LYS A 132 5 5 HELIX 5 5 PRO A 140 LEU A 145 5 6 SHEET 1 A 4 ALA A 49 ALA A 51 0 SHEET 2 A 4 ILE A 19 ILE A 28 -1 N VAL A 24 O GLY A 50 SHEET 3 A 4 LYS A 97 GLY A 112 1 O GLU A 99 N MSE A 21 SHEET 4 A 4 LEU A 72 PHE A 83 -1 N LYS A 80 O VAL A 104 SHEET 1 B 4 ALA A 49 ALA A 51 0 SHEET 2 B 4 ILE A 19 ILE A 28 -1 N VAL A 24 O GLY A 50 SHEET 3 B 4 LYS A 97 GLY A 112 1 O GLU A 99 N MSE A 21 SHEET 4 B 4 ARG A 89 THR A 91 -1 N TYR A 90 O VAL A 98 SHEET 1 C 2 LEU A 35 GLN A 38 0 SHEET 2 C 2 LEU A 124 PHE A 127 -1 O PHE A 127 N LEU A 35 LINK C PHE A 20 N MSE A 21 1555 1555 1.33 LINK C MSE A 21 N PRO A 22 1555 1555 1.34 CRYST1 64.000 64.000 59.010 90.00 90.00 120.00 P 32 2 1 6 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 0.015625 0.009021 0.000000 0.00000 SCALE2 0.000000 0.018042 0.000000 0.00000 SCALE3 0.000000 0.000000 0.016946 0.00000