HEADER STRUCTURAL GENOMICS, UNKNOWN FUNCTION 11-MAY-04 1WD5 TITLE CRYSTAL STRUCTURE OF TT1426 FROM THERMUS THERMOPHILUS HB8 COMPND MOL_ID: 1; COMPND 2 MOLECULE: HYPOTHETICAL PROTEIN TT1426; COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: THERMUS THERMOPHILUS; SOURCE 3 ORGANISM_TAXID: 274; SOURCE 4 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 5 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 6 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 7 EXPRESSION_SYSTEM_PLASMID: PET11A KEYWDS STRUCTURAL GENOMICS, HYPOTHETICAL PROTEIN, RIKEN STRUCTURAL KEYWDS 2 GENOMICS/PROTEOMICS INITIATIVE, RSGI, UNKNOWN FUNCTION EXPDTA X-RAY DIFFRACTION AUTHOR R.SHIBATA,M.KUKIMOTO-NIINO,K.MURAYAMA,M.SHIROUZU,S.YOKOYAMA, AUTHOR 2 RIKEN STRUCTURAL GENOMICS/PROTEOMICS INITIATIVE (RSGI) REVDAT 3 24-FEB-09 1WD5 1 VERSN REVDAT 2 08-MAR-05 1WD5 1 AUTHOR JRNL KEYWDS REMARK REVDAT 1 11-NOV-04 1WD5 0 JRNL AUTH M.KUKIMOTO-NIINO,R.SHIBATA,K.MURAYAMA,H.HAMANA, JRNL AUTH 2 M.NISHIMOTO,Y.BESSHO,T.TERADA,M.SHIROUZU, JRNL AUTH 3 S.KURAMITSU,S.YOKOYAMA JRNL TITL CRYSTAL STRUCTURE OF A PREDICTED JRNL TITL 2 PHOSPHORIBOSYLTRANSFERASE (TT1426) FROM THERMUS JRNL TITL 3 THERMOPHILUS HB8 AT 2.01 A RESOLUTION JRNL REF PROTEIN SCI. V. 14 823 2005 JRNL REFN ISSN 0961-8368 JRNL PMID 15689504 JRNL DOI 10.1110/PS.041229405 REMARK 1 REMARK 2 REMARK 2 RESOLUTION. 2.00 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 : NULL REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.00 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 36.76 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 DATA CUTOFF HIGH (ABS(F)) : 219596.220 REMARK 3 DATA CUTOFF LOW (ABS(F)) : 0.0000 REMARK 3 COMPLETENESS (WORKING+TEST) (%) : 88.1 REMARK 3 NUMBER OF REFLECTIONS : 18107 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) : 0.195 REMARK 3 FREE R VALUE : 0.227 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.900 REMARK 3 FREE R VALUE TEST SET COUNT : 1530 REMARK 3 ESTIMATED ERROR OF FREE R VALUE : 0.006 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) : 2.00 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.13 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 44.40 REMARK 3 REFLECTIONS IN BIN (WORKING SET) : 2561 REMARK 3 BIN R VALUE (WORKING SET) : 0.2520 REMARK 3 BIN FREE R VALUE : 0.2970 REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : 4.20 REMARK 3 BIN FREE R VALUE TEST SET COUNT : 113 REMARK 3 ESTIMATED ERROR OF BIN FREE R VALUE : 0.028 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 1578 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 12 REMARK 3 SOLVENT ATOMS : 224 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 6.60 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 21.90 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 4.50000 REMARK 3 B22 (A**2) : 4.50000 REMARK 3 B33 (A**2) : -8.99000 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) : 0.22 REMARK 3 ESD FROM SIGMAA (A) : 0.20 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) : 0.20 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 BOND LENGTHS (A) : 0.009 REMARK 3 BOND ANGLES (DEGREES) : 1.20 REMARK 3 DIHEDRAL ANGLES (DEGREES) : 22.30 REMARK 3 IMPROPER ANGLES (DEGREES) : 0.74 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) : 1.220 ; 1.500 REMARK 3 MAIN-CHAIN ANGLE (A**2) : 1.890 ; 2.000 REMARK 3 SIDE-CHAIN BOND (A**2) : 2.370 ; 2.000 REMARK 3 SIDE-CHAIN ANGLE (A**2) : 3.460 ; 2.500 REMARK 3 REMARK 3 BULK SOLVENT MODELING. REMARK 3 METHOD USED : FLAT MODEL REMARK 3 KSOL : 0.36 REMARK 3 BSOL : 57.80 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 : MES.PARAM REMARK 3 PARAMETER FILE 4 : NULL REMARK 3 TOPOLOGY FILE 1 : PROTEIN.TOP REMARK 3 TOPOLOGY FILE 2 : WATER.TOP REMARK 3 TOPOLOGY FILE 3 : MES.TOP REMARK 3 TOPOLOGY FILE 4 : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 1WD5 COMPLIES WITH FORMAT V. 3.15, 01-DEC-08 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 13-MAY-04. REMARK 100 THE RCSB ID CODE IS RCSB023449. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 05-APR-04 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : NULL REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : SPRING-8 REMARK 200 BEAMLINE : BL26B1 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.97910, 0.97938, 0.97400 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : RIGAKU JUPITER 210 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 31382 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.000 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 (%) : 95.3 REMARK 200 DATA REDUNDANCY : 7.380 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : 0.10700 REMARK 200 FOR THE DATA SET : 15.3700 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.00 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.08 REMARK 200 COMPLETENESS FOR SHELL (%) : 67.4 REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : 0.30300 REMARK 200 FOR SHELL : NULL REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: MAD REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MAD REMARK 200 SOFTWARE USED: SOLVE REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 59.80 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 3.10 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: NULL 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 25.64350 REMARK 290 SMTRY1 3 0.000000 -1.000000 0.000000 51.98500 REMARK 290 SMTRY2 3 1.000000 0.000000 0.000000 51.98500 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 12.82175 REMARK 290 SMTRY1 4 0.000000 1.000000 0.000000 51.98500 REMARK 290 SMTRY2 4 -1.000000 0.000000 0.000000 51.98500 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 38.46525 REMARK 290 SMTRY1 5 -1.000000 0.000000 0.000000 51.98500 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 51.98500 REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 12.82175 REMARK 290 SMTRY1 6 1.000000 0.000000 0.000000 51.98500 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 51.98500 REMARK 290 SMTRY3 6 0.000000 0.000000 -1.000000 38.46525 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 25.64350 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 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 ALA A 24 61.08 36.46 REMARK 500 ALA A 182 -85.46 -95.63 REMARK 500 REMARK 500 REMARK: NULL REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MES A 2955 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: TTK003001426 RELATED DB: TARGETDB DBREF 1WD5 A 1 208 UNP Q5SIB2 Q5SIB2_THET8 1 208 SEQRES 1 A 208 MSE ARG PHE ARG ASP ARG ARG HIS ALA GLY ALA LEU LEU SEQRES 2 A 208 ALA GLU ALA LEU ALA PRO LEU GLY LEU GLU ALA PRO VAL SEQRES 3 A 208 VAL LEU GLY LEU PRO ARG GLY GLY VAL VAL VAL ALA ASP SEQRES 4 A 208 GLU VAL ALA ARG ARG LEU GLY GLY GLU LEU ASP VAL VAL SEQRES 5 A 208 LEU VAL ARG LYS VAL GLY ALA PRO GLY ASN PRO GLU PHE SEQRES 6 A 208 ALA LEU GLY ALA VAL GLY GLU GLY GLY GLU LEU VAL LEU SEQRES 7 A 208 MSE PRO TYR ALA LEU ARG TYR ALA ASP GLN SER TYR LEU SEQRES 8 A 208 GLU ARG GLU ALA ALA ARG GLN ARG ASP VAL LEU ARG LYS SEQRES 9 A 208 ARG ALA GLU ARG TYR ARG ARG VAL ARG PRO LYS ALA ALA SEQRES 10 A 208 ARG LYS GLY ARG ASP VAL VAL LEU VAL ASP ASP GLY VAL SEQRES 11 A 208 ALA THR GLY ALA SER MSE GLU ALA ALA LEU SER VAL VAL SEQRES 12 A 208 PHE GLN GLU GLY PRO ARG ARG VAL VAL VAL ALA VAL PRO SEQRES 13 A 208 VAL ALA SER PRO GLU ALA VAL GLU ARG LEU LYS ALA ARG SEQRES 14 A 208 ALA GLU VAL VAL ALA LEU SER VAL PRO GLN ASP PHE ALA SEQRES 15 A 208 ALA VAL GLY ALA TYR TYR LEU ASP PHE GLY GLU VAL THR SEQRES 16 A 208 ASP GLU ASP VAL GLU ALA ILE LEU LEU GLU TRP ALA GLY MODRES 1WD5 MSE A 1 MET SELENOMETHIONINE MODRES 1WD5 MSE A 79 MET SELENOMETHIONINE MODRES 1WD5 MSE A 136 MET SELENOMETHIONINE HET MSE A 1 8 HET MSE A 79 8 HET MSE A 136 8 HET MES A2955 12 HETNAM MSE SELENOMETHIONINE HETNAM MES 2-(N-MORPHOLINO)-ETHANESULFONIC ACID FORMUL 1 MSE 3(C5 H11 N O2 SE) FORMUL 2 MES C6 H13 N O4 S FORMUL 3 HOH *224(H2 O) HELIX 1 1 ASP A 5 ALA A 18 1 14 HELIX 2 2 PRO A 19 GLY A 21 5 3 HELIX 3 3 ARG A 32 GLY A 46 1 15 HELIX 4 4 TYR A 81 ALA A 86 1 6 HELIX 5 5 ASP A 87 ARG A 113 1 27 HELIX 6 6 GLY A 133 GLN A 145 1 13 HELIX 7 7 SER A 159 ALA A 168 1 10 HELIX 8 8 ALA A 183 TYR A 188 5 6 HELIX 9 9 THR A 195 GLU A 205 1 11 SHEET 1 A 5 GLU A 48 VAL A 51 0 SHEET 2 A 5 VAL A 26 GLY A 29 1 N VAL A 27 O GLU A 48 SHEET 3 A 5 ASP A 122 VAL A 126 1 O VAL A 124 N LEU A 28 SHEET 4 A 5 ARG A 150 VAL A 157 1 O ALA A 154 N LEU A 125 SHEET 5 A 5 GLU A 171 SER A 176 1 O VAL A 173 N VAL A 153 SHEET 1 B 3 VAL A 54 ALA A 59 0 SHEET 2 B 3 ASN A 62 GLY A 71 -1 O LEU A 67 N VAL A 57 SHEET 3 B 3 LEU A 76 LEU A 78 -1 O VAL A 77 N ALA A 69 LINK C MSE A 1 N ARG A 2 1555 1555 1.33 LINK C LEU A 78 N MSE A 79 1555 1555 1.33 LINK C MSE A 79 N PRO A 80 1555 1555 1.34 LINK C SER A 135 N MSE A 136 1555 1555 1.33 LINK C MSE A 136 N GLU A 137 1555 1555 1.33 CISPEP 1 PRO A 31 ARG A 32 0 -1.06 SITE 1 AC1 6 LEU A 12 GLU A 15 TYR A 90 ARG A 93 SITE 2 AC1 6 ARG A 97 HOH A1170 CRYST1 103.970 103.970 51.287 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 0.009618 0.000000 0.000000 0.00000 SCALE2 0.000000 0.009618 0.000000 0.00000 SCALE3 0.000000 0.000000 0.019498 0.00000 HETATM 1 N MSE A 1 23.887 40.551 -19.527 1.00 48.72 N HETATM 2 CA MSE A 1 22.889 40.951 -20.563 1.00 48.52 C HETATM 3 C MSE A 1 22.377 42.358 -20.247 1.00 45.86 C HETATM 4 O MSE A 1 22.996 43.085 -19.468 1.00 45.36 O HETATM 5 CB MSE A 1 21.731 39.945 -20.577 1.00 53.21 C HETATM 6 CG MSE A 1 20.871 39.984 -21.831 1.00 59.07 C HETATM 7 SE MSE A 1 19.896 38.474 -22.046 1.00 72.29 SE HETATM 8 CE MSE A 1 20.997 37.481 -23.070 1.00 64.87 C