HEADER TRANSFERASE 31-MAY-03 1UFK TITLE CRYSTAL STRUCTURE OF TT0836 COMPND MOL_ID: 1; COMPND 2 MOLECULE: TT0836 PROTEIN; 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: PET-11A KEYWDS ADOMET-DEPENDENT METHYLTRANSFERASE-FOLD, STRUCTURAL GENOMICS, RIKEN KEYWDS 2 STRUCTURAL GENOMICS/PROTEOMICS INITIATIVE, RSGI, TRANSFERASE EXPDTA X-RAY DIFFRACTION AUTHOR T.KAMINISHI,H.SAKAI,C.TAKEMOTO-HORI,T.TERADA,N.NAKAGAWA,N.MAOKA, AUTHOR 2 S.KURAMITSU,M.SHIROUZU,S.YOKOYAMA,RIKEN STRUCTURAL AUTHOR 3 GENOMICS/PROTEOMICS INITIATIVE (RSGI) REVDAT 3 27-DEC-23 1UFK 1 REMARK REVDAT 2 24-FEB-09 1UFK 1 VERSN REVDAT 1 30-NOV-03 1UFK 0 JRNL AUTH T.KAMINISHI,H.SAKAI,C.TAKEMOTO-HORI,T.TERADA,N.NAKAGAWA, JRNL AUTH 2 N.MAOKA,S.KURAMITSU,M.SHIROUZU,S.YOKOYAMA JRNL TITL CRYSTAL STRUCTURE OF TT0836 JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. 1.90 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) : 1.90 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 47.80 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 DATA CUTOFF HIGH (ABS(F)) : 573313.470 REMARK 3 DATA CUTOFF LOW (ABS(F)) : 0.0000 REMARK 3 COMPLETENESS (WORKING+TEST) (%) : 94.4 REMARK 3 NUMBER OF REFLECTIONS : 21665 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) : 0.232 REMARK 3 FREE R VALUE : 0.250 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.800 REMARK 3 FREE R VALUE TEST SET COUNT : 1045 REMARK 3 ESTIMATED ERROR OF FREE R VALUE : 0.008 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) : 1.90 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.02 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 86.00 REMARK 3 REFLECTIONS IN BIN (WORKING SET) : 3102 REMARK 3 BIN R VALUE (WORKING SET) : 0.3390 REMARK 3 BIN FREE R VALUE : 0.3430 REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : 4.80 REMARK 3 BIN FREE R VALUE TEST SET COUNT : 156 REMARK 3 ESTIMATED ERROR OF BIN FREE R VALUE : 0.027 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 1919 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 0 REMARK 3 SOLVENT ATOMS : 88 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 17.70 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 38.10 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -5.42000 REMARK 3 B22 (A**2) : 17.00000 REMARK 3 B33 (A**2) : -11.57000 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : -2.16000 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM LUZZATI PLOT (A) : 0.27 REMARK 3 ESD FROM SIGMAA (A) : 0.30 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) : 0.29 REMARK 3 ESD FROM C-V SIGMAA (A) : 0.29 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 BOND LENGTHS (A) : 0.011 REMARK 3 BOND ANGLES (DEGREES) : 1.600 REMARK 3 DIHEDRAL ANGLES (DEGREES) : 25.00 REMARK 3 IMPROPER ANGLES (DEGREES) : 0.970 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) : 1.420 ; 1.500 REMARK 3 MAIN-CHAIN ANGLE (A**2) : 2.170 ; 2.000 REMARK 3 SIDE-CHAIN BOND (A**2) : 2.170 ; 2.000 REMARK 3 SIDE-CHAIN ANGLE (A**2) : 3.280 ; 2.500 REMARK 3 REMARK 3 BULK SOLVENT MODELING. REMARK 3 METHOD USED : FLAT MODEL REMARK 3 KSOL : 0.36 REMARK 3 BSOL : 60.42 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 : WATER.TOP REMARK 3 TOPOLOGY FILE 3 : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 1UFK COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 03-JUN-03. REMARK 100 THE DEPOSITION ID IS D_1000005771. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 09-JUN-02 REMARK 200 TEMPERATURE (KELVIN) : 90 REMARK 200 PH : 6.8 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 : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : MARRESEARCH REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 22573 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.900 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 (%) : 98.5 REMARK 200 DATA REDUNDANCY : 3.800 REMARK 200 R MERGE (I) : 0.04000 REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 28.5000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.90 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.97 REMARK 200 COMPLETENESS FOR SHELL (%) : 98.0 REMARK 200 DATA REDUNDANCY IN SHELL : 3.80 REMARK 200 R MERGE FOR SHELL (I) : 0.29400 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 <I/SIGMA(I)> FOR SHELL : 4.800 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MAD REMARK 200 SOFTWARE USED: SHARP REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 52.72 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.62 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 20MM MES, 700MM AMMONIUM SULFATE, REMARK 280 4%(V/V) DIOXANE, 160MM 1,6-HEXANEDIOL, PH 6.8, VAPOR DIFFUSION, REMARK 280 HANGING DROP, TEMPERATURE 293.0K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: C 1 2 1 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 40.93100 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 38.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 40.93100 REMARK 290 SMTRY2 4 0.000000 1.000000 0.000000 38.00000 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 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 GLY A 96 REMARK 465 MET A 97 REMARK 465 ALA A 98 REMARK 465 PHE A 99 REMARK 465 GLY A 100 REMARK 465 THR A 101 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 32 68.80 39.69 REMARK 500 ALA A 72 72.60 -165.63 REMARK 500 PRO A 73 136.83 -39.77 REMARK 500 SER A 175 -156.72 -122.21 REMARK 500 LEU A 192 -112.16 -125.61 REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: TTK003000836.4 RELATED DB: TARGETDB DBREF 1UFK A 1 254 UNP Q84BQ9 PRMA_THET8 1 254 SEQRES 1 A 254 MET TRP VAL TYR ARG LEU LYS GLY THR LEU GLU ALA LEU SEQRES 2 A 254 ASP PRO ILE LEU PRO GLY LEU PHE ASP GLY GLY ALA ARG SEQRES 3 A 254 GLY LEU TRP GLU ARG GLU GLY GLU VAL TRP ALA PHE PHE SEQRES 4 A 254 PRO ALA PRO VAL ASP LEU PRO TYR GLU GLY VAL TRP GLU SEQRES 5 A 254 GLU VAL GLY ASP GLU ASP TRP LEU GLU ALA TRP ARG ARG SEQRES 6 A 254 ASP LEU LYS PRO ALA LEU ALA PRO PRO PHE VAL VAL LEU SEQRES 7 A 254 ALA PRO TRP HIS THR TRP GLU GLY ALA GLU ILE PRO LEU SEQRES 8 A 254 VAL ILE GLU PRO GLY MET ALA PHE GLY THR GLY HIS HIS SEQRES 9 A 254 GLU THR THR ARG LEU ALA LEU LYS ALA LEU ALA ARG HIS SEQRES 10 A 254 LEU ARG PRO GLY ASP LYS VAL LEU ASP LEU GLY THR GLY SEQRES 11 A 254 SER GLY VAL LEU ALA ILE ALA ALA GLU LYS LEU GLY GLY SEQRES 12 A 254 LYS ALA LEU GLY VAL ASP ILE ASP PRO MET VAL LEU PRO SEQRES 13 A 254 GLN ALA GLU ALA ASN ALA LYS ARG ASN GLY VAL ARG PRO SEQRES 14 A 254 ARG PHE LEU GLU GLY SER LEU GLU ALA ALA LEU PRO PHE SEQRES 15 A 254 GLY PRO PHE ASP LEU LEU VAL ALA ASN LEU TYR ALA GLU SEQRES 16 A 254 LEU HIS ALA ALA LEU ALA PRO ARG TYR ARG GLU ALA LEU SEQRES 17 A 254 VAL PRO GLY GLY ARG ALA LEU LEU THR GLY ILE LEU LYS SEQRES 18 A 254 ASP ARG ALA PRO LEU VAL ARG GLU ALA MET ALA GLY ALA SEQRES 19 A 254 GLY PHE ARG PRO LEU GLU GLU ALA ALA GLU GLY GLU TRP SEQRES 20 A 254 VAL LEU LEU ALA TYR GLY ARG FORMUL 2 HOH *88(H2 O) HELIX 1 1 THR A 9 ASP A 14 1 6 HELIX 2 2 ILE A 16 GLY A 23 1 8 HELIX 3 3 GLY A 55 LEU A 67 1 13 HELIX 4 4 HIS A 104 LEU A 118 1 15 HELIX 5 5 GLY A 132 LEU A 141 1 10 HELIX 6 6 ASP A 151 MET A 153 5 3 HELIX 7 7 VAL A 154 ASN A 165 1 12 HELIX 8 8 SER A 175 LEU A 180 1 6 HELIX 9 9 PRO A 181 GLY A 183 5 3 HELIX 10 10 TYR A 193 ALA A 207 1 15 HELIX 11 11 ARG A 223 ALA A 234 1 12 SHEET 1 A 4 GLY A 27 ARG A 31 0 SHEET 2 A 4 GLU A 34 PHE A 39 -1 O GLU A 34 N ARG A 31 SHEET 3 A 4 TRP A 2 LYS A 7 -1 N TRP A 2 O PHE A 39 SHEET 4 A 4 VAL A 50 GLU A 53 -1 O GLU A 52 N VAL A 3 SHEET 1 B 3 ALA A 70 ALA A 72 0 SHEET 2 B 3 PHE A 75 LEU A 78 -1 O VAL A 77 N ALA A 70 SHEET 3 B 3 ILE A 89 VAL A 92 1 O ILE A 89 N VAL A 76 SHEET 1 C 7 ARG A 170 GLU A 173 0 SHEET 2 C 7 LYS A 144 ASP A 149 1 N GLY A 147 O ARG A 170 SHEET 3 C 7 LYS A 123 LEU A 127 1 N VAL A 124 O LYS A 144 SHEET 4 C 7 PHE A 185 ASN A 191 1 O VAL A 189 N LEU A 125 SHEET 5 C 7 LEU A 208 LEU A 220 1 O LEU A 215 N LEU A 188 SHEET 6 C 7 TRP A 247 GLY A 253 -1 O LEU A 250 N LEU A 216 SHEET 7 C 7 ARG A 237 GLU A 244 -1 N ALA A 242 O LEU A 249 CISPEP 1 PRO A 73 PRO A 74 0 0.24 CISPEP 2 GLY A 183 PRO A 184 0 -0.26 CRYST1 81.862 76.000 62.129 90.00 130.32 90.00 C 1 2 1 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 0.012216 0.000000 0.010367 0.00000 SCALE2 0.000000 0.013158 0.000000 0.00000 SCALE3 0.000000 0.000000 0.021111 0.00000