HEADER TRANSFERASE 01-NOV-04 1WS6 TITLE THE STRUCTURE OF THERMUS THERMPHILLUS HB8 HYPOTHETICAL PROTEIN TITLE 2 TTHA0928 COMPND MOL_ID: 1; COMPND 2 MOLECULE: METHYLTRANSFERASE; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: RESIDUES 15-185; COMPND 5 SYNONYM: HYPOTHETICAL PROTEIN TTHA0928; COMPND 6 EC: 2.1.1.-; COMPND 7 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: THERMUS THERMOPHILUS; SOURCE 3 ORGANISM_TAXID: 300852; SOURCE 4 STRAIN: HB8; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 7 EXPRESSION_SYSTEM_STRAIN: HMS174(DE3); SOURCE 8 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 9 EXPRESSION_SYSTEM_PLASMID: PET-11A KEYWDS METHYLTRANSFERASE, STRUCTURAL GENOMICS, RIKEN STRUCTURAL KEYWDS 2 GENOMICS/PROTEOMICS INITIATIVE, RSGI, TRANSFERASE EXPDTA X-RAY DIFFRACTION AUTHOR C.SASAKI,I.SUGIURA,S.SUGIO,T.TAMURA,K.INAGAKI,RIKEN STRUCTURAL AUTHOR 2 GENOMICS/PROTEOMICS INITIATIVE (RSGI) REVDAT 4 30-OCT-24 1WS6 1 SEQADV LINK REVDAT 3 13-JUL-11 1WS6 1 VERSN REVDAT 2 24-FEB-09 1WS6 1 VERSN REVDAT 1 07-FEB-06 1WS6 0 JRNL AUTH C.SASAKI,I.SUGIURA,S.SUGIO,T.TAMURA,K.INAGAKI JRNL TITL THE STRUCTURE OF THERMUS THERMPHILLUS HB8 HYPOTHETICAL JRNL TITL 2 PROTEIN TTHA0928 JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. 2.50 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : CNS 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) : 2.50 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 50.00 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) (%) : 94.4 REMARK 3 NUMBER OF REFLECTIONS : 7434 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 CROSS-VALIDATION METHOD : NULL REMARK 3 FREE R VALUE TEST SET SELECTION : RANDOM REMARK 3 R VALUE (WORKING SET) : 0.218 REMARK 3 FREE R VALUE : 0.283 REMARK 3 FREE R VALUE TEST SET SIZE (%) : NULL REMARK 3 FREE R VALUE TEST SET COUNT : 413 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) : 2.50 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.59 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : NULL REMARK 3 REFLECTIONS IN BIN (WORKING SET) : NULL REMARK 3 BIN R VALUE (WORKING SET) : 0.2744 REMARK 3 BIN FREE R VALUE : 0.2700 REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : NULL REMARK 3 BIN FREE R VALUE TEST SET COUNT : 38 REMARK 3 ESTIMATED ERROR OF BIN FREE R VALUE : NULL REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 1314 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 0 REMARK 3 SOLVENT ATOMS : 92 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 18.60 REMARK 3 MEAN B VALUE (OVERALL, A**2) : -0.04 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 1.02000 REMARK 3 B22 (A**2) : 1.02000 REMARK 3 B33 (A**2) : -2.03900 REMARK 3 B12 (A**2) : 0.43800 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) : NULL REMARK 3 ESD FROM SIGMAA (A) : NULL REMARK 3 LOW RESOLUTION CUTOFF (A) : NULL REMARK 3 REMARK 3 CROSS-VALIDATED ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM C-V LUZZATI PLOT (A) : NULL REMARK 3 ESD FROM C-V SIGMAA (A) : NULL REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 BOND LENGTHS (A) : 0.006 REMARK 3 BOND ANGLES (DEGREES) : 0.274 REMARK 3 DIHEDRAL ANGLES (DEGREES) : 23.99 REMARK 3 IMPROPER ANGLES (DEGREES) : 0.955 REMARK 3 REMARK 3 ISOTROPIC THERMAL MODEL : NULL 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 : 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 1WS6 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 02-NOV-04. REMARK 100 THE DEPOSITION ID IS D_1000023936. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 18-FEB-03 REMARK 200 TEMPERATURE (KELVIN) : 174 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 : BL12B2 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.88, 0.9795, 0.9795, 1.03 REMARK 200 MONOCHROMATOR : NULL 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 : 7434 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.500 REMARK 200 RESOLUTION RANGE LOW (A) : 50.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 2.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 100.0 REMARK 200 DATA REDUNDANCY : 6.700 REMARK 200 R MERGE (I) : 0.07700 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : NULL REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.50 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.59 REMARK 200 COMPLETENESS FOR SHELL (%) : 100.0 REMARK 200 DATA REDUNDANCY IN SHELL : 6.80 REMARK 200 R MERGE FOR SHELL (I) : 0.33500 REMARK 200 R SYM FOR SHELL (I) : NULL 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 (%): 54.57 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.71 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: PEG 10000, POTASSIUM THIOCYANATE, PH REMARK 280 6.5, MICRO-BATCH, TEMPERATURE 278K, MICROBATCH REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 31 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+1/3 REMARK 290 3555 -X+Y,-X,Z+2/3 REMARK 290 4555 Y,X,-Z REMARK 290 5555 X-Y,-Y,-Z+2/3 REMARK 290 6555 -X,-X+Y,-Z+1/3 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 33.88667 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 67.77333 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 67.77333 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 33.88667 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 32 -2.49 -55.13 REMARK 500 SER A 37 108.55 172.81 REMARK 500 ARG A 56 -134.42 57.23 REMARK 500 TYR A 134 -13.68 -48.52 REMARK 500 ALA A 139 -54.17 163.89 REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: TTK003001253.1 RELATED DB: TARGETDB DBREF 1WS6 A 15 185 GB 55772310 BAD70751 15 185 SEQADV 1WS6 PRO A 62 GB 55772310 LEU 62 CONFLICT SEQADV 1WS6 MSE A 130 GB 55772310 MET 130 MODIFIED RESIDUE SEQADV 1WS6 MSE A 136 GB 55772310 MET 136 MODIFIED RESIDUE SEQRES 1 A 171 VAL VAL ARG ILE LEU GLY GLY LYS ALA ARG GLY VAL ALA SEQRES 2 A 171 LEU LYS VAL PRO ALA SER ALA ARG PRO SER PRO VAL ARG SEQRES 3 A 171 LEU ARG LYS ALA LEU PHE ASP TYR LEU ARG LEU ARG TYR SEQRES 4 A 171 PRO ARG ARG GLY ARG PHE LEU ASP PRO PHE ALA GLY SER SEQRES 5 A 171 GLY ALA VAL GLY LEU GLU ALA ALA SER GLU GLY TRP GLU SEQRES 6 A 171 ALA VAL LEU VAL GLU LYS ASP PRO GLU ALA VAL ARG LEU SEQRES 7 A 171 LEU LYS GLU ASN VAL ARG ARG THR GLY LEU GLY ALA ARG SEQRES 8 A 171 VAL VAL ALA LEU PRO VAL GLU VAL PHE LEU PRO GLU ALA SEQRES 9 A 171 LYS ALA GLN GLY GLU ARG PHE THR VAL ALA PHE MSE ALA SEQRES 10 A 171 PRO PRO TYR ALA MSE ASP LEU ALA ALA LEU PHE GLY GLU SEQRES 11 A 171 LEU LEU ALA SER GLY LEU VAL GLU ALA GLY GLY LEU TYR SEQRES 12 A 171 VAL LEU GLN HIS PRO LYS ASP LEU TYR LEU PRO LEU GLY SEQRES 13 A 171 GLU ARG ARG VAL TYR GLY GLU ASN ALA LEU THR LEU VAL SEQRES 14 A 171 GLU VAL MODRES 1WS6 MSE A 130 MET SELENOMETHIONINE MODRES 1WS6 MSE A 136 MET SELENOMETHIONINE HET MSE A 130 8 HET MSE A 136 8 HETNAM MSE SELENOMETHIONINE FORMUL 1 MSE 2(C5 H11 N O2 SE) FORMUL 2 HOH *92(H2 O) HELIX 1 1 GLY A 20 ARG A 24 5 5 HELIX 2 2 PRO A 38 TYR A 53 1 16 HELIX 3 3 GLY A 67 GLU A 76 1 10 HELIX 4 4 ASP A 86 GLY A 101 1 16 HELIX 5 5 PRO A 110 GLN A 121 1 12 HELIX 6 6 ALA A 139 GLY A 149 1 11 SHEET 1 A 2 VAL A 16 ARG A 17 0 SHEET 2 A 2 ALA A 27 LEU A 28 -1 O LEU A 28 N VAL A 16 SHEET 1 B 7 ARG A 105 VAL A 107 0 SHEET 2 B 7 GLU A 79 VAL A 83 1 N LEU A 82 O VAL A 107 SHEET 3 B 7 ARG A 58 PRO A 62 1 N ASP A 61 O VAL A 81 SHEET 4 B 7 PHE A 125 MSE A 130 1 O VAL A 127 N LEU A 60 SHEET 5 B 7 VAL A 151 PRO A 162 1 O VAL A 158 N ALA A 128 SHEET 6 B 7 ASN A 178 GLU A 184 -1 O ALA A 179 N HIS A 161 SHEET 7 B 7 GLU A 171 TYR A 175 -1 N TYR A 175 O ASN A 178 LINK C PHE A 129 N MSE A 130 1555 1555 1.33 LINK C MSE A 130 N ALA A 131 1555 1555 1.33 LINK C ALA A 135 N MSE A 136 1555 1555 1.33 LINK C MSE A 136 N ASP A 137 1555 1555 1.33 CISPEP 1 ARG A 35 PRO A 36 0 -0.13 CRYST1 58.760 58.760 101.660 90.00 90.00 120.00 P 31 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 0.017018 0.009826 0.000000 0.00000 SCALE2 0.000000 0.019651 0.000000 0.00000 SCALE3 0.000000 0.000000 0.009837 0.00000