PDB Short entry for 1B02 HEADER TRANSFERASE 16-NOV-98 1B02 TITLE CRYSTAL STRUCTURE OF THYMIDYLATE SYNTHASE A FROM BACILLUS SUBTILIS COMPND MOL_ID: 1; COMPND 2 MOLECULE: PROTEIN (THYMIDYLATE SYNTHASE); COMPND 3 CHAIN: A; COMPND 4 EC: 2.1.1.45; COMPND 5 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: BACILLUS SUBTILIS; SOURCE 3 ORGANISM_TAXID: 1423; SOURCE 4 STRAIN: 168; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 7 EXPRESSION_SYSTEM_STRAIN: DH5ALPHA; SOURCE 8 EXPRESSION_SYSTEM_PLASMID: PET17XB KEYWDS TRANSFERASE, METHYLTRANSFERASE EXPDTA X-RAY DIFFRACTION AUTHOR K.M.FOX,F.MALEY,A.GARIBIAN,L.CHANGCHIEN,P.VANROEY REVDAT 6 09-AUG-23 1B02 1 REMARK LINK REVDAT 5 29-JAN-14 1B02 1 CRYST1 REVDAT 4 13-JUL-11 1B02 1 VERSN REVDAT 3 24-FEB-09 1B02 1 VERSN REVDAT 2 01-APR-03 1B02 1 JRNL REVDAT 1 29-MAR-99 1B02 0 JRNL AUTH K.M.FOX,F.MALEY,A.GARIBIAN,L.M.CHANGCHIEN,P.VAN ROEY JRNL TITL CRYSTAL STRUCTURE OF THYMIDYLATE SYNTHASE A FROM BACILLUS JRNL TITL 2 SUBTILIS. JRNL REF PROTEIN SCI. V. 8 538 1999 JRNL REFN ISSN 0961-8368 JRNL PMID 10091656 REMARK 2 REMARK 2 RESOLUTION. 2.50 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : X-PLOR 3.851 REMARK 3 AUTHORS : BRUNGER REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.50 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 100.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 DATA CUTOFF HIGH (ABS(F)) : 1000000.000 REMARK 3 DATA CUTOFF LOW (ABS(F)) : 0.0010 REMARK 3 COMPLETENESS (WORKING+TEST) (%) : 97.2 REMARK 3 NUMBER OF REFLECTIONS : 23755 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) : 0.194 REMARK 3 FREE R VALUE : 0.233 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 9.600 REMARK 3 FREE R VALUE TEST SET COUNT : 2280 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 : 8 REMARK 3 BIN RESOLUTION RANGE HIGH (A) : 2.50 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.61 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 87.70 REMARK 3 REFLECTIONS IN BIN (WORKING SET) : NULL REMARK 3 BIN R VALUE (WORKING SET) : 0.2970 REMARK 3 BIN FREE R VALUE : 0.3660 REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : 9.80 REMARK 3 BIN FREE R VALUE TEST SET COUNT : NULL 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 : 2315 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 54 REMARK 3 SOLVENT ATOMS : 84 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 29.70 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : NULL REMARK 3 B22 (A**2) : NULL REMARK 3 B33 (A**2) : NULL REMARK 3 B12 (A**2) : NULL REMARK 3 B13 (A**2) : NULL REMARK 3 B23 (A**2) : NULL 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) : 1.100 REMARK 3 DIHEDRAL ANGLES (DEGREES) : 26.50 REMARK 3 IMPROPER ANGLES (DEGREES) : 0.480 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) : 4.000 ; 1.500 REMARK 3 MAIN-CHAIN ANGLE (A**2) : 5.600 ; 2.000 REMARK 3 SIDE-CHAIN BOND (A**2) : 6.400 ; 2.000 REMARK 3 SIDE-CHAIN ANGLE (A**2) : 8.600 ; 2.500 REMARK 3 REMARK 3 NCS MODEL : CONSTRAINTS 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 : PARAM19.SOL REMARK 3 PARAMETER FILE 3 : NULL REMARK 3 TOPOLOGY FILE 1 : TOPHCSDX.PRO REMARK 3 TOPOLOGY FILE 2 : TOPH19.SOL REMARK 3 TOPOLOGY FILE 3 : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 1B02 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 18-NOV-98. REMARK 100 THE DEPOSITION ID IS D_1000000087. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : JUL-98 REMARK 200 TEMPERATURE (KELVIN) : 298 REMARK 200 PH : 6.25 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : N REMARK 200 RADIATION SOURCE : ROTATING ANODE REMARK 200 BEAMLINE : NULL REMARK 200 X-RAY GENERATOR MODEL : RIGAKU RU200 REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.5418 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : MSC MIRRORS REMARK 200 REMARK 200 DETECTOR TYPE : IMAGE PLATE REMARK 200 DETECTOR MANUFACTURER : RIGAKU RAXIS IV REMARK 200 INTENSITY-INTEGRATION SOFTWARE : DENZO REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 23792 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.500 REMARK 200 RESOLUTION RANGE LOW (A) : 30.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 0.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 96.0 REMARK 200 DATA REDUNDANCY : 4.600 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : 0.09400 REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : NULL REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.47 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.51 REMARK 200 COMPLETENESS FOR SHELL (%) : 79.3 REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : 0.34900 REMARK 200 <I/SIGMA(I)> FOR SHELL : NULL REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: AMORE REMARK 200 STARTING MODEL: 1TSN REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 50.00 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.80 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: PH 6.25 REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 21 21 21 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X+1/2,-Y,Z+1/2 REMARK 290 3555 -X,Y+1/2,-Z+1/2 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 27.78500 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 58.63000 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 52.50500 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 58.63000 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 27.78500 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 52.50500 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 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC REMARK 350 SOFTWARE USED: PISA 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 SER A 33 -87.04 -71.84 REMARK 500 SER A 45 80.62 53.22 REMARK 500 PRO A 56 94.36 -69.98 REMARK 500 TYR A 108 -120.35 44.64 REMARK 500 LEU A 119 -79.99 -108.59 REMARK 500 ASN A 137 58.72 -158.12 REMARK 500 HIS A 171 38.69 71.35 REMARK 500 LEU A 187 -70.56 -94.15 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 UFP A 280 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE C2F A 281 DBREF 1B02 A 1 279 UNP P42326 TYSA_BACSU 1 279 SEQRES 1 A 279 MET THR GLN PHE ASP LYS GLN TYR ASN SER ILE ILE LYS SEQRES 2 A 279 ASP ILE ILE ASN ASN GLY ILE SER ASP GLU GLU PHE ASP SEQRES 3 A 279 VAL ARG THR LYS TRP ASP SER ASP GLY THR PRO ALA HIS SEQRES 4 A 279 THR LEU SER VAL ILE SER LYS GLN MET ARG PHE ASP ASN SEQRES 5 A 279 SER GLU VAL PRO ILE LEU THR THR LYS LYS VAL ALA TRP SEQRES 6 A 279 LYS THR ALA ILE LYS GLU LEU LEU TRP ILE TRP GLN LEU SEQRES 7 A 279 LYS SER ASN ASP VAL ASN ASP LEU ASN MET MET GLY VAL SEQRES 8 A 279 HIS ILE TRP ASP GLN TRP LYS GLN GLU ASP GLY THR ILE SEQRES 9 A 279 GLY HIS ALA TYR GLY PHE GLN LEU GLY LYS LYS ASN ARG SEQRES 10 A 279 SER LEU ASN GLY GLU LYS VAL ASP GLN VAL ASP TYR LEU SEQRES 11 A 279 LEU HIS GLN LEU LYS ASN ASN PRO SER SER ARG ARG HIS SEQRES 12 A 279 ILE THR MET LEU TRP ASN PRO ASP GLU LEU ASP ALA MET SEQRES 13 A 279 ALA LEU THR PRO CYS VAL TYR GLU THR GLN TRP TYR VAL SEQRES 14 A 279 LYS HIS GLY LYS LEU HIS LEU GLU VAL ARG ALA ARG SER SEQRES 15 A 279 ASN ASP MET ALA LEU GLY ASN PRO PHE ASN VAL PHE GLN SEQRES 16 A 279 TYR ASN VAL LEU GLN ARG MET ILE ALA GLN VAL THR GLY SEQRES 17 A 279 TYR GLU LEU GLY GLU TYR ILE PHE ASN ILE GLY ASP CYS SEQRES 18 A 279 HIS VAL TYR THR ARG HIS ILE ASP ASN LEU LYS ILE GLN SEQRES 19 A 279 MET GLU ARG GLU GLN PHE GLU ALA PRO GLU LEU TRP ILE SEQRES 20 A 279 ASN PRO GLU VAL LYS ASP PHE TYR ASP PHE THR ILE ASP SEQRES 21 A 279 ASP PHE LYS LEU ILE ASN TYR LYS HIS GLY ASP LYS LEU SEQRES 22 A 279 LEU PHE GLU VAL ALA VAL HET UFP A 280 21 HET C2F A 281 33 HETNAM UFP 5-FLUORO-2'-DEOXYURIDINE-5'-MONOPHOSPHATE HETNAM C2F 5-METHYL-5,6,7,8-TETRAHYDROFOLIC ACID FORMUL 2 UFP C9 H12 F N2 O8 P FORMUL 3 C2F C20 H25 N7 O6 FORMUL 4 HOH *84(H2 O) HELIX 1 1 GLN A 3 ASN A 18 1 16 HELIX 2 2 TRP A 65 TRP A 76 1 12 HELIX 3 3 VAL A 83 MET A 88 1 6 HELIX 4 4 ASP A 95 TRP A 97 5 3 HELIX 5 5 TYR A 108 GLY A 113 5 6 HELIX 6 6 GLN A 126 ASN A 136 1 11 HELIX 7 7 LEU A 153 ALA A 155 5 3 HELIX 8 8 GLY A 188 THR A 207 1 20 HELIX 9 9 THR A 225 GLU A 236 5 12 HELIX 10 10 PHE A 254 ASP A 256 5 3 HELIX 11 11 ILE A 259 ASP A 261 5 3 SHEET 1 A 3 THR A 40 ILE A 44 0 SHEET 2 A 3 ASP A 220 TYR A 224 -1 N VAL A 223 O LEU A 41 SHEET 3 A 3 SER A 182 ASP A 184 1 N ASN A 183 O ASP A 220 SHEET 1 B 5 LYS A 46 PHE A 50 0 SHEET 2 B 5 TYR A 214 ILE A 218 -1 N ILE A 218 O LYS A 46 SHEET 3 B 5 LEU A 174 ALA A 180 1 N LEU A 176 O ILE A 215 SHEET 4 B 5 VAL A 162 VAL A 169 -1 N TYR A 168 O HIS A 175 SHEET 5 B 5 ILE A 144 MET A 146 -1 N THR A 145 O THR A 165 SHEET 1 C 2 GLU A 244 ILE A 247 0 SHEET 2 C 2 PHE A 262 ILE A 265 -1 N ILE A 265 O GLU A 244 SHEET 1 D 2 LYS A 115 SER A 118 0 SHEET 2 D 2 LYS A 123 ASP A 125 -1 N VAL A 124 O ASN A 116 LINK SG CYS A 161 C6 UFP A 280 1555 1555 1.72 LINK C5 UFP A 280 C11 C2F A 281 1555 1555 1.65 SITE 1 AC1 14 ARG A 28 TYR A 108 CYS A 161 ARG A 181 SITE 2 AC1 14 SER A 182 ASN A 183 ASP A 184 GLY A 188 SITE 3 AC1 14 ASN A 192 HIS A 222 TYR A 224 C2F A 281 SITE 4 AC1 14 HOH A 291 HOH A 313 SITE 1 AC2 14 ALA A 64 THR A 67 ILE A 93 TRP A 94 SITE 2 AC2 14 TRP A 97 ASP A 184 GLY A 188 ALA A 278 SITE 3 AC2 14 UFP A 280 HOH A 299 HOH A 332 HOH A 342 SITE 4 AC2 14 HOH A 351 HOH A 360 CRYST1 55.570 105.010 117.260 90.00 90.00 90.00 P 21 21 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 0.017995 0.000000 0.000000 0.00000 SCALE2 0.000000 0.009523 0.000000 0.00000 SCALE3 0.000000 0.000000 0.008528 0.00000 MTRIX1 1 -0.940100 0.321300 -0.114000 -7.35650 MTRIX2 1 0.322800 0.731400 -0.600800 24.60800 MTRIX3 1 -0.109700 -0.601600 -0.791300 66.70550