HEADER THYMIDINE PHOSPHORYLASE 14-JUN-90 1TPT TITLE THREE-DIMENSIONAL STRUCTURE OF THYMIDINE PHOSPHORYLASE FROM TITLE 2 ESCHERICHIA COLI AT 2.8 ANGSTROMS RESOLUTION COMPND MOL_ID: 1; COMPND 2 MOLECULE: THYMIDINE PHOSPHORYLASE; COMPND 3 CHAIN: A; COMPND 4 EC: 2.4.2.4; COMPND 5 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: ESCHERICHIA COLI; SOURCE 3 ORGANISM_TAXID: 562; SOURCE 4 EXPRESSION_SYSTEM_STRAIN: K12 KEYWDS THYMIDINE PHOSPHORYLASE EXPDTA X-RAY DIFFRACTION MDLTYP CA ATOMS ONLY, CHAIN A AUTHOR M.R.WALTER,W.J.COOK,L.B.COLE,S.A.SHORT,G.W.KOSZALKA,T.A.KRENITSKY, AUTHOR 2 S.E.EALICK REVDAT 5 14-FEB-24 1TPT 1 SEQADV REVDAT 4 24-FEB-09 1TPT 1 VERSN REVDAT 3 01-APR-03 1TPT 1 JRNL REVDAT 2 15-JUL-92 1TPT 1 FORMUL REVDAT 1 15-JUL-91 1TPT 0 JRNL AUTH M.R.WALTER,W.J.COOK,L.B.COLE,S.A.SHORT,G.W.KOSZALKA, JRNL AUTH 2 T.A.KRENITSKY,S.E.EALICK JRNL TITL THREE-DIMENSIONAL STRUCTURE OF THYMIDINE PHOSPHORYLASE FROM JRNL TITL 2 ESCHERICHIA COLI AT 2.8 A RESOLUTION. JRNL REF J.BIOL.CHEM. V. 265 14016 1990 JRNL REFN ISSN 0021-9258 JRNL PMID 2199449 REMARK 2 REMARK 2 RESOLUTION. 2.80 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PROLSQ REMARK 3 AUTHORS : KONNERT,HENDRICKSON REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.80 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : NULL REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : NULL REMARK 3 NUMBER OF REFLECTIONS : NULL REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 CROSS-VALIDATION METHOD : NULL REMARK 3 FREE R VALUE TEST SET SELECTION : NULL REMARK 3 R VALUE (WORKING + TEST SET) : 0.280 REMARK 3 R VALUE (WORKING SET) : NULL REMARK 3 FREE R VALUE : NULL REMARK 3 FREE R VALUE TEST SET SIZE (%) : NULL REMARK 3 FREE R VALUE TEST SET COUNT : NULL REMARK 3 REMARK 3 FIT/AGREEMENT OF MODEL WITH ALL DATA. REMARK 3 R VALUE (WORKING + TEST SET, NO CUTOFF) : NULL REMARK 3 R VALUE (WORKING SET, NO CUTOFF) : NULL REMARK 3 FREE R VALUE (NO CUTOFF) : NULL REMARK 3 FREE R VALUE TEST SET SIZE (%, NO CUTOFF) : NULL REMARK 3 FREE R VALUE TEST SET COUNT (NO CUTOFF) : NULL REMARK 3 TOTAL NUMBER OF REFLECTIONS (NO CUTOFF) : NULL REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 440 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 14 REMARK 3 SOLVENT ATOMS : 0 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : NULL 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 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 DISTANCE RESTRAINTS. RMS SIGMA REMARK 3 BOND LENGTH (A) : 0.011 ; NULL REMARK 3 ANGLE DISTANCE (A) : NULL ; NULL REMARK 3 INTRAPLANAR 1-4 DISTANCE (A) : NULL ; NULL REMARK 3 H-BOND OR METAL COORDINATION (A) : NULL ; NULL REMARK 3 REMARK 3 PLANE RESTRAINT (A) : NULL ; NULL REMARK 3 CHIRAL-CENTER RESTRAINT (A**3) : NULL ; NULL REMARK 3 REMARK 3 NON-BONDED CONTACT RESTRAINTS. REMARK 3 SINGLE TORSION (A) : NULL ; NULL REMARK 3 MULTIPLE TORSION (A) : NULL ; NULL REMARK 3 H-BOND (X...Y) (A) : NULL ; NULL REMARK 3 H-BOND (X-H...Y) (A) : NULL ; NULL REMARK 3 REMARK 3 CONFORMATIONAL TORSION ANGLE RESTRAINTS. REMARK 3 SPECIFIED (DEGREES) : NULL ; NULL REMARK 3 PLANAR (DEGREES) : NULL ; NULL REMARK 3 STAGGERED (DEGREES) : NULL ; NULL REMARK 3 TRANSVERSE (DEGREES) : NULL ; 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 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 1TPT COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY BNL. REMARK 100 THE DEPOSITION ID IS D_1000176792. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : NULL REMARK 200 TEMPERATURE (KELVIN) : NULL REMARK 200 PH : NULL REMARK 200 NUMBER OF CRYSTALS USED : NULL REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : NULL REMARK 200 RADIATION SOURCE : NULL REMARK 200 BEAMLINE : NULL REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : NULL REMARK 200 WAVELENGTH OR RANGE (A) : NULL REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : NULL REMARK 200 DETECTOR MANUFACTURER : NULL REMARK 200 INTENSITY-INTEGRATION SOFTWARE : NULL REMARK 200 DATA SCALING SOFTWARE : NULL REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : NULL REMARK 200 RESOLUTION RANGE HIGH (A) : NULL REMARK 200 RESOLUTION RANGE LOW (A) : NULL REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : NULL REMARK 200 DATA REDUNDANCY : NULL REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL 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) : NULL REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : NULL REMARK 200 COMPLETENESS FOR SHELL (%) : NULL REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 <I/SIGMA(I)> FOR SHELL : NULL REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: NULL REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: NULL REMARK 200 SOFTWARE USED: NULL REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 61.06 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 3.16 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: NULL REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 43 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+3/4 REMARK 290 4555 Y+1/2,-X+1/2,Z+1/4 REMARK 290 5555 -X+1/2,Y+1/2,-Z+3/4 REMARK 290 6555 X+1/2,-Y+1/2,-Z+1/4 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 33.75000 REMARK 290 SMTRY1 3 0.000000 -1.000000 0.000000 66.50000 REMARK 290 SMTRY2 3 1.000000 0.000000 0.000000 66.50000 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 50.62500 REMARK 290 SMTRY1 4 0.000000 1.000000 0.000000 66.50000 REMARK 290 SMTRY2 4 -1.000000 0.000000 0.000000 66.50000 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 16.87500 REMARK 290 SMTRY1 5 -1.000000 0.000000 0.000000 66.50000 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 66.50000 REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 50.62500 REMARK 290 SMTRY1 6 1.000000 0.000000 0.000000 66.50000 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 66.50000 REMARK 290 SMTRY3 6 0.000000 0.000000 -1.000000 16.87500 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 33.75000 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: DIMERIC 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 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT2 2 1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT3 2 0.000000 0.000000 -1.000000 0.00000 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: SO4 REMARK 800 EVIDENCE_CODE: AUTHOR REMARK 800 SITE_DESCRIPTION: SULFATE BINDING SITE REMARK 800 REMARK 800 SITE_IDENTIFIER: TDR REMARK 800 EVIDENCE_CODE: AUTHOR REMARK 800 SITE_DESCRIPTION: THYMINE BINDING SITE DBREF 1TPT A 1 440 UNP P07650 TYPH_ECOLI 1 441 SEQADV 1TPT A UNP P07650 PHE 136 DELETION SEQRES 1 A 440 LEU PHE LEU ALA GLN GLU ILE ILE ARG LYS LYS ARG ASP SEQRES 2 A 440 GLY HIS ALA LEU SER ASP GLU GLU ILE ARG PHE PHE ILE SEQRES 3 A 440 ASN GLY ILE ARG ASP ASN THR ILE SER GLU GLY GLN ILE SEQRES 4 A 440 ALA ALA LEU ALA MET THR ILE PHE PHE HIS ASP MET THR SEQRES 5 A 440 MET PRO GLU ARG VAL SER LEU THR MET ALA MET ARG ASP SEQRES 6 A 440 SER GLY THR VAL LEU ASP TRP LYS SER LEU HIS LEU ASN SEQRES 7 A 440 GLY PRO ILE VAL ASP LYS HIS SER THR GLY GLY VAL GLY SEQRES 8 A 440 ASP VAL THR SER LEU MET LEU GLY PRO MET VAL ALA ALA SEQRES 9 A 440 CYS GLY GLY TYR ILE PRO MET ILE SER GLY ARG GLY LEU SEQRES 10 A 440 GLY HIS THR GLY GLY THR LEU ASP LYS LEU GLU SER ILE SEQRES 11 A 440 PRO GLY PHE ASP ILE PHE PRO ASP ASP ASN ARG PHE ARG SEQRES 12 A 440 GLU ILE ILE LYS ASP VAL GLY VAL ALA ILE ILE GLY GLN SEQRES 13 A 440 THR SER SER LEU ALA PRO ALA ASP LYS ARG PHE TYR ALA SEQRES 14 A 440 THR ARG ASP ILE THR ALA THR VAL ASP SER ILE PRO LEU SEQRES 15 A 440 ILE THR ALA SER ILE LEU ALA LYS LYS LEU ALA GLU GLY SEQRES 16 A 440 LEU ASP ALA LEU VAL MET ASP VAL LYS VAL GLY SER GLY SEQRES 17 A 440 ALA PHE MET PRO THR TYR GLU LEU SER GLU ALA LEU ALA SEQRES 18 A 440 GLU ALA ILE VAL GLY VAL ALA ASN GLY ALA GLY VAL ARG SEQRES 19 A 440 THR THR ALA LEU LEU THR ASP MET ASN GLN VAL LEU ALA SEQRES 20 A 440 SER SER ALA GLY ASN ALA VAL GLU VAL ARG GLU ALA VAL SEQRES 21 A 440 GLN PHE LEU THR GLY GLU TYR ARG ASN PRO ARG LEU PHE SEQRES 22 A 440 ASP VAL THR MET ALA LEU CYS VAL GLU MET LEU ILE SER SEQRES 23 A 440 GLY LYS LEU ALA LYS ASP ASP ALA GLU ALA ARG ALA LYS SEQRES 24 A 440 LEU GLN ALA VAL LEU ASP ASN GLY LYS ALA ALA GLU VAL SEQRES 25 A 440 PHE GLY ARG MET VAL ALA ALA GLN LYS GLY PRO THR ASP SEQRES 26 A 440 PHE VAL GLU ASN TYR ALA LYS TYR LEU PRO THR ALA MET SEQRES 27 A 440 LEU THR LYS ALA VAL TYR ALA ASP THR GLU GLY PHE VAL SEQRES 28 A 440 SER GLU MET ASP THR ARG ALA LEU GLY MET ALA VAL VAL SEQRES 29 A 440 ALA MET GLY GLY GLY ARG ARG GLN ALA SER ASP THR ILE SEQRES 30 A 440 ASP TYR SER VAL GLY PHE THR ASP MET ALA ARG LEU GLY SEQRES 31 A 440 ASP GLN VAL ASP GLY GLN ARG PRO LEU ALA VAL ILE HIS SEQRES 32 A 440 ALA LYS ASP GLU ASN ASN TRP GLN GLU ALA ALA LYS ALA SEQRES 33 A 440 VAL LYS ALA ALA ILE LYS LEU ALA ASP LYS ALA PRO GLU SEQRES 34 A 440 SER THR PRO THR VAL TYR ARG ARG ILE SER GLU HET SO4 A 441 5 HET TDR A 442 9 HETNAM SO4 SULFATE ION HETNAM TDR THYMINE FORMUL 2 SO4 O4 S 2- FORMUL 3 TDR C5 H6 N2 O2 HELIX 1 H1 ALA A 4 ARG A 12 1 9 HELIX 2 H2 SER A 18 ASN A 32 1 15 HELIX 3 H3 SER A 35 HIS A 49 1 15 HELIX 4 H4 THR A 52 ASP A 65 1 14 HELIX 5 H5 THR A 94 CYS A 105 1 12 HELIX 6 H6 GLY A 122 ILE A 130 1 9 HELIX 7 H7 ASP A 138 VAL A 149 1 12 HELIX 8 H8 ALA A 163 THR A 174 1 12 HELIX 9 H9 SER A 179 ALA A 193 1 15 HELIX 10 H10 THR A 213 ASN A 229 1 17 HELIX 11 H11 ASN A 252 GLY A 265 1 14 HELIX 12 H12 PRO A 270 GLY A 287 1 18 HELIX 13 H13 ASP A 292 ASN A 306 1 15 HELIX 14 H14 LYS A 308 GLN A 320 1 13 HELIX 15 H15 TYR A 330 LEU A 334 1 5 HELIX 16 H16 SER A 352 GLY A 367 1 16 HELIX 17 H17 GLU A 407 ILE A 421 1 15 SHEET 1 A 6 GLY A 150 ILE A 154 0 SHEET 2 A 6 TYR A 108 SER A 113 1 SHEET 3 A 6 PRO A 80 THR A 87 1 SHEET 4 A 6 ASP A 197 VAL A 205 1 SHEET 5 A 6 ARG A 234 ASP A 241 1 SHEET 6 A 6 THR A 433 ILE A 438 -1 SHEET 1 B 4 SER A 248 ALA A 250 0 SHEET 2 B 4 GLY A 382 ALA A 387 -1 SHEET 3 B 4 LEU A 399 ALA A 404 -1 SHEET 4 B 4 LEU A 339 VAL A 343 -1 SITE 1 SO4 6 LYS A 84 HIS A 85 SER A 86 SER A 95 SITE 2 SO4 6 SER A 113 THR A 123 SITE 1 TDR 3 ARG A 171 SER A 186 LYS A 190 CRYST1 133.000 133.000 67.500 90.00 90.00 90.00 P 43 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 0.007519 0.000000 0.000000 0.00000 SCALE2 0.000000 0.007519 0.000000 0.00000 SCALE3 0.000000 0.000000 0.014815 0.00000