HEADER TRANSFERASE/DNA 06-DEC-04 1Y6G TITLE ALPHA-GLUCOSYLTRANSFERASE IN COMPLEX WITH UDP AND A 13_MER DNA TITLE 2 CONTAINING A HMU BASE AT 2.8 A RESOLUTION COMPND MOL_ID: 1; COMPND 2 MOLECULE: 5'-D(*GP*AP*TP*AP*CP*TP*(5HU)P*AP*GP*AP*TP*AP*G)-3'; COMPND 3 CHAIN: C; COMPND 4 ENGINEERED: YES; COMPND 5 MOL_ID: 2; COMPND 6 MOLECULE: 5'-D(*CP*TP*AP*TP*CP*TP*GP*AP*GP*TP*AP*T)-3'; COMPND 7 CHAIN: D; COMPND 8 ENGINEERED: YES; COMPND 9 MOL_ID: 3; COMPND 10 MOLECULE: DNA ALPHA-GLUCOSYLTRANSFERASE; COMPND 11 CHAIN: A, B; COMPND 12 SYNONYM: AGT; COMPND 13 EC: 2.4.1.26; COMPND 14 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 SYNTHETIC: YES; SOURCE 3 MOL_ID: 2; SOURCE 4 SYNTHETIC: YES; SOURCE 5 MOL_ID: 3; SOURCE 6 ORGANISM_SCIENTIFIC: ENTEROBACTERIA PHAGE T4; SOURCE 7 ORGANISM_TAXID: 10665; SOURCE 8 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 9 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 10 EXPRESSION_SYSTEM_STRAIN: XL1BLUE; SOURCE 11 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 12 EXPRESSION_SYSTEM_PLASMID: PROEXHTB KEYWDS TRANSFERASE, TRANSFERASE-DNA COMPLEX EXPDTA X-RAY DIFFRACTION AUTHOR L.LARIVIERE,N.SOMMER,S.MORERA REVDAT 5 25-OCT-23 1Y6G 1 REMARK REVDAT 4 22-JUL-20 1Y6G 1 REMARK SEQADV LINK REVDAT 3 24-FEB-09 1Y6G 1 VERSN REVDAT 2 04-OCT-05 1Y6G 1 JRNL REVDAT 1 30-AUG-05 1Y6G 0 JRNL AUTH L.LARIVIERE,N.SOMMER,S.MORERA JRNL TITL STRUCTURAL EVIDENCE OF A PASSIVE BASE-FLIPPING MECHANISM FOR JRNL TITL 2 AGT, AN UNUSUAL GT-B GLYCOSYLTRANSFERASE. JRNL REF J.MOL.BIOL. V. 352 139 2005 JRNL REFN ISSN 0022-2836 JRNL PMID 16081100 JRNL DOI 10.1016/J.JMB.2005.07.007 REMARK 2 REMARK 2 RESOLUTION. 2.80 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : CNS 1.0 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) : 2.80 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 20.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : 1.000 REMARK 3 DATA CUTOFF HIGH (ABS(F)) : NULL REMARK 3 DATA CUTOFF LOW (ABS(F)) : NULL REMARK 3 COMPLETENESS (WORKING+TEST) (%) : NULL REMARK 3 NUMBER OF REFLECTIONS : 23542 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) : 0.219 REMARK 3 FREE R VALUE : 0.287 REMARK 3 FREE R VALUE TEST SET SIZE (%) : NULL REMARK 3 FREE R VALUE TEST SET COUNT : 1120 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) : NULL REMARK 3 BIN RESOLUTION RANGE LOW (A) : NULL REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : NULL REMARK 3 REFLECTIONS IN BIN (WORKING SET) : NULL REMARK 3 BIN R VALUE (WORKING SET) : NULL REMARK 3 BIN FREE R VALUE : NULL REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : NULL 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 : 6439 REMARK 3 NUCLEIC ACID ATOMS : 510 REMARK 3 HETEROGEN ATOMS : 104 REMARK 3 SOLVENT ATOMS : 79 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 69.00 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 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) : 1.390 REMARK 3 BOND ANGLES (DEGREES) : NULL REMARK 3 DIHEDRAL ANGLES (DEGREES) : NULL REMARK 3 IMPROPER ANGLES (DEGREES) : NULL 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 1Y6G COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 08-DEC-04. REMARK 100 THE DEPOSITION ID IS D_1000031175. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 25-SEP-04 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 8.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : ESRF REMARK 200 BEAMLINE : ID14-1 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.934 REMARK 200 MONOCHROMATOR : 0.97 REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : MARRESEARCH REMARK 200 INTENSITY-INTEGRATION SOFTWARE : MOSFLM REMARK 200 DATA SCALING SOFTWARE : SCALA, CCP4 (SCALA) REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 23542 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.800 REMARK 200 RESOLUTION RANGE LOW (A) : 20.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 1.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.3 REMARK 200 DATA REDUNDANCY : 4.700 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : 0.08700 REMARK 200 FOR THE DATA SET : NULL REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.80 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.90 REMARK 200 COMPLETENESS FOR SHELL (%) : 99.1 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 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: 1Y6F REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 51.40 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.60 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: PEG 10000, PH 8.5, VAPOR DIFFUSION, REMARK 280 HANGING DROP, TEMPERATURE 298K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 1 21 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,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 60.26000 REMARK 290 SMTRY3 2 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: TETRAMERIC REMARK 350 APPLY THE FOLLOWING TO CHAINS: C, D, A, B 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 GLU A 1157 REMARK 465 THR A 1158 REMARK 465 VAL A 1159 REMARK 465 SER A 1160 REMARK 465 LEU A 1161 REMARK 465 PHE A 1162 REMARK 465 ASP A 1163 REMARK 465 ASP A 1164 REMARK 465 ILE A 1165 REMARK 465 GLU A 1166 REMARK 465 GLU A 1167 REMARK 465 THR B 1158 REMARK 465 VAL B 1159 REMARK 465 SER B 1160 REMARK 465 LEU B 1161 REMARK 465 PHE B 1162 REMARK 465 ASP B 1163 REMARK 465 ASP B 1164 REMARK 465 ILE B 1165 REMARK 465 GLU B 1166 REMARK 465 GLU B 1167 REMARK 470 REMARK 470 MISSING ATOM REMARK 470 THE FOLLOWING RESIDUES HAVE MISSING ATOMS (M=MODEL NUMBER; REMARK 470 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; REMARK 470 I=INSERTION CODE): REMARK 470 M RES CSSEQI ATOMS REMARK 470 ARG A1123 CG CD NE CZ NH1 NH2 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 CYS A1014 -144.54 -94.30 REMARK 500 ARG A1046 29.36 -69.96 REMARK 500 HIS A1052 -10.69 -161.57 REMARK 500 CYS A1075 167.83 172.83 REMARK 500 THR A1092 -73.55 -87.38 REMARK 500 LYS A1104 145.43 -35.32 REMARK 500 HIS A1116 -79.42 -112.79 REMARK 500 LEU A1119 -70.17 -48.27 REMARK 500 LEU A1121 18.06 -62.85 REMARK 500 ARG A1122 -12.15 -142.92 REMARK 500 LYS A1148 -71.00 -80.92 REMARK 500 VAL A1149 -80.43 -57.22 REMARK 500 SER A1185 19.95 -49.16 REMARK 500 THR A1186 -28.71 -143.20 REMARK 500 TRP A1188 80.22 -54.30 REMARK 500 VAL A1191 2.75 -50.46 REMARK 500 ASN A1195 85.96 -65.85 REMARK 500 MET A1196 -32.91 -38.98 REMARK 500 THR A1205 77.63 -67.36 REMARK 500 MET A1214 -72.01 -55.76 REMARK 500 PHE A1221 -62.88 -152.31 REMARK 500 ALA A1225 13.00 -60.84 REMARK 500 ARG A1236 33.97 -82.49 REMARK 500 LYS A1260 11.92 -60.60 REMARK 500 ASN A1262 88.49 -58.24 REMARK 500 PRO A1265 171.05 -56.69 REMARK 500 ASN A1266 73.73 46.42 REMARK 500 ASP A1273 -144.40 -68.86 REMARK 500 CYS A1274 109.52 -51.06 REMARK 500 GLU A1282 -70.56 -54.65 REMARK 500 GLN A1292 95.38 -165.08 REMARK 500 LEU A1293 65.00 -106.51 REMARK 500 LYS A1295 38.72 -76.76 REMARK 500 GLN A1302 -38.63 -149.47 REMARK 500 ARG A1303 -16.73 -168.39 REMARK 500 LYS A1323 -73.62 -37.15 REMARK 500 SER A1324 -53.38 -25.07 REMARK 500 VAL A1333 -77.54 -80.38 REMARK 500 PRO A1337 130.06 -30.62 REMARK 500 LEU A1338 -74.18 -52.32 REMARK 500 THR A1339 -24.96 -27.91 REMARK 500 ASP A1342 55.51 -103.62 REMARK 500 PHE A1348 115.01 -33.70 REMARK 500 ASP A1352 57.22 -102.13 REMARK 500 SER A1365 -60.82 -96.30 REMARK 500 ARG A1367 10.03 -55.64 REMARK 500 GLN A1385 54.09 -149.97 REMARK 500 HIS B1052 -14.81 -148.06 REMARK 500 LYS B1053 -1.42 -52.43 REMARK 500 LEU B1061 -55.17 -26.81 REMARK 500 REMARK 500 THIS ENTRY HAS 78 RAMACHANDRAN OUTLIERS. REMARK 500 REMARK 500 REMARK: NULL REMARK 525 REMARK 525 SOLVENT REMARK 525 REMARK 525 THE SOLVENT MOLECULES HAVE CHAIN IDENTIFIERS THAT REMARK 525 INDICATE THE POLYMER CHAIN WITH WHICH THEY ARE MOST REMARK 525 CLOSELY ASSOCIATED. THE REMARK LISTS ALL THE SOLVENT REMARK 525 MOLECULES WHICH ARE MORE THAN 5A AWAY FROM THE REMARK 525 NEAREST POLYMER CHAIN (M = MODEL NUMBER; REMARK 525 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE REMARK 525 NUMBER; I=INSERTION CODE): REMARK 525 REMARK 525 M RES CSSEQI REMARK 525 HOH A2049 DISTANCE = 7.28 ANGSTROMS REMARK 525 HOH A2067 DISTANCE = 7.73 ANGSTROMS REMARK 525 HOH A2077 DISTANCE = 7.93 ANGSTROMS REMARK 525 HOH B2037 DISTANCE = 7.52 ANGSTROMS REMARK 525 HOH B2043 DISTANCE = 5.84 ANGSTROMS REMARK 525 HOH B2049 DISTANCE = 10.10 ANGSTROMS REMARK 525 HOH B2057 DISTANCE = 5.95 ANGSTROMS REMARK 525 HOH B2059 DISTANCE = 8.89 ANGSTROMS REMARK 525 HOH B2066 DISTANCE = 7.71 ANGSTROMS REMARK 525 HOH B2068 DISTANCE = 6.76 ANGSTROMS REMARK 525 HOH B2070 DISTANCE = 10.61 ANGSTROMS REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CL B 2017 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE NCO A 1401 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE NCO B 2018 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE NCO D 1003 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE NCO A 1402 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE NCO B 2019 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC7 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE NCO A 1403 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC8 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE NCO B 2020 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC9 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE UDP A 1404 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE UDP B 2021 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE EDO B 2022 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 1XV5 RELATED DB: PDB REMARK 900 THE SAME PROTEIN IN COMPLEX WITH UDP REMARK 900 RELATED ID: 1Y6F RELATED DB: PDB REMARK 900 THE SAME PROTEIN IN COMPLEX WITH UDP-GLUCOSE AND DNA CONTAINING AN REMARK 900 ABASIC SITE REMARK 900 RELATED ID: 1Y8Z RELATED DB: PDB REMARK 900 THE SAME PROTEIN IN COMPLEX WITH UDP AND A 13-MER DNA CONTAINING A REMARK 900 HMU BASE AT 1.9 A RESOLUTION REMARK 900 RELATED ID: 1YA6 RELATED DB: PDB REMARK 900 THE SAME PROTEIN IN COMPLEX WITH UDP AND A 13-MER DNA CONTAINING A REMARK 900 CENTRAL A:G MISMATCH DBREF 1Y6G A 1001 1400 UNP P04519 GSTA_BPT4 1 400 DBREF 1Y6G B 1001 1400 UNP P04519 GSTA_BPT4 1 400 DBREF 1Y6G C 1 13 PDB 1Y6G 1Y6G 1 13 DBREF 1Y6G D 1 12 PDB 1Y6G 1Y6G 1 12 SEQADV 1Y6G MET A 998 UNP P04519 CLONING ARTIFACT SEQADV 1Y6G GLY A 999 UNP P04519 CLONING ARTIFACT SEQADV 1Y6G SER A 1000 UNP P04519 CLONING ARTIFACT SEQADV 1Y6G MET B 998 UNP P04519 CLONING ARTIFACT SEQADV 1Y6G GLY B 999 UNP P04519 CLONING ARTIFACT SEQADV 1Y6G SER B 1000 UNP P04519 CLONING ARTIFACT SEQRES 1 C 13 DG DA DT DA DC DT 5HU DA DG DA DT DA DG SEQRES 1 D 12 DC DT DA DT DC DT DG DA DG DT DA DT SEQRES 1 A 403 MET GLY SER MET ARG ILE CYS ILE PHE MET ALA ARG GLY SEQRES 2 A 403 LEU GLU GLY CYS GLY VAL THR LYS PHE SER LEU GLU GLN SEQRES 3 A 403 ARG ASP TRP PHE ILE LYS ASN GLY HIS GLU VAL THR LEU SEQRES 4 A 403 VAL TYR ALA LYS ASP LYS SER PHE THR ARG THR SER SER SEQRES 5 A 403 HIS ASP HIS LYS SER PHE SER ILE PRO VAL ILE LEU ALA SEQRES 6 A 403 LYS GLU TYR ASP LYS ALA LEU LYS LEU VAL ASN ASP CYS SEQRES 7 A 403 ASP ILE LEU ILE ILE ASN SER VAL PRO ALA THR SER VAL SEQRES 8 A 403 GLN GLU ALA THR ILE ASN ASN TYR LYS LYS LEU LEU ASP SEQRES 9 A 403 ASN ILE LYS PRO SER ILE ARG VAL VAL VAL TYR GLN HIS SEQRES 10 A 403 ASP HIS SER VAL LEU SER LEU ARG ARG ASN LEU GLY LEU SEQRES 11 A 403 GLU GLU THR VAL ARG ARG ALA ASP VAL ILE PHE SER HIS SEQRES 12 A 403 SER ASP ASN GLY ASP PHE ASN LYS VAL LEU MET LYS GLU SEQRES 13 A 403 TRP TYR PRO GLU THR VAL SER LEU PHE ASP ASP ILE GLU SEQRES 14 A 403 GLU ALA PRO THR VAL TYR ASN PHE GLN PRO PRO MET ASP SEQRES 15 A 403 ILE VAL LYS VAL ARG SER THR TYR TRP LYS ASP VAL SER SEQRES 16 A 403 GLU ILE ASN MET ASN ILE ASN ARG TRP ILE GLY ARG THR SEQRES 17 A 403 THR THR TRP LYS GLY PHE TYR GLN MET PHE ASP PHE HIS SEQRES 18 A 403 GLU LYS PHE LEU LYS PRO ALA GLY LYS SER THR VAL MET SEQRES 19 A 403 GLU GLY LEU GLU ARG SER PRO ALA PHE ILE ALA ILE LYS SEQRES 20 A 403 GLU LYS GLY ILE PRO TYR GLU TYR TYR GLY ASN ARG GLU SEQRES 21 A 403 ILE ASP LYS MET ASN LEU ALA PRO ASN GLN PRO ALA GLN SEQRES 22 A 403 ILE LEU ASP CYS TYR ILE ASN SER GLU MET LEU GLU ARG SEQRES 23 A 403 MET SER LYS SER GLY PHE GLY TYR GLN LEU SER LYS LEU SEQRES 24 A 403 ASN GLN LYS TYR LEU GLN ARG SER LEU GLU TYR THR HIS SEQRES 25 A 403 LEU GLU LEU GLY ALA CYS GLY THR ILE PRO VAL PHE TRP SEQRES 26 A 403 LYS SER THR GLY GLU ASN LEU LYS PHE ARG VAL ASP ASN SEQRES 27 A 403 THR PRO LEU THR SER HIS ASP SER GLY ILE ILE TRP PHE SEQRES 28 A 403 ASP GLU ASN ASP MET GLU SER THR PHE GLU ARG ILE LYS SEQRES 29 A 403 GLU LEU SER SER ASP ARG ALA LEU TYR ASP ARG GLU ARG SEQRES 30 A 403 GLU LYS ALA TYR GLU PHE LEU TYR GLN HIS GLN ASP SER SEQRES 31 A 403 SER PHE CYS PHE LYS GLU GLN PHE ASP ILE ILE THR LYS SEQRES 1 B 403 MET GLY SER MET ARG ILE CYS ILE PHE MET ALA ARG GLY SEQRES 2 B 403 LEU GLU GLY CYS GLY VAL THR LYS PHE SER LEU GLU GLN SEQRES 3 B 403 ARG ASP TRP PHE ILE LYS ASN GLY HIS GLU VAL THR LEU SEQRES 4 B 403 VAL TYR ALA LYS ASP LYS SER PHE THR ARG THR SER SER SEQRES 5 B 403 HIS ASP HIS LYS SER PHE SER ILE PRO VAL ILE LEU ALA SEQRES 6 B 403 LYS GLU TYR ASP LYS ALA LEU LYS LEU VAL ASN ASP CYS SEQRES 7 B 403 ASP ILE LEU ILE ILE ASN SER VAL PRO ALA THR SER VAL SEQRES 8 B 403 GLN GLU ALA THR ILE ASN ASN TYR LYS LYS LEU LEU ASP SEQRES 9 B 403 ASN ILE LYS PRO SER ILE ARG VAL VAL VAL TYR GLN HIS SEQRES 10 B 403 ASP HIS SER VAL LEU SER LEU ARG ARG ASN LEU GLY LEU SEQRES 11 B 403 GLU GLU THR VAL ARG ARG ALA ASP VAL ILE PHE SER HIS SEQRES 12 B 403 SER ASP ASN GLY ASP PHE ASN LYS VAL LEU MET LYS GLU SEQRES 13 B 403 TRP TYR PRO GLU THR VAL SER LEU PHE ASP ASP ILE GLU SEQRES 14 B 403 GLU ALA PRO THR VAL TYR ASN PHE GLN PRO PRO MET ASP SEQRES 15 B 403 ILE VAL LYS VAL ARG SER THR TYR TRP LYS ASP VAL SER SEQRES 16 B 403 GLU ILE ASN MET ASN ILE ASN ARG TRP ILE GLY ARG THR SEQRES 17 B 403 THR THR TRP LYS GLY PHE TYR GLN MET PHE ASP PHE HIS SEQRES 18 B 403 GLU LYS PHE LEU LYS PRO ALA GLY LYS SER THR VAL MET SEQRES 19 B 403 GLU GLY LEU GLU ARG SER PRO ALA PHE ILE ALA ILE LYS SEQRES 20 B 403 GLU LYS GLY ILE PRO TYR GLU TYR TYR GLY ASN ARG GLU SEQRES 21 B 403 ILE ASP LYS MET ASN LEU ALA PRO ASN GLN PRO ALA GLN SEQRES 22 B 403 ILE LEU ASP CYS TYR ILE ASN SER GLU MET LEU GLU ARG SEQRES 23 B 403 MET SER LYS SER GLY PHE GLY TYR GLN LEU SER LYS LEU SEQRES 24 B 403 ASN GLN LYS TYR LEU GLN ARG SER LEU GLU TYR THR HIS SEQRES 25 B 403 LEU GLU LEU GLY ALA CYS GLY THR ILE PRO VAL PHE TRP SEQRES 26 B 403 LYS SER THR GLY GLU ASN LEU LYS PHE ARG VAL ASP ASN SEQRES 27 B 403 THR PRO LEU THR SER HIS ASP SER GLY ILE ILE TRP PHE SEQRES 28 B 403 ASP GLU ASN ASP MET GLU SER THR PHE GLU ARG ILE LYS SEQRES 29 B 403 GLU LEU SER SER ASP ARG ALA LEU TYR ASP ARG GLU ARG SEQRES 30 B 403 GLU LYS ALA TYR GLU PHE LEU TYR GLN HIS GLN ASP SER SEQRES 31 B 403 SER PHE CYS PHE LYS GLU GLN PHE ASP ILE ILE THR LYS MODRES 1Y6G 5HU C 7 DU HET 5HU C 7 21 HET NCO D1003 7 HET NCO A1401 7 HET NCO A1402 7 HET NCO A1403 7 HET UDP A1404 25 HET CL B2017 1 HET NCO B2018 7 HET NCO B2019 7 HET NCO B2020 7 HET UDP B2021 25 HET EDO B2022 4 HETNAM 5HU 5-HYDROXYMETHYLURIDINE-2'-DEOXY-5'-MONOPHOSPHATE HETNAM NCO COBALT HEXAMMINE(III) HETNAM UDP URIDINE-5'-DIPHOSPHATE HETNAM CL CHLORIDE ION HETNAM EDO 1,2-ETHANEDIOL HETSYN EDO ETHYLENE GLYCOL FORMUL 1 5HU C10 H15 N2 O9 P FORMUL 5 NCO 7(CO H18 N6 3+) FORMUL 9 UDP 2(C9 H14 N2 O12 P2) FORMUL 10 CL CL 1- FORMUL 15 EDO C2 H6 O2 FORMUL 16 HOH *79(H2 O) HELIX 1 1 CYS A 1014 ASN A 1030 1 17 HELIX 2 2 GLU A 1064 ASN A 1073 1 10 HELIX 3 3 GLN A 1089 ILE A 1103 1 15 HELIX 4 4 LEU A 1119 ARG A 1123 5 5 HELIX 5 5 GLY A 1126 ALA A 1134 1 9 HELIX 6 6 LYS A 1148 TYR A 1155 1 8 HELIX 7 7 ASP A 1179 TRP A 1188 1 10 HELIX 8 8 THR A 1206 LYS A 1209 5 4 HELIX 9 9 GLY A 1210 PHE A 1221 1 12 HELIX 10 10 SER A 1237 ALA A 1239 5 3 HELIX 11 11 PHE A 1240 LYS A 1246 1 7 HELIX 12 12 ILE A 1276 SER A 1285 1 10 HELIX 13 13 GLU A 1306 GLY A 1313 1 8 HELIX 14 14 ALA A 1314 GLY A 1316 5 3 HELIX 15 15 LYS A 1323 LEU A 1329 1 7 HELIX 16 16 ASP A 1352 ASP A 1366 1 15 HELIX 17 17 ALA A 1368 ASP A 1386 1 19 HELIX 18 18 ASP A 1386 LYS A 1400 1 15 HELIX 19 19 CYS B 1014 ASN B 1030 1 17 HELIX 20 20 ILE B 1060 ASN B 1073 1 14 HELIX 21 21 GLN B 1089 ASN B 1102 1 14 HELIX 22 22 SER B 1117 ARG B 1122 1 6 HELIX 23 23 GLY B 1126 ALA B 1134 1 9 HELIX 24 24 VAL B 1149 TYR B 1155 1 7 HELIX 25 25 ASP B 1179 TRP B 1188 1 10 HELIX 26 26 ASP B 1190 ILE B 1194 5 5 HELIX 27 27 THR B 1206 LYS B 1209 5 4 HELIX 28 28 GLY B 1210 PHE B 1221 1 12 HELIX 29 29 LEU B 1222 GLY B 1226 5 5 HELIX 30 30 PRO B 1238 GLU B 1245 1 8 HELIX 31 31 GLU B 1257 MET B 1261 5 5 HELIX 32 32 ILE B 1276 LYS B 1286 1 11 HELIX 33 33 ASN B 1297 LEU B 1301 5 5 HELIX 34 34 GLU B 1306 CYS B 1315 1 10 HELIX 35 35 TRP B 1322 LEU B 1329 1 8 HELIX 36 36 ASP B 1352 SER B 1365 1 14 HELIX 37 37 ASP B 1366 ASP B 1386 1 21 HELIX 38 38 ASP B 1386 LYS B 1400 1 15 SHEET 1 A 7 ILE A1057 VAL A1059 0 SHEET 2 A 7 GLU A1033 ALA A1039 1 N LEU A1036 O ILE A1057 SHEET 3 A 7 ARG A1002 MET A1007 1 N ILE A1003 O GLU A1033 SHEET 4 A 7 ILE A1077 ILE A1080 1 O ILE A1079 N PHE A1006 SHEET 5 A 7 ARG A1108 TYR A1112 1 O VAL A1110 N LEU A1078 SHEET 6 A 7 VAL A1136 SER A1139 1 O PHE A1138 N VAL A1111 SHEET 7 A 7 TYR A1172 ASN A1173 1 O TYR A1172 N ILE A1137 SHEET 1 B 7 TYR A1250 TYR A1253 0 SHEET 2 B 7 ALA A1269 LEU A1272 1 O ILE A1271 N GLU A1251 SHEET 3 B 7 SER A1228 GLU A1232 1 N THR A1229 O GLN A1270 SHEET 4 B 7 ASN A1195 ILE A1202 1 N ASN A1199 O VAL A1230 SHEET 5 B 7 SER A1287 GLN A1292 1 O TYR A1291 N ARG A1200 SHEET 6 B 7 ILE A1318 TRP A1322 1 O ILE A1318 N GLY A1290 SHEET 7 B 7 ILE A1346 PHE A1348 1 O ILE A1346 N PRO A1319 SHEET 1 C 7 SER B1056 VAL B1059 0 SHEET 2 C 7 GLU B1033 ALA B1039 1 N LEU B1036 O ILE B1057 SHEET 3 C 7 ARG B1002 MET B1007 1 N ILE B1003 O GLU B1033 SHEET 4 C 7 ILE B1077 SER B1082 1 O ILE B1079 N PHE B1006 SHEET 5 C 7 ARG B1108 TYR B1112 1 O VAL B1110 N LEU B1078 SHEET 6 C 7 VAL B1136 SER B1139 1 O VAL B1136 N VAL B1111 SHEET 7 C 7 VAL B1171 ASN B1173 1 O TYR B1172 N ILE B1137 SHEET 1 D 6 TYR B1250 GLU B1251 0 SHEET 2 D 6 ALA B1269 LEU B1272 1 O ILE B1271 N GLU B1251 SHEET 3 D 6 SER B1228 GLU B1232 1 N MET B1231 O GLN B1270 SHEET 4 D 6 ASN B1195 ILE B1202 1 N ASN B1199 O SER B1228 SHEET 5 D 6 SER B1287 GLN B1292 1 O TYR B1291 N ARG B1200 SHEET 6 D 6 ILE B1318 PHE B1321 1 O VAL B1320 N GLN B1292 LINK O3' DT C 6 P 5HU C 7 1555 1555 1.61 LINK O3' 5HU C 7 P DA C 8 1555 1555 1.61 CISPEP 1 ALA A 1168 PRO A 1169 0 -0.37 CISPEP 2 ALA B 1168 PRO B 1169 0 -0.40 SITE 1 AC1 2 HIS B1114 NCO B2019 SITE 1 AC2 3 ARG A1132 ALA A1134 ASP A1135 SITE 1 AC3 4 ARG B1132 ARG B1133 ALA B1134 ASP B1135 SITE 1 AC4 3 TYR B1252 GLU B1257 DT D 10 SITE 1 AC5 4 THR A1086 SER A1087 VAL A1088 GLU A1090 SITE 1 AC6 6 HIS B1114 ASP B1115 HIS B1116 ARG B1204 SITE 2 AC6 6 CL B2017 UDP B2021 SITE 1 AC7 6 HIS A1114 ASP A1115 HIS A1116 ARG A1204 SITE 2 AC7 6 GLU A1306 UDP A1404 SITE 1 AC8 3 HOH A2014 ASP B1101 ASN B1102 SITE 1 AC9 15 CYS A1014 GLY A1015 ARG A1046 SER A1049 SITE 2 AC9 15 HIS A1050 ARG A1204 LYS A1209 CYS A1274 SITE 3 AC9 15 TYR A1275 ASN A1277 GLU A1306 TYR A1307 SITE 4 AC9 15 THR A1308 GLU A1311 NCO A1403 SITE 1 BC1 15 CYS B1014 GLY B1015 ARG B1046 SER B1049 SITE 2 BC1 15 HIS B1050 ARG B1204 LYS B1209 CYS B1274 SITE 3 BC1 15 TYR B1275 ASN B1277 GLU B1306 TYR B1307 SITE 4 BC1 15 THR B1308 GLU B1311 NCO B2019 SITE 1 BC2 1 LYS B1246 CRYST1 46.994 120.520 86.807 90.00 94.68 90.00 P 1 21 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 0.021279 0.000000 0.001742 0.00000 SCALE2 0.000000 0.008297 0.000000 0.00000 SCALE3 0.000000 0.000000 0.011558 0.00000