HEADER TRANSFERASE/DNA 14-DEC-04 1Y8Z TITLE ALPHA-GLUCOSYLTRANSFERASE IN COMPLEX WITH UDP AND A 13-MER DNA TITLE 2 CONTAINING A HMU BASE AT 1.9 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*G)-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 6 25-OCT-23 1Y8Z 1 REMARK LINK REVDAT 5 22-JUL-20 1Y8Z 1 REMARK SEQADV LINK REVDAT 4 13-JUL-11 1Y8Z 1 VERSN REVDAT 3 24-FEB-09 1Y8Z 1 VERSN REVDAT 2 04-OCT-05 1Y8Z 1 JRNL REVDAT 1 30-AUG-05 1Y8Z 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. 1.90 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) : 1.90 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) (%) : 99.0 REMARK 3 NUMBER OF REFLECTIONS : 62256 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) : 0.208 REMARK 3 FREE R VALUE : 0.250 REMARK 3 FREE R VALUE TEST SET SIZE (%) : NULL REMARK 3 FREE R VALUE TEST SET COUNT : 3141 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 : 6287 REMARK 3 NUCLEIC ACID ATOMS : 449 REMARK 3 HETEROGEN ATOMS : 110 REMARK 3 SOLVENT ATOMS : 494 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 25.00 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) : 0.005 REMARK 3 BOND ANGLES (DEGREES) : 1.212 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 1Y8Z COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 15-DEC-04. REMARK 100 THE DEPOSITION ID IS D_1000031266. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 23-JUL-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 : DENZO REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 62256 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.900 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 (%) : 99.0 REMARK 200 DATA REDUNDANCY : 7.000 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : 0.05800 REMARK 200 FOR THE DATA SET : 7.8000 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 (%) : 93.6 REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : 0.45000 REMARK 200 FOR SHELL : 2.200 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 (%): 41.60 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.10 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: PEG10000, 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 57.32750 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 ASP B 1142 REMARK 465 ASN B 1143 REMARK 465 GLY B 1144 REMARK 465 ASP B 1145 REMARK 465 PHE B 1146 REMARK 465 ASN B 1147 REMARK 465 LYS B 1148 REMARK 465 VAL B 1149 REMARK 465 LEU B 1150 REMARK 465 MET B 1151 REMARK 465 LYS B 1152 REMARK 465 GLU B 1153 REMARK 465 TRP B 1154 REMARK 465 TYR B 1155 REMARK 465 PRO B 1156 REMARK 465 GLU B 1157 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 465 ALA B 1168 REMARK 465 PRO B 1169 REMARK 465 THR B 1170 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 A1000 82.85 51.80 REMARK 500 CME A1014 -138.16 -111.74 REMARK 500 PHE A1055 -15.72 -143.09 REMARK 500 ASP A1074 48.51 -96.43 REMARK 500 HIS A1116 -77.39 -102.41 REMARK 500 PHE A1221 -52.17 -126.50 REMARK 500 GLU A1257 26.85 -149.08 REMARK 500 GLN A1302 -75.59 -137.06 REMARK 500 ASP A1352 65.32 -158.40 REMARK 500 GLN A1385 27.73 -142.76 REMARK 500 CME B1014 -136.41 -113.19 REMARK 500 ASN B1030 30.52 -98.74 REMARK 500 PHE B1055 -21.32 -143.24 REMARK 500 ASP B1074 49.31 -95.62 REMARK 500 HIS B1116 -76.89 -104.79 REMARK 500 PHE B1221 -53.85 -128.27 REMARK 500 ASN B1255 -0.93 -58.68 REMARK 500 GLU B1257 41.45 -108.66 REMARK 500 GLN B1298 -19.34 -49.41 REMARK 500 GLN B1302 -70.21 -133.04 REMARK 500 GLN B1385 29.16 -145.94 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 A 114 DISTANCE = 6.02 ANGSTROMS REMARK 525 HOH A 219 DISTANCE = 7.64 ANGSTROMS REMARK 525 HOH A 243 DISTANCE = 6.51 ANGSTROMS REMARK 525 HOH A 245 DISTANCE = 9.30 ANGSTROMS REMARK 525 HOH A 455 DISTANCE = 6.08 ANGSTROMS REMARK 525 HOH A 456 DISTANCE = 7.19 ANGSTROMS REMARK 525 HOH A 465 DISTANCE = 6.34 ANGSTROMS REMARK 525 HOH A 473 DISTANCE = 6.65 ANGSTROMS REMARK 525 HOH A 485 DISTANCE = 7.04 ANGSTROMS REMARK 525 HOH B 181 DISTANCE = 7.03 ANGSTROMS REMARK 525 HOH B 283 DISTANCE = 7.42 ANGSTROMS REMARK 525 HOH B 347 DISTANCE = 6.74 ANGSTROMS REMARK 525 HOH B 403 DISTANCE = 8.03 ANGSTROMS REMARK 525 HOH B 491 DISTANCE = 7.17 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 4001 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE NCO A 3001 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE NCO B 3002 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE NCO D 3003 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE NCO B 3004 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE NCO A 3005 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC7 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE UDP A 3006 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC8 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE UDP B 2001 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC9 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GOL A 5001 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GOL A 5002 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GOL A 5003 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GOL B 5004 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: 1Y6G RELATED DB: PDB REMARK 900 THE SAME PROTEIN IN COMPLEX WITH UDP AND A 13_MER DNA CONTAINING A REMARK 900 HMU BASE AT 2.8 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 1Y8Z A 1001 1400 UNP P04519 GSTA_BPT4 1 400 DBREF 1Y8Z B 1001 1400 UNP P04519 GSTA_BPT4 1 400 DBREF 1Y8Z C 1 13 PDB 1Y8Z 1Y8Z 1 13 DBREF 1Y8Z D 1 9 PDB 1Y8Z 1Y8Z 1 9 SEQADV 1Y8Z GLY A 999 UNP P04519 CLONING ARTIFACT SEQADV 1Y8Z SER A 1000 UNP P04519 CLONING ARTIFACT SEQADV 1Y8Z CME A 1014 UNP P04519 CYS 14 MODIFIED RESIDUE SEQADV 1Y8Z CME A 1274 UNP P04519 CYS 274 MODIFIED RESIDUE SEQADV 1Y8Z GLY B 999 UNP P04519 CLONING ARTIFACT SEQADV 1Y8Z SER B 1000 UNP P04519 CLONING ARTIFACT SEQADV 1Y8Z CME B 1014 UNP P04519 CYS 14 MODIFIED RESIDUE SEQADV 1Y8Z CME B 1274 UNP P04519 CYS 274 MODIFIED RESIDUE SEQRES 1 C 13 DG DA DT DA DC DT 5HU DA DG DA DT DA DG SEQRES 1 D 9 DC DT DA DT DC DT DG DA DG SEQRES 1 A 402 GLY SER MET ARG ILE CYS ILE PHE MET ALA ARG GLY LEU SEQRES 2 A 402 GLU GLY CME GLY VAL THR LYS PHE SER LEU GLU GLN ARG SEQRES 3 A 402 ASP TRP PHE ILE LYS ASN GLY HIS GLU VAL THR LEU VAL SEQRES 4 A 402 TYR ALA LYS ASP LYS SER PHE THR ARG THR SER SER HIS SEQRES 5 A 402 ASP HIS LYS SER PHE SER ILE PRO VAL ILE LEU ALA LYS SEQRES 6 A 402 GLU TYR ASP LYS ALA LEU LYS LEU VAL ASN ASP CYS ASP SEQRES 7 A 402 ILE LEU ILE ILE ASN SER VAL PRO ALA THR SER VAL GLN SEQRES 8 A 402 GLU ALA THR ILE ASN ASN TYR LYS LYS LEU LEU ASP ASN SEQRES 9 A 402 ILE LYS PRO SER ILE ARG VAL VAL VAL TYR GLN HIS ASP SEQRES 10 A 402 HIS SER VAL LEU SER LEU ARG ARG ASN LEU GLY LEU GLU SEQRES 11 A 402 GLU THR VAL ARG ARG ALA ASP VAL ILE PHE SER HIS SER SEQRES 12 A 402 ASP ASN GLY ASP PHE ASN LYS VAL LEU MET LYS GLU TRP SEQRES 13 A 402 TYR PRO GLU THR VAL SER LEU PHE ASP ASP ILE GLU GLU SEQRES 14 A 402 ALA PRO THR VAL TYR ASN PHE GLN PRO PRO MET ASP ILE SEQRES 15 A 402 VAL LYS VAL ARG SER THR TYR TRP LYS ASP VAL SER GLU SEQRES 16 A 402 ILE ASN MET ASN ILE ASN ARG TRP ILE GLY ARG THR THR SEQRES 17 A 402 THR TRP LYS GLY PHE TYR GLN MET PHE ASP PHE HIS GLU SEQRES 18 A 402 LYS PHE LEU LYS PRO ALA GLY LYS SER THR VAL MET GLU SEQRES 19 A 402 GLY LEU GLU ARG SER PRO ALA PHE ILE ALA ILE LYS GLU SEQRES 20 A 402 LYS GLY ILE PRO TYR GLU TYR TYR GLY ASN ARG GLU ILE SEQRES 21 A 402 ASP LYS MET ASN LEU ALA PRO ASN GLN PRO ALA GLN ILE SEQRES 22 A 402 LEU ASP CME TYR ILE ASN SER GLU MET LEU GLU ARG MET SEQRES 23 A 402 SER LYS SER GLY PHE GLY TYR GLN LEU SER LYS LEU ASN SEQRES 24 A 402 GLN LYS TYR LEU GLN ARG SER LEU GLU TYR THR HIS LEU SEQRES 25 A 402 GLU LEU GLY ALA CYS GLY THR ILE PRO VAL PHE TRP LYS SEQRES 26 A 402 SER THR GLY GLU ASN LEU LYS PHE ARG VAL ASP ASN THR SEQRES 27 A 402 PRO LEU THR SER HIS ASP SER GLY ILE ILE TRP PHE ASP SEQRES 28 A 402 GLU ASN ASP MET GLU SER THR PHE GLU ARG ILE LYS GLU SEQRES 29 A 402 LEU SER SER ASP ARG ALA LEU TYR ASP ARG GLU ARG GLU SEQRES 30 A 402 LYS ALA TYR GLU PHE LEU TYR GLN HIS GLN ASP SER SER SEQRES 31 A 402 PHE CYS PHE LYS GLU GLN PHE ASP ILE ILE THR LYS SEQRES 1 B 402 GLY SER MET ARG ILE CYS ILE PHE MET ALA ARG GLY LEU SEQRES 2 B 402 GLU GLY CME GLY VAL THR LYS PHE SER LEU GLU GLN ARG SEQRES 3 B 402 ASP TRP PHE ILE LYS ASN GLY HIS GLU VAL THR LEU VAL SEQRES 4 B 402 TYR ALA LYS ASP LYS SER PHE THR ARG THR SER SER HIS SEQRES 5 B 402 ASP HIS LYS SER PHE SER ILE PRO VAL ILE LEU ALA LYS SEQRES 6 B 402 GLU TYR ASP LYS ALA LEU LYS LEU VAL ASN ASP CYS ASP SEQRES 7 B 402 ILE LEU ILE ILE ASN SER VAL PRO ALA THR SER VAL GLN SEQRES 8 B 402 GLU ALA THR ILE ASN ASN TYR LYS LYS LEU LEU ASP ASN SEQRES 9 B 402 ILE LYS PRO SER ILE ARG VAL VAL VAL TYR GLN HIS ASP SEQRES 10 B 402 HIS SER VAL LEU SER LEU ARG ARG ASN LEU GLY LEU GLU SEQRES 11 B 402 GLU THR VAL ARG ARG ALA ASP VAL ILE PHE SER HIS SER SEQRES 12 B 402 ASP ASN GLY ASP PHE ASN LYS VAL LEU MET LYS GLU TRP SEQRES 13 B 402 TYR PRO GLU THR VAL SER LEU PHE ASP ASP ILE GLU GLU SEQRES 14 B 402 ALA PRO THR VAL TYR ASN PHE GLN PRO PRO MET ASP ILE SEQRES 15 B 402 VAL LYS VAL ARG SER THR TYR TRP LYS ASP VAL SER GLU SEQRES 16 B 402 ILE ASN MET ASN ILE ASN ARG TRP ILE GLY ARG THR THR SEQRES 17 B 402 THR TRP LYS GLY PHE TYR GLN MET PHE ASP PHE HIS GLU SEQRES 18 B 402 LYS PHE LEU LYS PRO ALA GLY LYS SER THR VAL MET GLU SEQRES 19 B 402 GLY LEU GLU ARG SER PRO ALA PHE ILE ALA ILE LYS GLU SEQRES 20 B 402 LYS GLY ILE PRO TYR GLU TYR TYR GLY ASN ARG GLU ILE SEQRES 21 B 402 ASP LYS MET ASN LEU ALA PRO ASN GLN PRO ALA GLN ILE SEQRES 22 B 402 LEU ASP CME TYR ILE ASN SER GLU MET LEU GLU ARG MET SEQRES 23 B 402 SER LYS SER GLY PHE GLY TYR GLN LEU SER LYS LEU ASN SEQRES 24 B 402 GLN LYS TYR LEU GLN ARG SER LEU GLU TYR THR HIS LEU SEQRES 25 B 402 GLU LEU GLY ALA CYS GLY THR ILE PRO VAL PHE TRP LYS SEQRES 26 B 402 SER THR GLY GLU ASN LEU LYS PHE ARG VAL ASP ASN THR SEQRES 27 B 402 PRO LEU THR SER HIS ASP SER GLY ILE ILE TRP PHE ASP SEQRES 28 B 402 GLU ASN ASP MET GLU SER THR PHE GLU ARG ILE LYS GLU SEQRES 29 B 402 LEU SER SER ASP ARG ALA LEU TYR ASP ARG GLU ARG GLU SEQRES 30 B 402 LYS ALA TYR GLU PHE LEU TYR GLN HIS GLN ASP SER SER SEQRES 31 B 402 PHE CYS PHE LYS GLU GLN PHE ASP ILE ILE THR LYS MODRES 1Y8Z 5HU C 7 DU MODRES 1Y8Z CME A 1014 CYS S,S-(2-HYDROXYETHYL)THIOCYSTEINE MODRES 1Y8Z CME A 1274 CYS S,S-(2-HYDROXYETHYL)THIOCYSTEINE MODRES 1Y8Z CME B 1014 CYS S,S-(2-HYDROXYETHYL)THIOCYSTEINE MODRES 1Y8Z CME B 1274 CYS S,S-(2-HYDROXYETHYL)THIOCYSTEINE HET 5HU C 7 21 HET CME A1014 10 HET CME A1274 10 HET CME B1014 10 HET CME B1274 10 HET NCO D3003 7 HET NCO A3001 7 HET NCO A3005 7 HET UDP A3006 25 HET GOL A5001 6 HET GOL A5002 6 HET GOL A5003 6 HET CL B4001 1 HET NCO B3002 7 HET NCO B3004 7 HET UDP B2001 25 HET GOL B5004 6 HETNAM 5HU 5-HYDROXYMETHYLURIDINE-2'-DEOXY-5'-MONOPHOSPHATE HETNAM CME S,S-(2-HYDROXYETHYL)THIOCYSTEINE HETNAM NCO COBALT HEXAMMINE(III) HETNAM UDP URIDINE-5'-DIPHOSPHATE HETNAM GOL GLYCEROL HETNAM CL CHLORIDE ION HETSYN GOL GLYCERIN; PROPANE-1,2,3-TRIOL FORMUL 1 5HU C10 H15 N2 O9 P FORMUL 3 CME 4(C5 H11 N O3 S2) FORMUL 5 NCO 5(CO H18 N6 3+) FORMUL 8 UDP 2(C9 H14 N2 O12 P2) FORMUL 9 GOL 4(C3 H8 O3) FORMUL 12 CL CL 1- FORMUL 17 HOH *494(H2 O) HELIX 1 1 CME A 1014 ASN A 1030 1 17 HELIX 2 2 PHE A 1044 SER A 1049 5 6 HELIX 3 3 GLU A 1064 ASN A 1073 1 10 HELIX 4 4 GLN A 1089 ASN A 1102 1 14 HELIX 5 5 SER A 1117 ARG A 1122 1 6 HELIX 6 6 GLY A 1126 ALA A 1134 1 9 HELIX 7 7 GLY A 1144 VAL A 1149 1 6 HELIX 8 8 VAL A 1149 TYR A 1155 1 7 HELIX 9 9 ASP A 1179 TRP A 1188 1 10 HELIX 10 10 ASP A 1190 ILE A 1194 5 5 HELIX 11 11 THR A 1206 LYS A 1209 5 4 HELIX 12 12 GLY A 1210 PHE A 1221 1 12 HELIX 13 13 ALA A 1239 GLY A 1247 1 9 HELIX 14 14 GLU A 1257 MET A 1261 5 5 HELIX 15 15 ILE A 1276 SER A 1285 1 10 HELIX 16 16 ASN A 1297 LEU A 1301 5 5 HELIX 17 17 GLU A 1306 GLY A 1316 1 11 HELIX 18 18 LYS A 1323 LEU A 1329 1 7 HELIX 19 19 PRO A 1337 HIS A 1341 5 5 HELIX 20 20 ASP A 1349 ASN A 1351 5 3 HELIX 21 21 ASP A 1352 SER A 1365 1 14 HELIX 22 22 ASP A 1366 ASP A 1386 1 21 HELIX 23 23 ASP A 1386 THR A 1399 1 14 HELIX 24 24 CME B 1014 ASN B 1030 1 17 HELIX 25 25 GLU B 1064 ASN B 1073 1 10 HELIX 26 26 GLN B 1089 ILE B 1103 1 15 HELIX 27 27 SER B 1117 ARG B 1122 1 6 HELIX 28 28 GLY B 1126 ALA B 1134 1 9 HELIX 29 29 ASP B 1179 TRP B 1188 1 10 HELIX 30 30 ASP B 1190 ILE B 1194 5 5 HELIX 31 31 THR B 1206 LYS B 1209 5 4 HELIX 32 32 GLY B 1210 PHE B 1221 1 12 HELIX 33 33 PRO B 1238 LYS B 1246 1 9 HELIX 34 34 GLU B 1257 MET B 1261 5 5 HELIX 35 35 ILE B 1276 SER B 1285 1 10 HELIX 36 36 GLU B 1306 CYS B 1315 1 10 HELIX 37 37 LYS B 1323 LEU B 1329 1 7 HELIX 38 38 PRO B 1337 HIS B 1341 5 5 HELIX 39 39 ASP B 1352 ASP B 1366 1 15 HELIX 40 40 ASP B 1366 ASP B 1386 1 21 HELIX 41 41 ASP B 1386 LYS B 1400 1 15 SHEET 1 A 7 SER A1056 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 VAL A1136 N VAL A1111 SHEET 7 A 7 VAL A1171 ASN A1173 1 O TYR A1172 N ILE A1137 SHEET 1 B 7 GLU A1251 TYR A1253 0 SHEET 2 B 7 GLN A1270 LEU A1272 1 O ILE A1271 N GLU A1251 SHEET 3 B 7 SER A1228 GLU A1232 1 N MET A1231 O GLN A1270 SHEET 4 B 7 ASN A1195 ILE A1202 1 N TRP A1201 O VAL A1230 SHEET 5 B 7 SER A1287 GLN A1292 1 O PHE A1289 N ARG A1200 SHEET 6 B 7 ILE A1318 TRP A1322 1 O VAL A1320 N GLN A1292 SHEET 7 B 7 ILE A1346 PHE A1348 1 O PHE A1348 N PHE A1321 SHEET 1 C 7 ILE B1057 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 ILE B1080 1 O ILE B1079 N PHE B1006 SHEET 5 C 7 ARG B1108 GLN B1113 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 TYR B1172 ASN B1173 1 O TYR B1172 N ILE B1137 SHEET 1 D 7 TYR B1250 TYR B1253 0 SHEET 2 D 7 ALA B1269 LEU B1272 1 O ILE B1271 N GLU B1251 SHEET 3 D 7 SER B1228 GLU B1232 1 N MET B1231 O GLN B1270 SHEET 4 D 7 ASN B1195 ILE B1202 1 N TRP B1201 O GLU B1232 SHEET 5 D 7 SER B1287 GLN B1292 1 O PHE B1289 N ARG B1200 SHEET 6 D 7 ILE B1318 TRP B1322 1 O VAL B1320 N GLN B1292 SHEET 7 D 7 ILE B1346 PHE B1348 1 O PHE B1348 N PHE B1321 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 LINK C GLY A1013 N CME A1014 1555 1555 1.33 LINK C CME A1014 N GLY A1015 1555 1555 1.33 LINK C ASP A1273 N CME A1274 1555 1555 1.32 LINK C CME A1274 N TYR A1275 1555 1555 1.33 LINK C GLY B1013 N CME B1014 1555 1555 1.33 LINK C CME B1014 N GLY B1015 1555 1555 1.33 LINK C ASP B1273 N CME B1274 1555 1555 1.33 LINK C CME B1274 N TYR B1275 1555 1555 1.33 SITE 1 AC1 6 HOH B 489 GLU B1012 CME B1014 GLY B1015 SITE 2 AC1 6 VAL B1016 THR B1017 SITE 1 AC2 6 HOH A 420 ARG A1132 ARG A1133 ALA A1134 SITE 2 AC2 6 ASP A1135 LYS B1400 SITE 1 AC3 5 LYS A1400 ARG B1132 ARG B1133 ALA B1134 SITE 2 AC3 5 ASP B1135 SITE 1 AC4 3 TYR B1252 GLU B1257 DG D 9 SITE 1 AC5 3 HOH B 287 ASP B1101 ASN B1102 SITE 1 AC6 4 THR A1086 VAL A1088 GLU A1090 LEU A1125 SITE 1 AC7 19 HOH A 46 HOH A 424 HOH A 479 GLY A1013 SITE 2 AC7 19 CME A1014 GLY A1015 ARG A1046 SER A1049 SITE 3 AC7 19 HIS A1050 ARG A1204 LYS A1209 CME A1274 SITE 4 AC7 19 TYR A1275 ASN A1277 MET A1280 GLU A1306 SITE 5 AC7 19 TYR A1307 THR A1308 GLU A1311 SITE 1 AC8 19 HOH B 71 HOH B 278 HOH B 334 GLY B1013 SITE 2 AC8 19 CME B1014 GLY B1015 LYS B1018 ARG B1046 SITE 3 AC8 19 SER B1049 HIS B1050 ARG B1204 LYS B1209 SITE 4 AC8 19 CME B1274 TYR B1275 ASN B1277 GLU B1306 SITE 5 AC8 19 TYR B1307 THR B1308 GLU B1311 SITE 1 AC9 3 GLY A1247 ILE A1248 TYR A1250 SITE 1 BC1 1 SER A1000 SITE 1 BC2 3 SER A1340 HIS A1341 ASP A1342 SITE 1 BC3 3 SER B1139 SER B1141 VAL B1171 CRYST1 41.263 114.655 86.143 90.00 89.49 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 0.024235 0.000000 -0.000216 0.00000 SCALE2 0.000000 0.008722 0.000000 0.00000 SCALE3 0.000000 0.000000 0.011609 0.00000