HEADER TRANSFERASE(GLUCOSYLTRANSFERASE) 09-JUN-94 1BGU TITLE CRYSTAL STRUCTURE OF THE DNA MODIFYING ENZYME BETA-GLUCOSYLTRANSFERASE TITLE 2 IN THE PRESENCE AND ABSENCE OF THE SUBSTRATE URIDINE DIPHOSPHOGLUCOSE COMPND MOL_ID: 1; COMPND 2 MOLECULE: BETA-GLUCOSYLTRANSFERASE; COMPND 3 CHAIN: A; COMPND 4 EC: 2.4.1.27; COMPND 5 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: ENTEROBACTERIA PHAGE T4; SOURCE 3 ORGANISM_TAXID: 10665 KEYWDS TRANSFERASE(GLUCOSYLTRANSFERASE) EXPDTA X-RAY DIFFRACTION MDLTYP CA ATOMS ONLY, CHAIN A AUTHOR A.VRIELINK,W.RUEGER,H.P.C.DRIESSEN,P.S.FREEMONT REVDAT 5 07-FEB-24 1BGU 1 REMARK REVDAT 4 29-NOV-17 1BGU 1 HELIX REVDAT 3 24-FEB-09 1BGU 1 VERSN REVDAT 2 01-APR-03 1BGU 1 JRNL REVDAT 1 15-OCT-94 1BGU 0 JRNL AUTH A.VRIELINK,W.RUGER,H.P.DRIESSEN,P.S.FREEMONT JRNL TITL CRYSTAL STRUCTURE OF THE DNA MODIFYING ENZYME JRNL TITL 2 BETA-GLUCOSYLTRANSFERASE IN THE PRESENCE AND ABSENCE OF THE JRNL TITL 3 SUBSTRATE URIDINE DIPHOSPHOGLUCOSE. JRNL REF EMBO J. V. 13 3413 1994 JRNL REFN ISSN 0261-4189 JRNL PMID 8062817 REMARK 1 REMARK 1 REFERENCE 1 REMARK 1 AUTH P.S.FREEMONT,W.RUEGER REMARK 1 TITL CRYSTALLIZATION AND PRELIMINARY X-RAY STUDIES OF T4 PHAGE REMARK 1 TITL 2 BETA-GLUCOSYLTRANSFERASE REMARK 1 REF J.MOL.BIOL. V. 203 525 1988 REMARK 1 REFN ISSN 0022-2836 REMARK 1 REFERENCE 2 REMARK 1 AUTH J.TOMASCHEWSKI,H.GRAM,J.W.CRABB,W.RUGER REMARK 1 TITL T4-INDUCED ALPHA-AND BETA-GLUCOSYLTRANSFERASE: CLONING OF REMARK 1 TITL 2 THE GENES AND A COMPARISON OF THEIR PRODUCTS BASED ON REMARK 1 TITL 3 SEQUENCING DATA REMARK 1 REF NUCLEIC ACIDS RES. V. 13 7551 1985 REMARK 1 REFN ISSN 0305-1048 REMARK 2 REMARK 2 RESOLUTION. 2.20 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : X-PLOR REMARK 3 AUTHORS : BRUNGER REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.20 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 10.00 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) (%) : NULL REMARK 3 NUMBER OF REFLECTIONS : 20885 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 SET) : 0.191 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 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 : 328 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 25 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 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) : 0.011 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 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: REMARK 3 THE COORDINATES ARE PRESENTED IN A COORDINATE FRAME THAT IS REMARK 3 TRANSLATED BY 1/4*151.920 ALONG A AND 1/4*52.26 ALONG B. REMARK 3 THUS THE TRANSFORMATION PRESENTED ON *SCALE* RECORDS BELOW REMARK 3 IS NOT THE DEFAULT. REMARK 3 REMARK 3 THE DICTIONARY FOR THE UDP PORTION OF THE SUBSTRATE WAS REMARK 3 BUILT USING THE CHARM MINIMIZATION WITHIN QUANTA. REMARK 4 REMARK 4 1BGU 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_1000171740. 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 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 FOR SHELL : NULL REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: NULL REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: NULL REMARK 200 SOFTWARE USED: X-PLOR REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 52.14 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.57 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: NULL REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 21 21 2 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,-Y,Z REMARK 290 3555 -X+1/2,Y+1/2,-Z 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 0.00000 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 75.96000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 26.13000 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 75.96000 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 26.13000 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 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 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 SER A 68 REMARK 465 ILE A 69 REMARK 465 ASN A 70 REMARK 465 PHE A 71 REMARK 465 PHE A 72 REMARK 465 GLY A 73 REMARK 465 GLY A 74 REMARK 465 LYS A 75 REMARK 465 PRO A 76 REMARK 465 TRP A 109 REMARK 465 PRO A 110 REMARK 465 ASN A 111 REMARK 465 VAL A 112 REMARK 465 LYS A 113 REMARK 465 ASN A 114 REMARK 465 ARG A 115 REMARK 465 PRO A 116 REMARK 465 TRP A 117 REMARK 465 ALA A 118 REMARK 465 TYR A 119 REMARK 465 LEU A 120 REMARK 465 TYR A 121 REMARK 465 THR A 122 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE UDP A 353 DBREF 1BGU A 1 351 UNP P04547 GSTB_BPT4 1 351 SEQRES 1 A 351 MET LYS ILE ALA ILE ILE ASN MET GLY ASN ASN VAL ILE SEQRES 2 A 351 ASN PHE LYS THR VAL PRO SER SER GLU THR ILE TYR LEU SEQRES 3 A 351 PHE LYS VAL ILE SER GLU MET GLY LEU ASN VAL ASP ILE SEQRES 4 A 351 ILE SER LEU LYS ASN GLY VAL TYR THR LYS SER PHE ASP SEQRES 5 A 351 GLU VAL ASP VAL ASN ASP TYR ASP ARG LEU ILE VAL VAL SEQRES 6 A 351 ASN SER SER ILE ASN PHE PHE GLY GLY LYS PRO ASN LEU SEQRES 7 A 351 ALA ILE LEU SER ALA GLN LYS PHE MET ALA LYS TYR LYS SEQRES 8 A 351 SER LYS ILE TYR TYR LEU PHE THR ASP ILE ARG LEU PRO SEQRES 9 A 351 PHE SER GLN SER TRP PRO ASN VAL LYS ASN ARG PRO TRP SEQRES 10 A 351 ALA TYR LEU TYR THR GLU GLU GLU LEU LEU ILE LYS SER SEQRES 11 A 351 PRO ILE LYS VAL ILE SER GLN GLY ILE ASN LEU ASP ILE SEQRES 12 A 351 ALA LYS ALA ALA HIS LYS LYS VAL ASP ASN VAL ILE GLU SEQRES 13 A 351 PHE GLU TYR PHE PRO ILE GLU GLN TYR LYS ILE HIS MET SEQRES 14 A 351 ASN ASP PHE GLN LEU SER LYS PRO THR LYS LYS THR LEU SEQRES 15 A 351 ASP VAL ILE TYR GLY GLY SER PHE ARG SER GLY GLN ARG SEQRES 16 A 351 GLU SER LYS MET VAL GLU PHE LEU PHE ASP THR GLY LEU SEQRES 17 A 351 ASN ILE GLU PHE PHE GLY ASN ALA ARG GLU LYS GLN PHE SEQRES 18 A 351 LYS ASN PRO LYS TYR PRO TRP THR LYS ALA PRO VAL PHE SEQRES 19 A 351 THR GLY LYS ILE PRO MET ASN MET VAL SER GLU LYS ASN SEQRES 20 A 351 SER GLN ALA ILE ALA ALA LEU ILE ILE GLY ASP LYS ASN SEQRES 21 A 351 TYR ASN ASP ASN PHE ILE THR LEU ARG VAL TRP GLU THR SEQRES 22 A 351 MET ALA SER ASP ALA VAL MET LEU ILE ASP GLU GLU PHE SEQRES 23 A 351 ASP THR LYS HIS ARG ILE ILE ASN ASP ALA ARG PHE TYR SEQRES 24 A 351 VAL ASN ASN ARG ALA GLU LEU ILE ASP ARG VAL ASN GLU SEQRES 25 A 351 LEU LYS HIS SER ASP VAL LEU ARG LYS GLU MET LEU SER SEQRES 26 A 351 ILE GLN HIS ASP ILE LEU ASN LYS THR ARG ALA LYS LYS SEQRES 27 A 351 ALA GLU TRP GLN ASP ALA PHE LYS LYS ALA ILE ASP LEU HET UDP A 353 25 HETNAM UDP URIDINE-5'-DIPHOSPHATE FORMUL 2 UDP C9 H14 N2 O12 P2 HELIX 1 H1 VAL A 18 ILE A 30 1 13 HELIX 2 H1A PHE A 51 GLU A 53 5 3 HELIX 3 H1B ASP A 55 ASP A 58 5 4 HELIX 4 H2 LEU A 78 MET A 87 1 10 HELIX 5 H3 ASP A 100 LEU A 103 1 4 HELIX 6 H4 GLU A 124 LEU A 127 1 4 HELIX 7 H5 ASN A 140 HIS A 148 1 9 HELIX 8 H6 ILE A 162 TYR A 165 1 4 HELIX 9 H7 GLU A 196 LEU A 203 1 8 HELIX 10 H8 ARG A 217 PHE A 221 5 5 HELIX 11 H9 VAL A 243 ASN A 247 1 5 HELIX 12 H10 LEU A 268 ALA A 275 1 8 HELIX 13 10A GLU A 284 ASP A 287 5 4 HELIX 14 10B ASP A 295 PHE A 298 5 4 HELIX 15 H11 ARG A 303 HIS A 315 1 13 HELIX 16 H12 ASP A 317 THR A 334 1 18 HELIX 17 H13 LYS A 338 ALA A 348 1 11 SHEET 1 A 7 THR A 48 SER A 50 0 SHEET 2 A 7 ASN A 36 SER A 41 1 SHEET 3 A 7 MET A 1 ASN A 7 1 SHEET 4 A 7 ARG A 61 VAL A 65 1 SHEET 5 A 7 ILE A 94 PHE A 98 1 SHEET 6 A 7 ILE A 132 SER A 136 1 SHEET 7 A 7 ILE A 155 TYR A 159 1 SHEET 1 B 6 VAL A 233 PHE A 234 0 SHEET 2 B 6 ILE A 210 PHE A 213 1 SHEET 3 B 6 LEU A 182 GLY A 187 1 SHEET 4 B 6 ALA A 250 ILE A 255 1 SHEET 5 B 6 VAL A 279 ASP A 283 1 SHEET 6 B 6 TYR A 299 VAL A 300 1 SITE 1 AC1 4 GLY A 188 GLY A 214 LYS A 237 MET A 240 CRYST1 151.920 52.260 52.740 90.00 90.00 90.00 P 21 21 2 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 0.006582 0.000000 0.000000 -0.25000 SCALE2 0.000000 0.019135 0.000000 -0.25000 SCALE3 0.000000 0.000000 0.018961 0.00000