HEADER TRANSFERASE 18-JUN-01 1JEJ TITLE T4 PHAGE APO BGT COMPND MOL_ID: 1; COMPND 2 MOLECULE: DNA BETA-GLUCOSYLTRANSFERASE; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: BGT; COMPND 5 EC: 2.4.1.27; COMPND 6 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: ENTEROBACTERIA PHAGE T4; SOURCE 3 ORGANISM_TAXID: 10665; SOURCE 4 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 5 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS GLYCOSYLTRANSFERASE, TRANSFERASE EXPDTA X-RAY DIFFRACTION AUTHOR S.MORERA,L.LARIVIERE,J.KURZECK,U.ASCHKE-SONNENBORN,P.S.FREEMONT, AUTHOR 2 J.JANIN,W.RUGER REVDAT 3 16-AUG-23 1JEJ 1 REMARK REVDAT 2 24-FEB-09 1JEJ 1 VERSN REVDAT 1 15-AUG-01 1JEJ 0 JRNL AUTH S.MORERA,L.LARIVIERE,J.KURZECK,U.ASCHKE-SONNENBORN, JRNL AUTH 2 P.S.FREEMONT,J.JANIN,W.RUGER JRNL TITL HIGH RESOLUTION CRYSTAL STRUCTURES OF T4 PHAGE JRNL TITL 2 BETA-GLUCOSYLTRANSFERASE: INDUCED FIT AND EFFECT OF JRNL TITL 3 SUBSTRATE AND METAL BINDING. JRNL REF J.MOL.BIOL. V. 311 569 2001 JRNL REFN ISSN 0022-2836 JRNL PMID 11493010 JRNL DOI 10.1006/JMBI.2001.4905 REMARK 1 REMARK 1 REFERENCE 1 REMARK 1 TITL T4 PHAGE BETA-GLUCOSYLTRANSFERASE: SUBSTRATE BINDING AND REMARK 1 TITL 2 PROPOSED CATALYTIC MECHANISM REMARK 1 REF J.MOL.BIOL. V. 292 717 1999 REMARK 1 REFN ISSN 0022-2836 REMARK 2 REMARK 2 RESOLUTION. 2.50 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) : 2.50 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 20.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : 2.000 REMARK 3 DATA CUTOFF HIGH (ABS(F)) : NULL REMARK 3 DATA CUTOFF LOW (ABS(F)) : NULL REMARK 3 COMPLETENESS (WORKING+TEST) (%) : 100.0 REMARK 3 NUMBER OF REFLECTIONS : 14639 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) : 0.197 REMARK 3 FREE R VALUE : 0.264 REMARK 3 FREE R VALUE TEST SET SIZE (%) : NULL REMARK 3 FREE R VALUE TEST SET COUNT : 720 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 : 2869 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 0 REMARK 3 SOLVENT ATOMS : 178 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 49.00 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) : 0.007 REMARK 3 BOND ANGLES (DEGREES) : 1.260 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 1JEJ COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 26-JUN-01. REMARK 100 THE DEPOSITION ID IS D_1000013683. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 09-MAY-00 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 7.5 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 : NULL 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 : 14639 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.500 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 (%) : 100.0 REMARK 200 DATA REDUNDANCY : 5.100 REMARK 200 R MERGE (I) : 0.04400 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 16.5000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.50 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.59 REMARK 200 COMPLETENESS FOR SHELL (%) : 100.0 REMARK 200 DATA REDUNDANCY IN SHELL : 5.10 REMARK 200 R MERGE FOR SHELL (I) : 0.22300 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: PDB ENTRY 1QKJ REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 53.52 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.65 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: PEG 10000, PH 7.5, VAPOR DIFFUSION, REMARK 280 HANGING DROP, TEMPERATURE 291K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 41 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,X,Z+1/4 REMARK 290 4555 Y,-X,Z+3/4 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 61.16950 REMARK 290 SMTRY1 3 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 30.58475 REMARK 290 SMTRY1 4 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY2 4 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 91.75425 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 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 ILE A 13 -46.46 -141.29 REMARK 500 ASN A 14 -146.43 -153.41 REMARK 500 LEU A 103 59.23 -110.69 REMARK 500 ARG A 191 126.11 -172.46 REMARK 500 LYS A 237 155.70 -44.11 REMARK 500 ASP A 258 120.13 -170.06 REMARK 500 ASN A 262 120.31 -16.52 REMARK 500 ASP A 263 25.48 49.12 REMARK 500 ASN A 264 -69.75 -136.72 REMARK 500 ASP A 287 72.11 -152.61 REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 1JG6 RELATED DB: PDB REMARK 900 T4 PHAGE BGT IN COMPLEX WITH UDP REMARK 900 RELATED ID: 1JG7 RELATED DB: PDB REMARK 900 T4 PHAGE BGT IN COMPLEX WITH UDP AND MN2+ REMARK 900 RELATED ID: 1BGT RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF THE DNA MODIFYING ENZYME -GLUCOSYLTRANSFERASE REMARK 900 IN THE PRESENCE AND ABSENCE OF THE SUBSTRATE URIDINE REMARK 900 DIPHOSPHOGLUCOSE REMARK 900 RELATED ID: 1BGU RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF THE DNA MODIFYING ENZYME -GLUCOSYLTRANSFERASE REMARK 900 IN THE PRESENCE AND ABSENCE OF THE SUBSTRATE URIDINE REMARK 900 DIPHOSPHOGLUCOSE REMARK 900 RELATED ID: 1C3J RELATED DB: PDB REMARK 900 T4 PHAGE -GLUCOSYLTRANSFERASE: SUBSTRATE BINDING AND PROPOSED REMARK 900 CATALYTIC MECHANISM REMARK 900 RELATED ID: 1QKJ RELATED DB: PDB REMARK 900 T4 PHAGE B-GLUCOSYLTRANSFERASE, SUBSTRATE BINDING AND PROPOSED REMARK 900 CATALYTIC MECHANISM DBREF 1JEJ 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 FORMUL 2 HOH *178(H2 O) HELIX 1 1 THR A 17 GLU A 32 1 16 HELIX 2 2 ASP A 52 VAL A 54 5 3 HELIX 3 3 ASP A 55 TYR A 59 5 5 HELIX 4 4 PHE A 71 LYS A 75 5 5 HELIX 5 5 ASN A 77 TYR A 90 1 14 HELIX 6 6 SER A 108 LYS A 113 1 6 HELIX 7 7 TRP A 117 TYR A 121 5 5 HELIX 8 8 THR A 122 LEU A 127 1 6 HELIX 9 9 ASN A 140 HIS A 148 1 9 HELIX 10 10 PRO A 161 ILE A 167 5 7 HELIX 11 11 GLY A 193 PHE A 204 1 12 HELIX 12 12 ARG A 217 PHE A 221 5 5 HELIX 13 13 MET A 242 SER A 248 1 7 HELIX 14 14 THR A 267 ALA A 275 1 9 HELIX 15 15 GLU A 285 THR A 288 5 4 HELIX 16 16 ASP A 295 ARG A 297 5 3 HELIX 17 17 ASN A 302 SER A 316 1 15 HELIX 18 18 SER A 316 ALA A 336 1 21 HELIX 19 19 LYS A 337 ILE A 349 1 13 SHEET 1 A 7 LYS A 49 SER A 50 0 SHEET 2 A 7 ASN A 36 SER A 41 1 O ILE A 39 N LYS A 49 SHEET 3 A 7 LYS A 2 ASN A 7 1 N ILE A 3 O ASN A 36 SHEET 4 A 7 ARG A 61 VAL A 65 1 O ARG A 61 N ALA A 4 SHEET 5 A 7 ILE A 94 PHE A 98 1 O TYR A 95 N VAL A 64 SHEET 6 A 7 ILE A 132 SER A 136 1 N LYS A 133 O ILE A 94 SHEET 7 A 7 VAL A 154 TYR A 159 1 N ILE A 155 O ILE A 132 SHEET 1 B 6 VAL A 233 PHE A 234 0 SHEET 2 B 6 ILE A 210 PHE A 213 1 O ILE A 210 N VAL A 233 SHEET 3 B 6 LEU A 182 GLY A 187 1 O VAL A 184 N GLU A 211 SHEET 4 B 6 ALA A 250 ILE A 255 1 N ILE A 251 O LEU A 182 SHEET 5 B 6 VAL A 279 ASP A 283 1 N VAL A 279 O ILE A 251 SHEET 6 B 6 TYR A 299 VAL A 300 1 N VAL A 300 O ILE A 282 CRYST1 59.369 59.369 122.339 90.00 90.00 90.00 P 41 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 0.016844 0.000000 0.000000 0.00000 SCALE2 0.000000 0.016844 0.000000 0.00000 SCALE3 0.000000 0.000000 0.008174 0.00000