HEADER TRANSFERASE 06-NOV-07 2VFZ TITLE CRYSTAL STRUCTURE OF ALPHA-1,3 GALACTOSYLTRANSFERASE (R365K) IN TITLE 2 COMPLEX WITH UDP-2F-GALACTOSE COMPND MOL_ID: 1; COMPND 2 MOLECULE: N-ACETYLLACTOSAMINIDE ALPHA-1,3-GALACTOSYL TRANSFERASE; COMPND 3 CHAIN: A, B; COMPND 4 FRAGMENT: CATALYTIC DOMAIN, RESIDUES 80-368; COMPND 5 SYNONYM: GALACTOSYLTRANSFERASE, UDP-GALACTOSE BETA-D-GALACTOSYL-1,4- COMPND 6 N-ACETYL- D-GLUCOSAMINIDE ALPHA-1,3-GALACTOSYLTRANSFERASE; COMPND 7 EC: 2.4.1.151, 2.4.1.87; COMPND 8 ENGINEERED: YES; COMPND 9 MUTATION: YES; COMPND 10 OTHER_DETAILS: URIDINE-5'-DIPHOSPHATE-2-DEOXY-2-FLUOROGALACTOSE COMPND 11 MANGANESE ION SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: BOS TAURUS; SOURCE 3 ORGANISM_COMMON: BOVINE; SOURCE 4 ORGANISM_TAXID: 9913; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 7 EXPRESSION_SYSTEM_STRAIN: BL21 (DE3); SOURCE 8 EXPRESSION_SYSTEM_PLASMID: PET15B KEYWDS 3 GALACTOSYLTRANSFERASE, MANGANESE, TRANSFERASE, GLYCOPROTEIN, METAL- KEYWDS 2 BINDING, GT, R365K, ALPHA-1, MEMBRANE, ALPHA GT, GALACTOSE, ENZYME KEYWDS 3 MECHANISM, GLYCOSYLTRANSFERASE, GALACTOSYLTRANSFERASE, SUBSTRATE KEYWDS 4 SPECIFICITY, SIGNAL-ANCHOR, TRANSMEMBRANE, GOLGI APPARATUS EXPDTA X-RAY DIFFRACTION AUTHOR H.JAMALUDDIN,P.TUMBALE,S.G.WITHERS,K.R.ACHARYA,K.BREW REVDAT 3 08-MAY-24 2VFZ 1 LINK REVDAT 2 24-FEB-09 2VFZ 1 VERSN REVDAT 1 13-NOV-07 2VFZ 0 SPRSDE 13-NOV-07 2VFZ 2JCF JRNL AUTH H.JAMALUDDIN,P.TUMBALE,S.G.WITHERS,K.R.ACHARYA,K.BREW JRNL TITL CONFORMATIONAL CHANGES INDUCED BY BINDING UDP-2F-GALACTOSE JRNL TITL 2 TO ALPHA-1,3 GALACTOSYLTRANSFERASE-IMPLICATIONS FOR JRNL TITL 3 CATALYSIS JRNL REF J.MOL.BIOL. V. 369 1270 2007 JRNL REFN ISSN 0022-2836 JRNL PMID 17493636 JRNL DOI 10.1016/J.JMB.2007.04.012 REMARK 2 REMARK 2 RESOLUTION. 2.40 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : CNS 1.1 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 : NULL REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.40 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 25.06 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 DATA CUTOFF HIGH (ABS(F)) : 290930.030 REMARK 3 DATA CUTOFF LOW (ABS(F)) : NULL REMARK 3 COMPLETENESS (WORKING+TEST) (%) : 87.9 REMARK 3 NUMBER OF REFLECTIONS : 23881 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 CROSS-VALIDATION METHOD : THROUGHOUT REMARK 3 FREE R VALUE TEST SET SELECTION : RANDOM REMARK 3 R VALUE (WORKING SET) : 0.178 REMARK 3 FREE R VALUE : 0.233 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.800 REMARK 3 FREE R VALUE TEST SET COUNT : 1157 REMARK 3 ESTIMATED ERROR OF FREE R VALUE : 0.007 REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : 6 REMARK 3 BIN RESOLUTION RANGE HIGH (A) : 2.40 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.55 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 71.60 REMARK 3 REFLECTIONS IN BIN (WORKING SET) : 3059 REMARK 3 BIN R VALUE (WORKING SET) : 0.2310 REMARK 3 BIN FREE R VALUE : 0.2720 REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : 5.40 REMARK 3 BIN FREE R VALUE TEST SET COUNT : 173 REMARK 3 ESTIMATED ERROR OF BIN FREE R VALUE : 0.021 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 4654 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 74 REMARK 3 SOLVENT ATOMS : 497 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 24.70 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 29.00 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -3.36000 REMARK 3 B22 (A**2) : 3.95000 REMARK 3 B33 (A**2) : -0.59000 REMARK 3 B12 (A**2) : -3.29000 REMARK 3 B13 (A**2) : 2.40000 REMARK 3 B23 (A**2) : -14.76000 REMARK 3 REMARK 3 ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM LUZZATI PLOT (A) : 0.24 REMARK 3 ESD FROM SIGMAA (A) : 0.26 REMARK 3 LOW RESOLUTION CUTOFF (A) : 5.00 REMARK 3 REMARK 3 CROSS-VALIDATED ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM C-V LUZZATI PLOT (A) : 0.33 REMARK 3 ESD FROM C-V SIGMAA (A) : 0.32 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 BOND LENGTHS (A) : 0.013 REMARK 3 BOND ANGLES (DEGREES) : 1.500 REMARK 3 DIHEDRAL ANGLES (DEGREES) : 23.90 REMARK 3 IMPROPER ANGLES (DEGREES) : 4.170 REMARK 3 REMARK 3 ISOTROPIC THERMAL MODEL : RESTRAINED REMARK 3 REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. RMS SIGMA REMARK 3 MAIN-CHAIN BOND (A**2) : 1.160 ; 1.500 REMARK 3 MAIN-CHAIN ANGLE (A**2) : 1.860 ; 2.000 REMARK 3 SIDE-CHAIN BOND (A**2) : 1.760 ; 2.000 REMARK 3 SIDE-CHAIN ANGLE (A**2) : 2.550 ; 2.500 REMARK 3 REMARK 3 BULK SOLVENT MODELING. REMARK 3 METHOD USED : FLAT MODEL REMARK 3 KSOL : 0.40 REMARK 3 BSOL : 66.03 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 : PROTEIN_REP.PARAM REMARK 3 PARAMETER FILE 2 : WATER_REP.PARAM REMARK 3 PARAMETER FILE 3 : ION.PARAM REMARK 3 PARAMETER FILE 4 : UPF-ONO-3-GOL.PAR REMARK 3 PARAMETER FILE 5 : NULL REMARK 3 TOPOLOGY FILE 1 : PROTEIN.TOP REMARK 3 TOPOLOGY FILE 2 : WATER.TOP REMARK 3 TOPOLOGY FILE 3 : ION.TOP REMARK 3 TOPOLOGY FILE 4 : UPF-ONO-3-GOL.TOP REMARK 3 TOPOLOGY FILE 5 : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: BULK SOLVENT MODEL USED REMARK 4 REMARK 4 2VFZ COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 06-NOV-07. REMARK 100 THE DEPOSITION ID IS D_1290034301. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 07-DEC-05 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 8 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : SRS REMARK 200 BEAMLINE : PX14.1 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.977, 1.48 REMARK 200 MONOCHROMATOR : SI(111) REMARK 200 OPTICS : MIRRORS REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC CCD REMARK 200 INTENSITY-INTEGRATION SOFTWARE : DENZO REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 27634 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.400 REMARK 200 RESOLUTION RANGE LOW (A) : 50.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 0.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 89.9 REMARK 200 DATA REDUNDANCY : 4.000 REMARK 200 R MERGE (I) : 0.05000 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 11.5000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.40 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.49 REMARK 200 COMPLETENESS FOR SHELL (%) : 67.2 REMARK 200 DATA REDUNDANCY IN SHELL : 1.90 REMARK 200 R MERGE FOR SHELL (I) : 0.13000 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 4.440 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: MOLREP REMARK 200 STARTING MODEL: NONE REMARK 200 REMARK 200 REMARK: NONE REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 59.00 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 3.00 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 10% PEG 6000, 0.1M TRIS-HCL, PH 8.0 REMARK 280 AND 12-20% MPD REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,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 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 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PQS REMARK 350 TOTAL BURIED SURFACE AREA: 1450 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 28410 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -12.6 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: 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 400 REMARK 400 COMPOUND REMARK 400 ENGINEERED RESIDUE IN CHAIN A, ARG 365 TO LYS REMARK 400 ENGINEERED RESIDUE IN CHAIN B, ARG 365 TO LYS 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 80 REMARK 465 SER A 81 REMARK 465 GLU A 360 REMARK 465 TYR A 361 REMARK 465 ASN A 362 REMARK 465 VAL A 363 REMARK 465 VAL A 364 REMARK 465 LYS A 365 REMARK 465 ASN A 366 REMARK 465 ASN A 367 REMARK 465 VAL A 368 REMARK 465 GLU B 1080 REMARK 465 SER B 1081 REMARK 465 LYS B 1082 REMARK 465 VAL B 1364 REMARK 465 LYS B 1365 REMARK 465 ASN B 1366 REMARK 465 ASN B 1367 REMARK 465 VAL B 1368 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 VAL B1363 CB CG1 CG2 REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS IN SAME ASYMMETRIC UNIT REMARK 500 REMARK 500 THE FOLLOWING ATOMS ARE IN CLOSE CONTACT. REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI DISTANCE REMARK 500 NH2 ARG A 263 O HOH A 2187 2.18 REMARK 500 REMARK 500 REMARK: NULL 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 TYR A 143 -33.68 -132.32 REMARK 500 HIS A 213 -35.12 -158.33 REMARK 500 PHE A 234 78.03 -119.78 REMARK 500 HIS A 315 -131.65 48.55 REMARK 500 CYS A 338 66.06 -171.42 REMARK 500 HIS B1213 -38.59 -151.85 REMARK 500 ASP B1227 49.47 -76.07 REMARK 500 PHE B1234 78.38 -119.85 REMARK 500 THR B1259 51.03 -90.14 REMARK 500 HIS B1315 -133.37 51.18 REMARK 500 CYS B1338 69.56 -173.15 REMARK 500 LEU B1345 88.53 -156.58 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 A2044 DISTANCE = 6.99 ANGSTROMS REMARK 525 HOH A2048 DISTANCE = 9.93 ANGSTROMS REMARK 525 HOH A2049 DISTANCE = 8.50 ANGSTROMS REMARK 525 HOH A2050 DISTANCE = 8.00 ANGSTROMS REMARK 525 HOH A2051 DISTANCE = 6.64 ANGSTROMS REMARK 525 HOH A2053 DISTANCE = 6.11 ANGSTROMS REMARK 525 HOH A2055 DISTANCE = 8.65 ANGSTROMS REMARK 525 HOH A2059 DISTANCE = 5.89 ANGSTROMS REMARK 525 HOH A2063 DISTANCE = 7.35 ANGSTROMS REMARK 525 HOH A2069 DISTANCE = 6.22 ANGSTROMS REMARK 525 HOH A2070 DISTANCE = 6.26 ANGSTROMS REMARK 525 HOH A2099 DISTANCE = 7.77 ANGSTROMS REMARK 525 HOH A2128 DISTANCE = 5.90 ANGSTROMS REMARK 525 HOH A2139 DISTANCE = 6.39 ANGSTROMS REMARK 525 HOH B2079 DISTANCE = 6.35 ANGSTROMS REMARK 525 HOH B2082 DISTANCE = 5.87 ANGSTROMS REMARK 525 HOH B2108 DISTANCE = 6.85 ANGSTROMS REMARK 525 HOH B2114 DISTANCE = 7.22 ANGSTROMS REMARK 525 HOH B2115 DISTANCE = 7.77 ANGSTROMS REMARK 525 HOH B2119 DISTANCE = 6.08 ANGSTROMS REMARK 525 HOH B2135 DISTANCE = 5.95 ANGSTROMS REMARK 525 HOH B2139 DISTANCE = 7.72 ANGSTROMS REMARK 525 HOH B2140 DISTANCE = 8.04 ANGSTROMS REMARK 525 HOH B2141 DISTANCE = 5.85 ANGSTROMS REMARK 525 HOH B2142 DISTANCE = 5.90 ANGSTROMS REMARK 525 HOH B2152 DISTANCE = 6.01 ANGSTROMS REMARK 525 HOH B2162 DISTANCE = 6.62 ANGSTROMS REMARK 525 HOH B2164 DISTANCE = 7.15 ANGSTROMS REMARK 525 HOH B2203 DISTANCE = 6.85 ANGSTROMS REMARK 620 REMARK 620 METAL COORDINATION REMARK 620 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 620 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE): REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MN A1361 MN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP A 227 OD1 REMARK 620 2 ASP A 227 OD2 53.8 REMARK 620 3 UPF A1360 O1A 85.6 77.4 REMARK 620 4 UPF A1360 O1B 144.1 92.9 72.9 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MN B2365 MN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP B1225 OD2 REMARK 620 2 ASP B1227 OD2 147.0 REMARK 620 3 ASP B1227 OD1 93.7 53.4 REMARK 620 4 HOH B2247 O 105.2 84.3 104.6 REMARK 620 5 UPF B2364 O1A 88.5 86.5 78.4 165.6 REMARK 620 6 UPF B2364 O1B 116.2 95.1 142.8 89.1 80.8 REMARK 620 N 1 2 3 4 5 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE UPF A1360 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MN A1361 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE UPF B2364 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MN B2365 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 1FG5 RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF BOVINE ALPHA-1,3- REMARK 900 GALACTOSYLTRANSFERASECATALYTIC DOMAIN. REMARK 900 RELATED ID: 1GWV RELATED DB: PDB REMARK 900 STRUCTURAL BASIS OF ORDERED BINDING OF DONOR AND ACCEPTOR REMARK 900 SUBSTRATES TO THE RETAINING GLYCOSYLTRANSFERASE: ALPHA -1,3 REMARK 900 GALACTOSYLTRANSFERASE REMARK 900 RELATED ID: 1GX0 RELATED DB: PDB REMARK 900 STRUCTURAL BASIS OF ORDERED BINDING OF DONOR AND ACCEPTOR REMARK 900 SUBSTRATES TO THE RETAINING GLYCOSYLTRANSFERASE: ALPHA -1,3 REMARK 900 GALACTOSYLTRANSFERASE REMARK 900 RELATED ID: 1GX4 RELATED DB: PDB REMARK 900 STRUCTURAL BASIS OF ORDERED BINDING OF DONOR AND ACCEPTOR REMARK 900 SUBSTRATES TO THE RETAINING GLYCOSYLTRANSFERASE: ALPHA -1,3 REMARK 900 GALACTOSYLTRANSFERASE REMARK 900 RELATED ID: 1K4V RELATED DB: PDB REMARK 900 1.53 A CRYSTAL STRUCTURE OF THE BETA- GALACTOSIDE-ALPHA-1,3- REMARK 900 GALACTOSYLTRANSFERASE IN COMPLEX WITH UDP REMARK 900 RELATED ID: 1O7Q RELATED DB: PDB REMARK 900 ROLES OF INDIVIDUAL RESIDUES OF ALPHA-1,3 GALACTOSYLTRANSFERASES IN REMARK 900 SUBSTRATE BINDING AND CATALYSIS REMARK 900 RELATED ID: 1VZT RELATED DB: PDB REMARK 900 ROLES ON INDIVIDUAL RESIDUES OF ALPHA-1,3 GALACTOSYLTRANSFERASES IN REMARK 900 SUBSTRATE BINDING AND CATALYSIS REMARK 900 RELATED ID: 1VZX RELATED DB: PDB REMARK 900 ROLES OF ACTIVE SITE TRYPTOPHANS IN SUBSTRATE BINDING AND CATALYSIS REMARK 900 BY ALPHA-1, 3 GALACTOSYLTRANSFERASE REMARK 900 RELATED ID: 2JCJ RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF ALPHA-1,3 GALACTOSYLTRANSFERASE (C-TERMINUS REMARK 900 TRUNCATED MUTANT-C3) IN COMPLEX WITH UDP AND TRIS REMARK 900 RELATED ID: 1G8O RELATED DB: PDB REMARK 900 CRYSTALLOGRAPHIC STRUCTURE OF THE NATIVE BOVINE ALPHA-1,3- REMARK 900 GALACTOSYLTRANSFERASE CATALYTIC DOMAIN REMARK 900 RELATED ID: 1G93 RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF THE BOVINE CATALYTIC DOMAIN OF ALPHA-1,3- REMARK 900 GALACTOSYLTRANSFERASE IN THE PRESENCE OF UDP-GALACTOSE REMARK 900 RELATED ID: 1GWW RELATED DB: PDB REMARK 900 STRUCTURAL BASIS OF ORDERED BINDING OF DONOR AND ACCEPTOR REMARK 900 SUBSTRATES TO THE RETAINING GLYCOSYLTRANSFERASE: ALPHA -1,3 REMARK 900 GALACTOSYLTRANSFERASE REMARK 900 RELATED ID: 1O7O RELATED DB: PDB REMARK 900 ROLES OF INDIVIDUAL RESIDUES OF ALPHA-1,3 GALACTOSYLTRANSFERASES IN REMARK 900 SUBSTRATE BINDING AND CATALYSIS REMARK 900 RELATED ID: 1VZU RELATED DB: PDB REMARK 900 ROLES OF ACTIVE SITE TRYPTOPHANS IN SUBSTRATE BINDING AND CATALYSIS REMARK 900 BY ALPHA-1, 3 GALACTOSYLTRANSFERASE REMARK 900 RELATED ID: 2JCK RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF ALPHA-1,3 GALACTOSYLTRANSFERASE (R365K) IN REMARK 900 COMPLEX WITH UDP AND 2 MANGANESE ION REMARK 900 RELATED ID: 2JCL RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF ALPHA-1,3 GALACTOSYLTRANSFERASE (R365K) IN THE REMARK 900 ABSENCE OF LIGANDS REMARK 900 RELATED ID: 2JCO RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF WILD TYPE ALPHA-1,3 GALACTOSYLTRANSFERASE IN REMARK 900 THE ABSENCE OF LIGANDS DBREF 2VFZ A 80 368 UNP P14769 GGTA1_BOVIN 80 368 DBREF 2VFZ B 1080 1368 UNP P14769 GGTA1_BOVIN 80 368 SEQADV 2VFZ LYS A 365 UNP P14769 ARG 365 ENGINEERED MUTATION SEQADV 2VFZ LYS B 1365 UNP P14769 ARG 365 ENGINEERED MUTATION SEQRES 1 A 289 GLU SER LYS LEU LYS LEU SER ASP TRP PHE ASN PRO PHE SEQRES 2 A 289 LYS ARG PRO GLU VAL VAL THR MET THR LYS TRP LYS ALA SEQRES 3 A 289 PRO VAL VAL TRP GLU GLY THR TYR ASN ARG ALA VAL LEU SEQRES 4 A 289 ASP ASN TYR TYR ALA LYS GLN LYS ILE THR VAL GLY LEU SEQRES 5 A 289 THR VAL PHE ALA VAL GLY ARG TYR ILE GLU HIS TYR LEU SEQRES 6 A 289 GLU GLU PHE LEU THR SER ALA ASN LYS HIS PHE MET VAL SEQRES 7 A 289 GLY HIS PRO VAL ILE PHE TYR ILE MET VAL ASP ASP VAL SEQRES 8 A 289 SER ARG MET PRO LEU ILE GLU LEU GLY PRO LEU ARG SER SEQRES 9 A 289 PHE LYS VAL PHE LYS ILE LYS PRO GLU LYS ARG TRP GLN SEQRES 10 A 289 ASP ILE SER MET MET ARG MET LYS THR ILE GLY GLU HIS SEQRES 11 A 289 ILE VAL ALA HIS ILE GLN HIS GLU VAL ASP PHE LEU PHE SEQRES 12 A 289 CYS MET ASP VAL ASP GLN VAL PHE GLN ASP LYS PHE GLY SEQRES 13 A 289 VAL GLU THR LEU GLY GLU SER VAL ALA GLN LEU GLN ALA SEQRES 14 A 289 TRP TRP TYR LYS ALA ASP PRO ASN ASP PHE THR TYR GLU SEQRES 15 A 289 ARG ARG LYS GLU SER ALA ALA TYR ILE PRO PHE GLY GLU SEQRES 16 A 289 GLY ASP PHE TYR TYR HIS ALA ALA ILE PHE GLY GLY THR SEQRES 17 A 289 PRO THR GLN VAL LEU ASN ILE THR GLN GLU CYS PHE LYS SEQRES 18 A 289 GLY ILE LEU LYS ASP LYS LYS ASN ASP ILE GLU ALA GLN SEQRES 19 A 289 TRP HIS ASP GLU SER HIS LEU ASN LYS TYR PHE LEU LEU SEQRES 20 A 289 ASN LYS PRO THR LYS ILE LEU SER PRO GLU TYR CYS TRP SEQRES 21 A 289 ASP TYR HIS ILE GLY LEU PRO ALA ASP ILE LYS LEU VAL SEQRES 22 A 289 LYS MET SER TRP GLN THR LYS GLU TYR ASN VAL VAL LYS SEQRES 23 A 289 ASN ASN VAL SEQRES 1 B 289 GLU SER LYS LEU LYS LEU SER ASP TRP PHE ASN PRO PHE SEQRES 2 B 289 LYS ARG PRO GLU VAL VAL THR MET THR LYS TRP LYS ALA SEQRES 3 B 289 PRO VAL VAL TRP GLU GLY THR TYR ASN ARG ALA VAL LEU SEQRES 4 B 289 ASP ASN TYR TYR ALA LYS GLN LYS ILE THR VAL GLY LEU SEQRES 5 B 289 THR VAL PHE ALA VAL GLY ARG TYR ILE GLU HIS TYR LEU SEQRES 6 B 289 GLU GLU PHE LEU THR SER ALA ASN LYS HIS PHE MET VAL SEQRES 7 B 289 GLY HIS PRO VAL ILE PHE TYR ILE MET VAL ASP ASP VAL SEQRES 8 B 289 SER ARG MET PRO LEU ILE GLU LEU GLY PRO LEU ARG SER SEQRES 9 B 289 PHE LYS VAL PHE LYS ILE LYS PRO GLU LYS ARG TRP GLN SEQRES 10 B 289 ASP ILE SER MET MET ARG MET LYS THR ILE GLY GLU HIS SEQRES 11 B 289 ILE VAL ALA HIS ILE GLN HIS GLU VAL ASP PHE LEU PHE SEQRES 12 B 289 CYS MET ASP VAL ASP GLN VAL PHE GLN ASP LYS PHE GLY SEQRES 13 B 289 VAL GLU THR LEU GLY GLU SER VAL ALA GLN LEU GLN ALA SEQRES 14 B 289 TRP TRP TYR LYS ALA ASP PRO ASN ASP PHE THR TYR GLU SEQRES 15 B 289 ARG ARG LYS GLU SER ALA ALA TYR ILE PRO PHE GLY GLU SEQRES 16 B 289 GLY ASP PHE TYR TYR HIS ALA ALA ILE PHE GLY GLY THR SEQRES 17 B 289 PRO THR GLN VAL LEU ASN ILE THR GLN GLU CYS PHE LYS SEQRES 18 B 289 GLY ILE LEU LYS ASP LYS LYS ASN ASP ILE GLU ALA GLN SEQRES 19 B 289 TRP HIS ASP GLU SER HIS LEU ASN LYS TYR PHE LEU LEU SEQRES 20 B 289 ASN LYS PRO THR LYS ILE LEU SER PRO GLU TYR CYS TRP SEQRES 21 B 289 ASP TYR HIS ILE GLY LEU PRO ALA ASP ILE LYS LEU VAL SEQRES 22 B 289 LYS MET SER TRP GLN THR LYS GLU TYR ASN VAL VAL LYS SEQRES 23 B 289 ASN ASN VAL HET UPF A1360 36 HET MN A1361 1 HET UPF B2364 36 HET MN B2365 1 HETNAM UPF URIDINE-5'-DIPHOSPHATE-2-DEOXY-2-FLUOROGALACTOSE HETNAM MN MANGANESE (II) ION HETSYN UPF URIDINE-5'-MONOPHOSPHATE 2-DEOXY-2-FLUORO- HETSYN 2 UPF GALACTOPYRANOSYL-MONOPHOSPHATE ESTER FORMUL 3 UPF 2(C15 H23 F N2 O16 P2) FORMUL 4 MN 2(MN 2+) FORMUL 7 HOH *497(H2 O) HELIX 1 1 LYS A 84 PHE A 89 1 6 HELIX 2 2 ASN A 90 ARG A 94 5 5 HELIX 3 3 ASN A 114 LYS A 126 1 13 HELIX 4 4 ARG A 138 TYR A 143 1 6 HELIX 5 5 TYR A 143 PHE A 155 1 13 HELIX 6 6 ASP A 169 MET A 173 5 5 HELIX 7 7 ARG A 194 MET A 201 1 8 HELIX 8 8 MET A 201 HIS A 213 1 13 HELIX 9 9 ILE A 214 GLU A 217 5 4 HELIX 10 10 GLY A 235 LEU A 239 5 5 HELIX 11 11 ASP A 254 PHE A 258 5 5 HELIX 12 12 THR A 287 ASN A 308 1 22 HELIX 13 13 HIS A 315 ASN A 327 1 13 HELIX 14 14 PRO A 335 CYS A 338 5 4 HELIX 15 15 ASP A 340 GLY A 344 5 5 HELIX 16 16 LYS B 1084 PHE B 1089 1 6 HELIX 17 17 ASN B 1090 ARG B 1094 5 5 HELIX 18 18 ASN B 1114 LYS B 1126 1 13 HELIX 19 19 ARG B 1138 PHE B 1155 1 18 HELIX 20 20 ASP B 1169 MET B 1173 5 5 HELIX 21 21 ARG B 1194 VAL B 1218 1 25 HELIX 22 22 GLY B 1235 LEU B 1239 5 5 HELIX 23 23 ASP B 1254 PHE B 1258 5 5 HELIX 24 24 THR B 1287 ASN B 1308 1 22 HELIX 25 25 HIS B 1315 ASN B 1327 1 13 HELIX 26 26 PRO B 1335 CYS B 1338 5 4 HELIX 27 27 ASP B 1340 GLY B 1344 5 5 SHEET 1 AA 8 VAL A 107 VAL A 108 0 SHEET 2 AA 8 LYS A 331 LEU A 333 1 O ILE A 332 N VAL A 108 SHEET 3 AA 8 SER A 242 LEU A 246 1 O ALA A 244 N LEU A 333 SHEET 4 AA 8 TYR A 279 GLY A 286 -1 N HIS A 280 O GLN A 245 SHEET 5 AA 8 PHE A 220 MET A 224 -1 O LEU A 221 N GLY A 286 SHEET 6 AA 8 VAL A 129 ALA A 135 1 O GLY A 130 N PHE A 222 SHEET 7 AA 8 VAL A 161 VAL A 167 1 O ILE A 162 N LEU A 131 SHEET 8 AA 8 ARG A 182 LYS A 188 1 O SER A 183 N PHE A 163 SHEET 1 AB 2 GLN A 228 PHE A 230 0 SHEET 2 AB 2 MET A 354 TRP A 356 -1 O SER A 355 N VAL A 229 SHEET 1 BA 8 VAL B1107 VAL B1108 0 SHEET 2 BA 8 LYS B1331 LEU B1333 1 O ILE B1332 N VAL B1108 SHEET 3 BA 8 SER B1242 LEU B1246 1 O SER B1242 N LYS B1331 SHEET 4 BA 8 TYR B1279 GLY B1286 -1 N HIS B1280 O GLN B1245 SHEET 5 BA 8 PHE B1220 MET B1224 -1 O LEU B1221 N GLY B1286 SHEET 6 BA 8 VAL B1129 ALA B1135 1 O GLY B1130 N PHE B1222 SHEET 7 BA 8 VAL B1161 VAL B1167 1 O ILE B1162 N LEU B1131 SHEET 8 BA 8 ARG B1182 LYS B1188 1 O SER B1183 N PHE B1163 SHEET 1 BB 2 GLN B1228 PHE B1230 0 SHEET 2 BB 2 MET B1354 TRP B1356 -1 O SER B1355 N VAL B1229 LINK OD1 ASP A 227 MN MN A1361 1555 1555 2.38 LINK OD2 ASP A 227 MN MN A1361 1555 1555 2.46 LINK O1A UPF A1360 MN MN A1361 1555 1555 2.44 LINK O1B UPF A1360 MN MN A1361 1555 1555 2.49 LINK OD2 ASP B1225 MN MN B2365 1555 1555 2.44 LINK OD2 ASP B1227 MN MN B2365 1555 1555 2.49 LINK OD1 ASP B1227 MN MN B2365 1555 1555 2.40 LINK O HOH B2247 MN MN B2365 1555 1555 2.46 LINK O1A UPF B2364 MN MN B2365 1555 1555 2.21 LINK O1B UPF B2364 MN MN B2365 1555 1555 2.35 SITE 1 AC1 17 PHE A 134 VAL A 136 TYR A 139 ILE A 198 SITE 2 AC1 17 SER A 199 ARG A 202 ASP A 225 VAL A 226 SITE 3 AC1 17 ASP A 227 HIS A 280 ALA A 281 ALA A 282 SITE 4 AC1 17 HIS A 315 ASP A 316 GLU A 317 LYS A 359 SITE 5 AC1 17 MN A1361 SITE 1 AC2 3 ASP A 225 ASP A 227 UPF A1360 SITE 1 AC3 21 PHE A 92 PHE B1134 ALA B1135 VAL B1136 SITE 2 AC3 21 TYR B1139 TRP B1195 ILE B1198 SER B1199 SITE 3 AC3 21 ARG B1202 ASP B1225 VAL B1226 ASP B1227 SITE 4 AC3 21 HIS B1280 ALA B1281 ALA B1282 HIS B1315 SITE 5 AC3 21 ASP B1316 GLU B1317 LYS B1359 HOH B2246 SITE 6 AC3 21 MN B2365 SITE 1 AC4 4 ASP B1225 ASP B1227 HOH B2247 UPF B2364 CRYST1 44.735 64.759 66.468 83.34 83.95 70.14 P 1 2 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 0.022354 -0.008074 -0.001683 0.00000 SCALE2 0.000000 0.016418 -0.001413 0.00000 SCALE3 0.000000 0.000000 0.015185 0.00000