HEADER TRANSFERASE 18-APR-08 2VS5 TITLE THE BINDING OF UDP-GALACTOSE BY AN ACTIVE SITE MUTANT OF ALPHA-1,3 TITLE 2 GALACTOSYLTRANSFERASE (ALPHA3GT) COMPND MOL_ID: 1; COMPND 2 MOLECULE: N-ACETYLLACTOSAMINIDE ALPHA-1,3-GALACTOSYLTRANSFERASE; COMPND 3 CHAIN: A, B; COMPND 4 FRAGMENT: RESIDUES 80-365; COMPND 5 SYNONYM: GALACTOSYLTRANSFERASE, UDP-GALACTOSE\: BETA-D-GALACTOSYL-1, COMPND 6 4-N-ACETYL-D-GLUCOSAMINIDE ALPHA-1,3-GALACTOSYLTRANSFERASE, ALPHA-1,3 COMPND 7 GALACTOSYLTRANSFERASE; COMPND 8 EC: 2.4.1.87; COMPND 9 ENGINEERED: YES; COMPND 10 MUTATION: YES 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 MANGANESE, TRANSFERASE, GLYCOPROTEIN, METAL-BINDING, ACTIVE-SITE KEYWDS 2 MUTANT, GLYCOSYLTRANSFERASE, N-ACETYL LACTOSAMINE, SIGNAL-ANCHOR, KEYWDS 3 TRANSMEMBRANE, GOLGI APPARATUS, GT, UDP, MEMBRANE, ALPHA3GT, KEYWDS 4 GALACTOSE, ALPHA-3GT EXPDTA X-RAY DIFFRACTION AUTHOR P.TUMBALE,H.JAMALUDDIN,N.THIYAGARAJAN,K.BREW,K.R.ACHARYA REVDAT 5 13-DEC-23 2VS5 1 LINK REVDAT 4 24-FEB-09 2VS5 1 VERSN REVDAT 3 19-AUG-08 2VS5 1 JRNL REVDAT 2 05-AUG-08 2VS5 1 JRNL REVDAT 1 15-JUL-08 2VS5 0 JRNL AUTH P.TUMBALE,H.JAMALUDDIN,N.THIYAGARAJAN,K.BREW,K.R.ACHARYA JRNL TITL STRUCTURAL BASIS OF UDP-GALACTOSE BINDING BY ALPHA- JRNL TITL 2 1,3-GALACTOSYLTRANSFERASE (ALPHA3GT): ROLE OF NEGATIVE JRNL TITL 3 CHARGE ON ASPARTIC ACID 316 IN STRUCTURE AND ACTIVITY. JRNL REF BIOCHEMISTRY V. 47 8711 2008 JRNL REFN ISSN 0006-2960 JRNL PMID 18651752 JRNL DOI 10.1021/BI800852A REMARK 2 REMARK 2 RESOLUTION. 1.82 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : CNS 1.2 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) : 1.82 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 24.57 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 DATA CUTOFF HIGH (ABS(F)) : 164786.090 REMARK 3 DATA CUTOFF LOW (ABS(F)) : 0.0000 REMARK 3 COMPLETENESS (WORKING+TEST) (%) : 75.9 REMARK 3 NUMBER OF REFLECTIONS : 51818 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) : 0.236 REMARK 3 FREE R VALUE : 0.242 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 12.100 REMARK 3 FREE R VALUE TEST SET COUNT : 6257 REMARK 3 ESTIMATED ERROR OF FREE R VALUE : 0.003 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) : 1.82 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.93 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 54.50 REMARK 3 REFLECTIONS IN BIN (WORKING SET) : 5426 REMARK 3 BIN R VALUE (WORKING SET) : 0.3330 REMARK 3 BIN FREE R VALUE : 0.3220 REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : 11.30 REMARK 3 BIN FREE R VALUE TEST SET COUNT : 690 REMARK 3 ESTIMATED ERROR OF BIN FREE R VALUE : 0.012 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 4640 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 83 REMARK 3 SOLVENT ATOMS : 723 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 13.40 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 18.80 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -0.48000 REMARK 3 B22 (A**2) : 4.65000 REMARK 3 B33 (A**2) : -4.17000 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : 0.00000 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM LUZZATI PLOT (A) : 0.27 REMARK 3 ESD FROM SIGMAA (A) : 0.29 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) : 0.28 REMARK 3 ESD FROM C-V SIGMAA (A) : 0.28 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 BOND LENGTHS (A) : 0.006 REMARK 3 BOND ANGLES (DEGREES) : 1.300 REMARK 3 DIHEDRAL ANGLES (DEGREES) : 23.70 REMARK 3 IMPROPER ANGLES (DEGREES) : 0.810 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) : 0.000 ; 1.500 REMARK 3 MAIN-CHAIN ANGLE (A**2) : 0.000 ; 2.000 REMARK 3 SIDE-CHAIN BOND (A**2) : 0.000 ; 2.000 REMARK 3 SIDE-CHAIN ANGLE (A**2) : 0.000 ; 2.500 REMARK 3 REMARK 3 BULK SOLVENT MODELING. REMARK 3 METHOD USED : FLAT MODEL REMARK 3 KSOL : 0.40 REMARK 3 BSOL : 32.98 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 : GDU-MPD.PAR REMARK 3 PARAMETER FILE 4 : ION.PARAM 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 : GDU-MPD.TOP REMARK 3 TOPOLOGY FILE 4 : ION.TOP REMARK 3 TOPOLOGY FILE 5 : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: BULK SOLVENT MODEL USED REMARK 4 REMARK 4 2VS5 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 18-APR-08. REMARK 100 THE DEPOSITION ID IS D_1290035941. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 09-NOV-05 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 6.0 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : SRS REMARK 200 BEAMLINE : PX14.2 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.979 REMARK 200 MONOCHROMATOR : SI(III) 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 : 68394 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.820 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 (%) : 97.9 REMARK 200 DATA REDUNDANCY : 6.400 REMARK 200 R MERGE (I) : 0.10000 REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 7.8000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.82 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.89 REMARK 200 COMPLETENESS FOR SHELL (%) : 97.9 REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : 0.52000 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 <I/SIGMA(I)> FOR SHELL : 2.500 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: PDB ENTRY 1K4V REMARK 200 REMARK 200 REMARK: NONE REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 55.60 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.80 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: PROTEIN: 10 % GLYCEROL, 20 MM MES-NAOH REMARK 280 PH 6.0, 10 MM MNCL2, 10 MM UDP-GAL, MOTHER LIQUOR: 10 % PEG 6000, REMARK 280 0.1 M TRIS-HCL PH 8.0, 8 % MPD REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 21 21 21 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X+1/2,-Y,Z+1/2 REMARK 290 3555 -X,Y+1/2,-Z+1/2 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 43.51350 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 47.31500 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 45.68500 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 47.31500 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 43.51350 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 45.68500 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000 REMARK 290 REMARK 290 REMARK: NULL REMARK 300 REMARK 300 BIOMOLECULE: 1, 2 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 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC REMARK 350 SOFTWARE USED: PQS 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 350 REMARK 350 BIOMOLECULE: 2 REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: MONOMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC REMARK 350 SOFTWARE USED: PQS REMARK 350 APPLY THE FOLLOWING TO CHAINS: 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, GLU 317 TO GLN REMARK 400 ENGINEERED RESIDUE IN CHAIN B, GLU 317 TO GLN 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 LYS A 82 REMARK 465 GLU B 80 REMARK 465 SER B 81 REMARK 465 GLU B 360 REMARK 465 TYR B 361 REMARK 465 ASN B 362 REMARK 465 VAL B 363 REMARK 465 VAL B 364 REMARK 465 ARG B 365 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 LYS A 359 CB CG CD CE NZ REMARK 470 GLU A 360 CB CG CD OE1 OE2 REMARK 470 TYR A 361 CB CG CD1 CD2 CE1 CE2 CZ REMARK 470 TYR A 361 OH REMARK 470 ASN A 362 CB CG OD1 ND2 REMARK 470 VAL A 363 CB CG1 CG2 REMARK 470 VAL A 364 CB CG1 CG2 REMARK 470 LYS B 359 CA C O CB CG CD CE REMARK 470 LYS B 359 NZ 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 O HOH B 2183 O HOH B 2337 1.75 REMARK 500 O HOH B 2079 O HOH B 2101 1.96 REMARK 500 O HOH A 2199 O HOH A 2202 2.09 REMARK 500 O HOH B 2027 O HOH B 2186 2.11 REMARK 500 OG1 THR A 358 O HOH A 2343 2.11 REMARK 500 O HOH A 2109 O HOH A 2273 2.19 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 MET A 173 102.21 -52.09 REMARK 500 HIS A 213 -39.60 -150.31 REMARK 500 HIS A 315 -128.14 42.54 REMARK 500 CYS A 338 67.79 -160.93 REMARK 500 LEU A 345 73.24 -152.13 REMARK 500 THR A 358 -51.56 -19.30 REMARK 500 LYS A 359 -38.08 122.73 REMARK 500 GLU A 360 -129.89 109.85 REMARK 500 TYR A 361 -10.67 109.96 REMARK 500 ASN A 362 -83.45 -133.04 REMARK 500 VAL A 363 -144.46 -76.98 REMARK 500 VAL A 364 -53.45 68.94 REMARK 500 ILE B 176 171.42 -55.35 REMARK 500 HIS B 213 -38.24 -152.54 REMARK 500 HIS B 315 -127.16 41.64 REMARK 500 CYS B 338 61.67 -160.53 REMARK 500 THR B 358 163.94 -46.38 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 = 6.03 ANGSTROMS REMARK 525 HOH A2072 DISTANCE = 6.33 ANGSTROMS REMARK 525 HOH B2064 DISTANCE = 6.14 ANGSTROMS REMARK 525 HOH B2083 DISTANCE = 6.07 ANGSTROMS REMARK 525 HOH B2085 DISTANCE = 6.49 ANGSTROMS REMARK 525 HOH B2097 DISTANCE = 5.97 ANGSTROMS REMARK 525 HOH B2100 DISTANCE = 6.51 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 A1366 MN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP A 225 OD2 REMARK 620 2 ASP A 227 OD1 102.2 REMARK 620 3 GDU A1368 O1A 97.8 81.3 REMARK 620 4 HOH A2348 O 100.1 105.5 158.9 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MN B1360 MN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP B 225 OD2 REMARK 620 2 ASP B 227 OD2 153.9 REMARK 620 3 ASP B 227 OD1 99.4 55.4 REMARK 620 4 GDU B1361 O2B 113.3 89.2 142.9 REMARK 620 5 GDU B1361 O1A 93.7 77.8 83.2 77.7 REMARK 620 6 HOH B2364 O 100.6 92.8 103.2 88.2 163.1 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 MN A1366 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MN A1367 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GDU A1368 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MN B1360 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GDU B1361 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MPD B1362 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 2VS4 RELATED DB: PDB REMARK 900 THE BINDING OF UDP-GALACTOSE BY AN ACTIVE SITE MUTANT OF ALPHA-1,3 REMARK 900 GALACTOSYLTRANSFERASE (ALPHA3GT) 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: 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: 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: 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: 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: 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: 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: 2VFZ RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF ALPHA-1,3 GALACTOSYLTRANSFERASE (R365K) IN REMARK 900 COMPLEX WITH UDP-2F-GALACTOSE 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: 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: 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: 1G8O RELATED DB: PDB REMARK 900 CRYSTALLOGRAPHIC STRUCTURE OF THE NATIVE BOVINE ALPHA-1,3- REMARK 900 GALACTOSYLTRANSFERASE CATALYTIC DOMAIN REMARK 900 RELATED ID: 2VS3 RELATED DB: PDB REMARK 900 THE BINDING OF UDP-GALACTOSE BY AN ACTIVE SITE MUTANT OF ALPHA-1,3 REMARK 900 GALACTOSYLTRANSFERASE (ALPHA3GT) 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: 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: 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 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: 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 DBREF 2VS5 A 80 365 UNP P14769 GGTA1_BOVIN 80 365 DBREF 2VS5 B 80 365 UNP P14769 GGTA1_BOVIN 80 365 SEQADV 2VS5 GLN A 317 UNP P14769 GLU 317 ENGINEERED MUTATION SEQADV 2VS5 GLN B 317 UNP P14769 GLU 317 ENGINEERED MUTATION SEQRES 1 A 286 GLU SER LYS LEU LYS LEU SER ASP TRP PHE ASN PRO PHE SEQRES 2 A 286 LYS ARG PRO GLU VAL VAL THR MET THR LYS TRP LYS ALA SEQRES 3 A 286 PRO VAL VAL TRP GLU GLY THR TYR ASN ARG ALA VAL LEU SEQRES 4 A 286 ASP ASN TYR TYR ALA LYS GLN LYS ILE THR VAL GLY LEU SEQRES 5 A 286 THR VAL PHE ALA VAL GLY ARG TYR ILE GLU HIS TYR LEU SEQRES 6 A 286 GLU GLU PHE LEU THR SER ALA ASN LYS HIS PHE MET VAL SEQRES 7 A 286 GLY HIS PRO VAL ILE PHE TYR ILE MET VAL ASP ASP VAL SEQRES 8 A 286 SER ARG MET PRO LEU ILE GLU LEU GLY PRO LEU ARG SER SEQRES 9 A 286 PHE LYS VAL PHE LYS ILE LYS PRO GLU LYS ARG TRP GLN SEQRES 10 A 286 ASP ILE SER MET MET ARG MET LYS THR ILE GLY GLU HIS SEQRES 11 A 286 ILE VAL ALA HIS ILE GLN HIS GLU VAL ASP PHE LEU PHE SEQRES 12 A 286 CYS MET ASP VAL ASP GLN VAL PHE GLN ASP LYS PHE GLY SEQRES 13 A 286 VAL GLU THR LEU GLY GLU SER VAL ALA GLN LEU GLN ALA SEQRES 14 A 286 TRP TRP TYR LYS ALA ASP PRO ASN ASP PHE THR TYR GLU SEQRES 15 A 286 ARG ARG LYS GLU SER ALA ALA TYR ILE PRO PHE GLY GLU SEQRES 16 A 286 GLY ASP PHE TYR TYR HIS ALA ALA ILE PHE GLY GLY THR SEQRES 17 A 286 PRO THR GLN VAL LEU ASN ILE THR GLN GLU CYS PHE LYS SEQRES 18 A 286 GLY ILE LEU LYS ASP LYS LYS ASN ASP ILE GLU ALA GLN SEQRES 19 A 286 TRP HIS ASP GLN SER HIS LEU ASN LYS TYR PHE LEU LEU SEQRES 20 A 286 ASN LYS PRO THR LYS ILE LEU SER PRO GLU TYR CYS TRP SEQRES 21 A 286 ASP TYR HIS ILE GLY LEU PRO ALA ASP ILE LYS LEU VAL SEQRES 22 A 286 LYS MET SER TRP GLN THR LYS GLU TYR ASN VAL VAL ARG SEQRES 1 B 286 GLU SER LYS LEU LYS LEU SER ASP TRP PHE ASN PRO PHE SEQRES 2 B 286 LYS ARG PRO GLU VAL VAL THR MET THR LYS TRP LYS ALA SEQRES 3 B 286 PRO VAL VAL TRP GLU GLY THR TYR ASN ARG ALA VAL LEU SEQRES 4 B 286 ASP ASN TYR TYR ALA LYS GLN LYS ILE THR VAL GLY LEU SEQRES 5 B 286 THR VAL PHE ALA VAL GLY ARG TYR ILE GLU HIS TYR LEU SEQRES 6 B 286 GLU GLU PHE LEU THR SER ALA ASN LYS HIS PHE MET VAL SEQRES 7 B 286 GLY HIS PRO VAL ILE PHE TYR ILE MET VAL ASP ASP VAL SEQRES 8 B 286 SER ARG MET PRO LEU ILE GLU LEU GLY PRO LEU ARG SER SEQRES 9 B 286 PHE LYS VAL PHE LYS ILE LYS PRO GLU LYS ARG TRP GLN SEQRES 10 B 286 ASP ILE SER MET MET ARG MET LYS THR ILE GLY GLU HIS SEQRES 11 B 286 ILE VAL ALA HIS ILE GLN HIS GLU VAL ASP PHE LEU PHE SEQRES 12 B 286 CYS MET ASP VAL ASP GLN VAL PHE GLN ASP LYS PHE GLY SEQRES 13 B 286 VAL GLU THR LEU GLY GLU SER VAL ALA GLN LEU GLN ALA SEQRES 14 B 286 TRP TRP TYR LYS ALA ASP PRO ASN ASP PHE THR TYR GLU SEQRES 15 B 286 ARG ARG LYS GLU SER ALA ALA TYR ILE PRO PHE GLY GLU SEQRES 16 B 286 GLY ASP PHE TYR TYR HIS ALA ALA ILE PHE GLY GLY THR SEQRES 17 B 286 PRO THR GLN VAL LEU ASN ILE THR GLN GLU CYS PHE LYS SEQRES 18 B 286 GLY ILE LEU LYS ASP LYS LYS ASN ASP ILE GLU ALA GLN SEQRES 19 B 286 TRP HIS ASP GLN SER HIS LEU ASN LYS TYR PHE LEU LEU SEQRES 20 B 286 ASN LYS PRO THR LYS ILE LEU SER PRO GLU TYR CYS TRP SEQRES 21 B 286 ASP TYR HIS ILE GLY LEU PRO ALA ASP ILE LYS LEU VAL SEQRES 22 B 286 LYS MET SER TRP GLN THR LYS GLU TYR ASN VAL VAL ARG HET MN A1366 1 HET MN A1367 1 HET GDU A1368 36 HET MN B1360 1 HET GDU B1361 36 HET MPD B1362 8 HETNAM MN MANGANESE (II) ION HETNAM GDU GALACTOSE-URIDINE-5'-DIPHOSPHATE HETNAM MPD (4S)-2-METHYL-2,4-PENTANEDIOL HETSYN GDU UDP-D-GALACTOPYRANOSE FORMUL 3 MN 3(MN 2+) FORMUL 5 GDU 2(C15 H24 N2 O17 P2) FORMUL 8 MPD C6 H14 O2 FORMUL 9 HOH *723(H2 O) HELIX 1 1 LYS A 84 TRP A 88 5 5 HELIX 2 2 ASN A 90 ARG A 94 5 5 HELIX 3 3 ASN A 114 GLN A 125 1 12 HELIX 4 4 ARG A 138 PHE A 155 1 18 HELIX 5 5 ASP A 169 MET A 173 5 5 HELIX 6 6 ARG A 194 VAL A 218 1 25 HELIX 7 7 GLY A 235 LEU A 239 5 5 HELIX 8 8 ASP A 254 PHE A 258 5 5 HELIX 9 9 THR A 287 ASN A 308 1 22 HELIX 10 10 TRP A 314 ASN A 327 1 14 HELIX 11 11 PRO A 335 CYS A 338 5 4 HELIX 12 12 ASP A 340 GLY A 344 5 5 HELIX 13 13 LYS B 84 TRP B 88 5 5 HELIX 14 14 ASN B 90 ARG B 94 5 5 HELIX 15 15 ASN B 114 LYS B 126 1 13 HELIX 16 16 ARG B 138 PHE B 155 1 18 HELIX 17 17 ASP B 169 MET B 173 5 5 HELIX 18 18 ARG B 194 MET B 201 1 8 HELIX 19 19 MET B 201 HIS B 213 1 13 HELIX 20 20 ILE B 214 GLU B 217 5 4 HELIX 21 21 GLY B 235 LEU B 239 5 5 HELIX 22 22 ASP B 254 PHE B 258 5 5 HELIX 23 23 THR B 287 ASN B 308 1 22 HELIX 24 24 TRP B 314 ASN B 327 1 14 HELIX 25 25 PRO B 335 CYS B 338 5 4 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 B 107 VAL B 108 0 SHEET 2 BA 8 LYS B 331 LEU B 333 1 O ILE B 332 N VAL B 108 SHEET 3 BA 8 SER B 242 LEU B 246 1 O ALA B 244 N LEU B 333 SHEET 4 BA 8 TYR B 279 GLY B 286 -1 N HIS B 280 O GLN B 245 SHEET 5 BA 8 PHE B 220 MET B 224 -1 O LEU B 221 N GLY B 286 SHEET 6 BA 8 VAL B 129 ALA B 135 1 O GLY B 130 N PHE B 222 SHEET 7 BA 8 VAL B 161 VAL B 167 1 O ILE B 162 N LEU B 131 SHEET 8 BA 8 ARG B 182 LYS B 188 1 O SER B 183 N PHE B 163 SHEET 1 BB 2 GLN B 228 PHE B 230 0 SHEET 2 BB 2 MET B 354 TRP B 356 -1 O SER B 355 N VAL B 229 LINK OD2 ASP A 225 MN MN A1366 1555 1555 2.26 LINK OD1 ASP A 227 MN MN A1366 1555 1555 2.30 LINK OD2 ASP A 340 MN MN A1367 1555 1555 2.27 LINK MN MN A1366 O1A GDU A1368 1555 1555 2.38 LINK MN MN A1366 O HOH A2348 1555 1555 2.25 LINK OD2 ASP B 225 MN MN B1360 1555 1555 2.25 LINK OD2 ASP B 227 MN MN B1360 1555 1555 2.47 LINK OD1 ASP B 227 MN MN B1360 1555 1555 2.26 LINK MN MN B1360 O2B GDU B1361 1555 1555 2.38 LINK MN MN B1360 O1A GDU B1361 1555 1555 2.24 LINK MN MN B1360 O HOH B2364 1555 1555 2.33 SITE 1 AC1 5 ASP A 225 ASP A 227 GDU A1368 HOH A2348 SITE 2 AC1 5 HOH A2354 SITE 1 AC2 3 ASP A 340 HIS A 342 HOH A2349 SITE 1 AC3 27 PHE A 134 ALA A 135 VAL A 136 TYR A 139 SITE 2 AC3 27 TRP A 195 ILE A 198 SER A 199 ARG A 202 SITE 3 AC3 27 ASP A 225 VAL A 226 ASP A 227 HIS A 280 SITE 4 AC3 27 ALA A 281 ALA A 282 TRP A 314 HIS A 315 SITE 5 AC3 27 ASP A 316 GLN A 317 VAL A 364 ARG A 365 SITE 6 AC3 27 MN A1366 HOH A2205 HOH A2350 HOH A2351 SITE 7 AC3 27 HOH A2352 HOH A2353 HOH A2354 SITE 1 AC4 4 ASP B 225 ASP B 227 GDU B1361 HOH B2364 SITE 1 AC5 24 PHE B 134 ALA B 135 VAL B 136 TYR B 139 SITE 2 AC5 24 TRP B 195 ILE B 198 SER B 199 ARG B 202 SITE 3 AC5 24 ASP B 225 VAL B 226 ASP B 227 HIS B 280 SITE 4 AC5 24 ALA B 281 ALA B 282 TRP B 314 HIS B 315 SITE 5 AC5 24 ASP B 316 GLN B 317 MN B1360 HOH B2217 SITE 6 AC5 24 HOH B2329 HOH B2365 HOH B2366 HOH B2367 SITE 1 AC6 4 ARG B 194 ASP B 197 LYS B 306 HOH B2167 CRYST1 87.027 91.370 94.630 90.00 90.00 90.00 P 21 21 21 8 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 0.011491 0.000000 0.000000 0.00000 SCALE2 0.000000 0.010945 0.000000 0.00000 SCALE3 0.000000 0.000000 0.010567 0.00000