HEADER TRANSFERASE 26-DEC-06 2JCK TITLE CRYSTAL STRUCTURE OF ALPHA-1,3 GALACTOSYLTRANSFERASE (R365K) IN TITLE 2 COMPLEX WITH UDP AND 2 MANGANESE ION COMPND MOL_ID: 1; COMPND 2 MOLECULE: N-ACETYLLACTOSAMINIDE ALPHA-1,3-GALACTOSYLTRANSFERASE; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: CATALYTIC DOMAIN, RESIDUES 80-368; COMPND 5 SYNONYM: GALACTOSYLTRANSFERASE, UDP-GALACTOSE\: BETA-D-GALACTOSYL-1, COMPND 6 4-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 (UDP), 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 SUBSTRATE SPECIFICITY, 3 GALACTOSYLTRANSFERASE, ALPHA-1, ENZYME KEYWDS 2 MECHANISM, GLYCOSYLTRANSFERASE GALACTOSYLTRANSFERASE, TRANSMEMBRANE, KEYWDS 3 GOLGI APPARATUS, GLYCOPROTEIN, METAL-BINDING, SIGNAL-ANCHOR, KEYWDS 4 MEMBRANE, MANGANESE, TRANSFERASE, GLYCOSYLTRANSFERASE EXPDTA X-RAY DIFFRACTION AUTHOR H.JAMALUDDIN,P.TUMBALE,S.G.WITHERS,K.R.ACHARYA,K.BREW REVDAT 4 13-DEC-23 2JCK 1 LINK REVDAT 3 24-FEB-09 2JCK 1 VERSN REVDAT 2 05-JUN-07 2JCK 1 JRNL REVDAT 1 22-MAY-07 2JCK 0 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. 1.80 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) : 1.80 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 24.84 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 DATA CUTOFF HIGH (ABS(F)) : 188273.080 REMARK 3 DATA CUTOFF LOW (ABS(F)) : 0.0000 REMARK 3 COMPLETENESS (WORKING+TEST) (%) : 90.6 REMARK 3 NUMBER OF REFLECTIONS : 31104 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) : 0.182 REMARK 3 FREE R VALUE : 0.192 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 3.300 REMARK 3 FREE R VALUE TEST SET COUNT : 1015 REMARK 3 ESTIMATED ERROR OF FREE R VALUE : 0.006 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) : 1.80 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.91 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 91.60 REMARK 3 REFLECTIONS IN BIN (WORKING SET) : 4994 REMARK 3 BIN R VALUE (WORKING SET) : 0.2140 REMARK 3 BIN FREE R VALUE : 0.2130 REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : 3.30 REMARK 3 BIN FREE R VALUE TEST SET COUNT : 168 REMARK 3 ESTIMATED ERROR OF BIN FREE R VALUE : 0.016 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 2315 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 27 REMARK 3 SOLVENT ATOMS : 409 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 13.20 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 17.60 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -1.98000 REMARK 3 B22 (A**2) : -2.83000 REMARK 3 B33 (A**2) : 4.81000 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : -3.03000 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM LUZZATI PLOT (A) : 0.18 REMARK 3 ESD FROM SIGMAA (A) : 0.13 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) : 0.19 REMARK 3 ESD FROM C-V SIGMAA (A) : 0.14 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 BOND LENGTHS (A) : 0.007 REMARK 3 BOND ANGLES (DEGREES) : 1.390 REMARK 3 DIHEDRAL ANGLES (DEGREES) : 23.50 REMARK 3 IMPROPER ANGLES (DEGREES) : 0.920 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) : 0.650 ; 1.500 REMARK 3 MAIN-CHAIN ANGLE (A**2) : 1.060 ; 2.000 REMARK 3 SIDE-CHAIN BOND (A**2) : 1.090 ; 2.000 REMARK 3 SIDE-CHAIN ANGLE (A**2) : 1.650 ; 2.500 REMARK 3 REMARK 3 BULK SOLVENT MODELING. REMARK 3 METHOD USED : FLAT MODEL REMARK 3 KSOL : 0.38 REMARK 3 BSOL : 49.23 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 : ION.PARAM REMARK 3 PARAMETER FILE 3 : WATER_REP.PARAM REMARK 3 PARAMETER FILE 4 : UDP.PAR REMARK 3 PARAMETER FILE 5 : NULL REMARK 3 TOPOLOGY FILE 1 : PROTEIN.TOP REMARK 3 TOPOLOGY FILE 2 : UDP.TOP REMARK 3 TOPOLOGY FILE 3 : NULL REMARK 3 TOPOLOGY FILE 4 : NULL REMARK 3 TOPOLOGY FILE 5 : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 2JCK COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 26-DEC-06. REMARK 100 THE DEPOSITION ID IS D_1290030927. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 25-SEP-05 REMARK 200 TEMPERATURE (KELVIN) : 100.0 REMARK 200 PH : 8.00 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) : 1.488 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 : 34457 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.800 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 (%) : 91.7 REMARK 200 DATA REDUNDANCY : 4.500 REMARK 200 R MERGE (I) : 0.10000 REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 9.0000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.80 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.86 REMARK 200 COMPLETENESS FOR SHELL (%) : 93.6 REMARK 200 DATA REDUNDANCY IN SHELL : 4.60 REMARK 200 R MERGE FOR SHELL (I) : 0.21000 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 <I/SIGMA(I)> FOR SHELL : 5.140 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: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 55.00 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.76 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.1M TRIS-HCL, PH 8.0, 10% PEG 6000, REMARK 280 AND 5% MPD, PH 8.00 REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: C 1 2 1 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 61.41200 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 34.12550 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 61.41200 REMARK 290 SMTRY2 4 0.000000 1.000000 0.000000 34.12550 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 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 375 REMARK 375 SPECIAL POSITION REMARK 375 THE FOLLOWING ATOMS ARE FOUND TO BE WITHIN 0.15 ANGSTROMS REMARK 375 OF A SYMMETRY RELATED ATOM AND ARE ASSUMED TO BE ON SPECIAL REMARK 375 POSITIONS. REMARK 375 REMARK 375 ATOM RES CSSEQI REMARK 375 HOH A2200 LIES ON A SPECIAL POSITION. REMARK 400 REMARK 400 COMPOUND REMARK 400 ENGINEERED RESIDUE IN CHAIN A, 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 1080 REMARK 465 SER A 1081 REMARK 465 LYS A 1082 REMARK 465 TYR A 1361 REMARK 465 ASN A 1362 REMARK 465 VAL A 1363 REMARK 465 VAL A 1364 REMARK 465 LYS A 1365 REMARK 465 ASN A 1366 REMARK 465 ASN A 1367 REMARK 465 VAL A 1368 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 A 2137 O HOH A 2138 1.93 REMARK 500 O HOH A 2244 O HOH A 2327 1.95 REMARK 500 O HOH A 2120 O HOH A 2121 1.97 REMARK 500 O HOH A 2086 O HOH A 2087 2.00 REMARK 500 O HOH A 2055 O HOH A 2271 2.04 REMARK 500 NE ARG A 1172 O HOH A 2198 2.05 REMARK 500 CB LYS A 1306 O HOH A 2347 2.05 REMARK 500 O HOH A 2345 O HOH A 2347 2.05 REMARK 500 O HOH A 2057 O HOH A 2374 2.06 REMARK 500 NH1 ARG A 1172 O HOH A 2199 2.10 REMARK 500 O HOH A 2128 O HOH A 2132 2.13 REMARK 500 O HOH A 2076 O HOH A 2329 2.17 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS REMARK 500 REMARK 500 THE FOLLOWING ATOMS THAT ARE RELATED BY CRYSTALLOGRAPHIC REMARK 500 SYMMETRY ARE IN CLOSE CONTACT. AN ATOM LOCATED WITHIN 0.15 REMARK 500 ANGSTROMS OF A SYMMETRY RELATED ATOM IS ASSUMED TO BE ON A REMARK 500 SPECIAL POSITION AND IS, THEREFORE, LISTED IN REMARK 375 REMARK 500 INSTEAD OF REMARK 500. ATOMS WITH NON-BLANK ALTERNATE REMARK 500 LOCATION INDICATORS ARE NOT INCLUDED IN THE CALCULATIONS. REMARK 500 REMARK 500 DISTANCE CUTOFF: REMARK 500 2.2 ANGSTROMS FOR CONTACTS NOT INVOLVING HYDROGEN ATOMS REMARK 500 1.6 ANGSTROMS FOR CONTACTS INVOLVING HYDROGEN ATOMS REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI SSYMOP DISTANCE REMARK 500 O HOH A 2171 O HOH A 2316 4545 1.96 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: COVALENT BOND LENGTHS REMARK 500 REMARK 500 THE STEREOCHEMICAL PARAMETERS OF THE FOLLOWING RESIDUES REMARK 500 HAVE VALUES WHICH DEVIATE FROM EXPECTED VALUES BY MORE REMARK 500 THAN 6*RMSD (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 500 IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT: (10X,I3,1X,2(A3,1X,A1,I4,A1,1X,A4,3X),1X,F6.3) REMARK 500 REMARK 500 EXPECTED VALUES PROTEIN: ENGH AND HUBER, 1999 REMARK 500 EXPECTED VALUES NUCLEIC ACID: CLOWNEY ET AL 1996 REMARK 500 REMARK 500 M RES CSSEQI ATM1 RES CSSEQI ATM2 DEVIATION REMARK 500 ARG A1172 CZ ARG A1172 NH1 -0.086 REMARK 500 ARG A1172 CZ ARG A1172 NH2 -0.159 REMARK 500 LYS A1300 CE LYS A1300 NZ -0.164 REMARK 500 LYS A1306 C LYS A1306 O -0.133 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: COVALENT BOND ANGLES REMARK 500 REMARK 500 THE STEREOCHEMICAL PARAMETERS OF THE FOLLOWING RESIDUES REMARK 500 HAVE VALUES WHICH DEVIATE FROM EXPECTED VALUES BY MORE REMARK 500 THAN 6*RMSD (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 500 IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT: (10X,I3,1X,A3,1X,A1,I4,A1,3(1X,A4,2X),12X,F5.1) REMARK 500 REMARK 500 EXPECTED VALUES PROTEIN: ENGH AND HUBER, 1999 REMARK 500 EXPECTED VALUES NUCLEIC ACID: CLOWNEY ET AL 1996 REMARK 500 REMARK 500 M RES CSSEQI ATM1 ATM2 ATM3 REMARK 500 ARG A1172 NE - CZ - NH1 ANGL. DEV. = 6.7 DEGREES REMARK 500 LYS A1300 CD - CE - NZ ANGL. DEV. = -17.7 DEGREES 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 ILE A1176 171.40 -59.57 REMARK 500 HIS A1213 -35.43 -149.38 REMARK 500 THR A1259 41.64 -85.02 REMARK 500 HIS A1315 -126.99 38.31 REMARK 500 CYS A1338 71.81 -168.41 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 A2086 DISTANCE = 6.15 ANGSTROMS REMARK 525 HOH A2088 DISTANCE = 5.93 ANGSTROMS REMARK 525 HOH A2090 DISTANCE = 6.11 ANGSTROMS REMARK 525 HOH A2093 DISTANCE = 6.09 ANGSTROMS REMARK 525 HOH A2096 DISTANCE = 6.10 ANGSTROMS REMARK 525 HOH A2100 DISTANCE = 6.59 ANGSTROMS REMARK 525 HOH A2102 DISTANCE = 6.75 ANGSTROMS REMARK 525 HOH A2103 DISTANCE = 5.91 ANGSTROMS REMARK 525 HOH A2104 DISTANCE = 8.92 ANGSTROMS REMARK 525 HOH A2106 DISTANCE = 7.16 ANGSTROMS REMARK 525 HOH A2107 DISTANCE = 7.88 ANGSTROMS REMARK 525 HOH A2108 DISTANCE = 6.37 ANGSTROMS REMARK 525 HOH A2109 DISTANCE = 6.64 ANGSTROMS REMARK 525 HOH A2110 DISTANCE = 7.19 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 A3362 MN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP A1225 OD2 REMARK 620 2 ASP A1227 OD1 102.0 REMARK 620 3 ASP A1227 OD2 157.2 55.6 REMARK 620 4 HOH A2406 O 103.8 95.5 77.0 REMARK 620 5 UDP A3361 O1A 92.7 86.6 90.2 162.5 REMARK 620 6 UDP A3361 O1B 97.5 158.8 105.3 87.9 84.1 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 A3362 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MN A3363 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE UDP A3361 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: 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: 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: 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: 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: 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: 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: 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: 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: 2JCF 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: 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: 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 2JCK A 1080 1368 UNP P14769 GGTA1_BOVIN 80 368 SEQADV 2JCK LYS A 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 HET UDP A3361 25 HET MN A3362 1 HET MN A3363 1 HETNAM UDP URIDINE-5'-DIPHOSPHATE HETNAM MN MANGANESE (II) ION FORMUL 2 UDP C9 H14 N2 O12 P2 FORMUL 3 MN 2(MN 2+) FORMUL 5 HOH *409(H2 O) HELIX 1 1 LYS A 1084 PHE A 1089 1 6 HELIX 2 2 ASN A 1090 ARG A 1094 5 5 HELIX 3 3 ASN A 1114 LYS A 1126 1 13 HELIX 4 4 ARG A 1138 PHE A 1155 1 18 HELIX 5 5 ASP A 1169 MET A 1173 5 5 HELIX 6 6 ARG A 1194 HIS A 1213 1 20 HELIX 7 7 HIS A 1213 VAL A 1218 1 6 HELIX 8 8 GLY A 1235 LEU A 1239 5 5 HELIX 9 9 ASP A 1254 PHE A 1258 5 5 HELIX 10 10 THR A 1287 ASN A 1308 1 22 HELIX 11 11 TRP A 1314 ASN A 1327 1 14 HELIX 12 12 PRO A 1335 CYS A 1338 5 4 HELIX 13 13 ASP A 1340 GLY A 1344 5 5 SHEET 1 AA 8 VAL A1107 VAL A1108 0 SHEET 2 AA 8 LYS A1331 LEU A1333 1 O ILE A1332 N VAL A1108 SHEET 3 AA 8 SER A1242 LEU A1246 1 O SER A1242 N LYS A1331 SHEET 4 AA 8 TYR A1279 GLY A1286 -1 N HIS A1280 O GLN A1245 SHEET 5 AA 8 PHE A1220 MET A1224 -1 O LEU A1221 N GLY A1286 SHEET 6 AA 8 VAL A1129 ALA A1135 1 O GLY A1130 N PHE A1222 SHEET 7 AA 8 VAL A1161 VAL A1167 1 O ILE A1162 N LEU A1131 SHEET 8 AA 8 ARG A1182 LYS A1188 1 O SER A1183 N PHE A1163 SHEET 1 AB 2 GLN A1228 PHE A1230 0 SHEET 2 AB 2 MET A1354 TRP A1356 -1 O SER A1355 N VAL A1229 LINK OD2 ASP A1225 MN MN A3362 1555 1555 2.22 LINK OD1 ASP A1227 MN MN A3362 1555 1555 2.20 LINK OD2 ASP A1227 MN MN A3362 1555 1555 2.51 LINK O HOH A2406 MN MN A3362 1555 1555 2.40 LINK O1A UDP A3361 MN MN A3362 1555 1555 2.34 LINK O1B UDP A3361 MN MN A3362 1555 1555 2.30 SITE 1 AC1 4 ASP A1225 ASP A1227 HOH A2406 UDP A3361 SITE 1 AC2 4 GLN A1247 HIS A1280 GLU A1317 HOH A2407 SITE 1 AC3 19 LYS A1102 LYS A1104 PHE A1134 ALA A1135 SITE 2 AC3 19 VAL A1136 TYR A1139 ILE A1198 SER A1199 SITE 3 AC3 19 ARG A1202 ASP A1225 VAL A1226 ASP A1227 SITE 4 AC3 19 GLU A1360 HOH A2257 HOH A2403 HOH A2404 SITE 5 AC3 19 HOH A2405 HOH A2407 MN A3362 CRYST1 122.824 68.251 44.732 90.00 90.19 90.00 C 1 2 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 0.008142 0.000000 0.000028 0.00000 SCALE2 0.000000 0.014652 0.000000 0.00000 SCALE3 0.000000 0.000000 0.022355 0.00000