HEADER TRANSFERASE 26-DEC-06 2JCL TITLE CRYSTAL STRUCTURE OF ALPHA-1,3 GALACTOSYLTRANSFERASE (R365K) IN THE TITLE 2 ABSENCE OF LIGANDS COMPND MOL_ID: 1; COMPND 2 MOLECULE: N-ACETYLLACTOSAMINIDE ALPHA-1,3-GALACTOSYLTRANSFERASE; COMPND 3 CHAIN: A, B; 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: SULPHATE 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 TRANSMEMBRANE, GOLGI APPARATUS, ENZYME MECHANISM, GLYCOPROTEIN, KEYWDS 2 METAL-BINDING, SIGNAL-ANCHOR, ALPHA-1, MEMBRANE, MANGANESE, KEYWDS 3 TRANSFERASE, GLYCOSYLTRANSFERASE, SUBSTRATE SPECIFICITY EXPDTA X-RAY DIFFRACTION AUTHOR H.JAMALUDDIN,P.TUMBALE,S.G.WITHERS,K.R.ACHARYA,K.BREW REVDAT 4 13-DEC-23 2JCL 1 REMARK REVDAT 3 24-FEB-09 2JCL 1 VERSN REVDAT 2 05-JUN-07 2JCL 1 JRNL REVDAT 1 22-MAY-07 2JCL 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. 3.29 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.2.0019 REMARK 3 AUTHORS : MURSHUDOV,SKUBAK,LEBEDEV,PANNU,STEINER, REMARK 3 : NICHOLLS,WINN,LONG,VAGIN REMARK 3 REMARK 3 REFINEMENT TARGET : MAXIMUM LIKELIHOOD REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 3.29 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 25.81 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 99.1 REMARK 3 NUMBER OF REFLECTIONS : 17707 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 + TEST SET) : 0.208 REMARK 3 R VALUE (WORKING SET) : 0.205 REMARK 3 FREE R VALUE : 0.280 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.100 REMARK 3 FREE R VALUE TEST SET COUNT : 960 REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : 20 REMARK 3 BIN RESOLUTION RANGE HIGH (A) : 3.29 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 3.38 REMARK 3 REFLECTION IN BIN (WORKING SET) : 1212 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 95.48 REMARK 3 BIN R VALUE (WORKING SET) : 0.2540 REMARK 3 BIN FREE R VALUE SET COUNT : 76 REMARK 3 BIN FREE R VALUE : 0.2710 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 4612 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 25 REMARK 3 SOLVENT ATOMS : 61 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 36.12 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 0.14000 REMARK 3 B22 (A**2) : -0.19000 REMARK 3 B33 (A**2) : 0.05000 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 OVERALL COORDINATE ERROR. REMARK 3 ESU BASED ON R VALUE (A): NULL REMARK 3 ESU BASED ON FREE R VALUE (A): 0.487 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.342 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 20.290 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.902 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.835 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 4778 ; 0.015 ; 0.022 REMARK 3 BOND LENGTHS OTHERS (A): NULL ; NULL ; NULL REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 6478 ; 1.544 ; 1.938 REMARK 3 BOND ANGLES OTHERS (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 552 ; 6.676 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 230 ;39.741 ;24.000 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 826 ;20.637 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 18 ;21.265 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 672 ; 0.103 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 3626 ; 0.005 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): 2950 ; 0.259 ; 0.200 REMARK 3 NON-BONDED CONTACTS OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): 3311 ; 0.335 ; 0.200 REMARK 3 NON-BONDED TORSION OTHERS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): 262 ; 0.161 ; 0.200 REMARK 3 H-BOND (X...Y) OTHERS (A): NULL ; NULL ; NULL REMARK 3 POTENTIAL METAL-ION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 POTENTIAL METAL-ION OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY VDW REFINED ATOMS (A): 38 ; 0.227 ; 0.200 REMARK 3 SYMMETRY VDW OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY METAL-ION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY METAL-ION OTHERS (A): NULL ; NULL ; NULL REMARK 3 REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. COUNT RMS WEIGHT REMARK 3 MAIN-CHAIN BOND REFINED ATOMS (A**2): 2815 ; 0.795 ; 1.500 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 4500 ; 1.419 ; 2.000 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 2285 ; 1.409 ; 3.000 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 1978 ; 2.352 ; 4.500 REMARK 3 SIDE-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 LONG RANGE B REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 LONG RANGE B OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 REMARK 3 ANISOTROPIC THERMAL FACTOR RESTRAINTS. COUNT RMS WEIGHT REMARK 3 RIGID-BOND RESTRAINTS (A**2): NULL ; NULL ; NULL REMARK 3 SPHERICITY; FREE ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SPHERICITY; BONDED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 REMARK 3 NCS RESTRAINTS STATISTICS REMARK 3 NUMBER OF DIFFERENT NCS GROUPS : NULL REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : NULL REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : MASK REMARK 3 PARAMETERS FOR MASK CALCULATION REMARK 3 VDW PROBE RADIUS : 1.40 REMARK 3 ION PROBE RADIUS : 0.80 REMARK 3 SHRINKAGE RADIUS : 0.80 REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: HYDROGENS HAVE BEEN ADDED IN THE RIDING REMARK 3 POSITIONS. THE ELECTRON DENSITY FOR REGION BETWEEN RESIDUES REMARK 3 A1191 TO A 1199 IS DISORDERED REMARK 4 REMARK 4 2JCL 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_1290030934. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 09-JUN-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 : PX9.6 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.87 REMARK 200 MONOCHROMATOR : SI 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 : 18881 REMARK 200 RESOLUTION RANGE HIGH (A) : 3.300 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 (%) : 99.8 REMARK 200 DATA REDUNDANCY : 11.70 REMARK 200 R MERGE (I) : 0.20000 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 7.6000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 3.30 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 3.42 REMARK 200 COMPLETENESS FOR SHELL (%) : 99.9 REMARK 200 DATA REDUNDANCY IN SHELL : 96.00 REMARK 200 R MERGE FOR SHELL (I) : 0.62000 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 2.450 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 (%): 72.00 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 4.42 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.3M SODIUM CACODYLATE BUFFER, PH 6.5, REMARK 280 1.4M SODIUM ACETATE, 2% DIOXANE, PH 8.00 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 47.96500 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 60.74500 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 51.63000 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 60.74500 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 47.96500 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 51.63000 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, 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 1080 REMARK 465 SER A 1081 REMARK 465 LYS A 1359 REMARK 465 GLU A 1360 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 465 GLU B 2080 REMARK 465 SER B 2081 REMARK 465 LYS B 2359 REMARK 465 GLU B 2360 REMARK 465 TYR B 2361 REMARK 465 ASN B 2362 REMARK 465 VAL B 2363 REMARK 465 VAL B 2364 REMARK 465 LYS B 2365 REMARK 465 ASN B 2366 REMARK 465 ASN B 2367 REMARK 465 VAL B 2368 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 ILE B 2198 N MET B 2201 2.12 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 TRP A1339 CB TRP A1339 CG -0.114 REMARK 500 ASP B2197 C ILE B2198 N 0.167 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 ASP B2197 O - C - N ANGL. DEV. = -10.6 DEGREES REMARK 500 ILE B2198 CA - C - N ANGL. DEV. = 21.9 DEGREES REMARK 500 ILE B2198 O - C - N ANGL. DEV. = -27.4 DEGREES REMARK 500 SER B2199 C - N - CA ANGL. DEV. = 29.9 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 LEU A1083 97.18 -165.21 REMARK 500 TRP A1088 -19.16 -140.86 REMARK 500 GLU A1096 -32.60 -33.22 REMARK 500 LYS A1102 9.46 -57.61 REMARK 500 TYR A1143 -43.14 -133.17 REMARK 500 THR A1149 -59.32 -27.63 REMARK 500 PRO A1191 -167.19 -64.09 REMARK 500 GLU A1192 -99.16 -61.46 REMARK 500 TRP A1195 -47.80 -27.52 REMARK 500 ILE A1198 -74.60 -29.73 REMARK 500 HIS A1213 -43.83 -144.69 REMARK 500 ASP A1227 48.93 -79.50 REMARK 500 ASN A1256 1.65 -61.96 REMARK 500 THR A1259 51.99 -67.11 REMARK 500 HIS A1315 -152.71 64.44 REMARK 500 CYS A1338 59.61 -150.11 REMARK 500 LEU A1345 79.76 -170.64 REMARK 500 LEU A1351 102.97 -168.20 REMARK 500 SER B2086 38.76 -71.69 REMARK 500 GLU B2096 -33.45 -33.33 REMARK 500 ARG B2138 -36.46 -38.57 REMARK 500 HIS B2142 -79.69 -34.59 REMARK 500 TYR B2143 -88.48 -96.05 REMARK 500 LEU B2144 -80.27 9.75 REMARK 500 GLU B2145 -72.73 -39.86 REMARK 500 ASP B2197 38.68 -63.90 REMARK 500 ILE B2198 -56.96 5.92 REMARK 500 HIS B2213 -39.01 -140.93 REMARK 500 LYS B2233 113.39 -38.73 REMARK 500 ALA B2253 -179.01 -68.94 REMARK 500 THR B2259 43.56 -69.84 REMARK 500 LYS B2300 -37.71 -37.03 REMARK 500 LYS B2304 -70.41 -57.88 REMARK 500 ASP B2305 -62.29 -16.74 REMARK 500 ASP B2309 70.61 47.36 REMARK 500 GLN B2313 -62.62 -10.10 REMARK 500 HIS B2315 -140.65 48.75 REMARK 500 CYS B2338 58.90 -143.36 REMARK 500 LEU B2345 82.10 -28.27 REMARK 500 LYS B2350 -70.80 -76.46 REMARK 500 TRP B2356 -135.31 -75.48 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: NON-CIS, NON-TRANS REMARK 500 REMARK 500 THE FOLLOWING PEPTIDE BONDS DEVIATE SIGNIFICANTLY FROM BOTH REMARK 500 CIS AND TRANS CONFORMATION. CIS BONDS, IF ANY, ARE LISTED REMARK 500 ON CISPEP RECORDS. TRANS IS DEFINED AS 180 +/- 30 AND REMARK 500 CIS IS DEFINED AS 0 +/- 30 DEGREES. REMARK 500 MODEL OMEGA REMARK 500 ASP B 2197 ILE B 2198 -148.71 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: MAIN CHAIN PLANARITY REMARK 500 REMARK 500 THE FOLLOWING RESIDUES HAVE A PSEUDO PLANARITY REMARK 500 TORSION ANGLE, C(I) - CA(I) - N(I+1) - O(I), GREATER REMARK 500 10.0 DEGREES. (M=MODEL NUMBER; RES=RESIDUE NAME; REMARK 500 C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; REMARK 500 I=INSERTION CODE). REMARK 500 REMARK 500 M RES CSSEQI ANGLE REMARK 500 ASP B2197 -13.18 REMARK 500 ILE B2198 -19.42 REMARK 500 REMARK 500 REMARK: NULL REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SO4 B3360 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SO4 B3361 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SO4 B3362 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SO4 B3363 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SO4 B3364 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: 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: 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: 2JCO RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF WILD TYPE ALPHA-1,3 GALACTOSYLTRANSFERASE IN REMARK 900 THE ABSENCE OF LIGANDS REMARK 999 REMARK 999 SEQUENCE REMARK 999 THE RESIDUE RANGE FOR THIS PROTEIN CONSTRUCT IS FROM 80 TO REMARK 999 368. THE RESIDUE RANGE MODELLED IN THE STRUCTURE IS 82-358 REMARK 999 FOR MOL A AND MOL B. MUTATION IS R365K. DBREF 2JCL A 1080 1368 UNP P14769 GGTA1_BOVIN 80 368 DBREF 2JCL B 2080 2368 UNP P14769 GGTA1_BOVIN 80 368 SEQADV 2JCL LYS A 1365 UNP P14769 ARG 365 ENGINEERED MUTATION SEQADV 2JCL LYS B 2365 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 SO4 B3360 5 HET SO4 B3361 5 HET SO4 B3362 5 HET SO4 B3363 5 HET SO4 B3364 5 HETNAM SO4 SULFATE ION FORMUL 3 SO4 5(O4 S 2-) FORMUL 8 HOH *61(H2 O) HELIX 1 1 LYS A 1084 TRP A 1088 5 5 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 GLY A 1137 TYR A 1143 1 7 HELIX 5 5 TYR A 1143 PHE A 1155 1 13 HELIX 6 6 ASP A 1197 HIS A 1213 1 17 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 HIS A 1315 ASN A 1327 1 13 HELIX 12 12 PRO A 1335 CYS A 1338 5 4 HELIX 13 13 ASP A 1340 GLY A 1344 5 5 HELIX 14 14 ASN B 2090 ARG B 2094 5 5 HELIX 15 15 ASN B 2114 LYS B 2126 1 13 HELIX 16 16 ARG B 2138 TYR B 2143 1 6 HELIX 17 17 LEU B 2144 PHE B 2155 1 12 HELIX 18 18 ASP B 2169 MET B 2173 5 5 HELIX 19 19 LYS B 2190 GLN B 2196 5 7 HELIX 20 20 ILE B 2198 HIS B 2213 1 16 HELIX 21 21 HIS B 2213 VAL B 2218 1 6 HELIX 22 22 GLY B 2235 LEU B 2239 5 5 HELIX 23 23 GLN B 2247 TYR B 2251 5 5 HELIX 24 24 ASP B 2254 PHE B 2258 5 5 HELIX 25 25 THR B 2287 ASN B 2308 1 22 HELIX 26 26 TRP B 2314 ASN B 2327 1 14 HELIX 27 27 PRO B 2335 CYS B 2338 5 4 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 ALA A1244 N LEU A1333 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 SHEET 1 BA 8 VAL B2107 VAL B2108 0 SHEET 2 BA 8 LYS B2331 LEU B2333 1 O ILE B2332 N VAL B2108 SHEET 3 BA 8 SER B2242 GLN B2245 1 O SER B2242 N LYS B2331 SHEET 4 BA 8 ILE B2283 GLY B2286 -1 O GLY B2285 N VAL B2243 SHEET 5 BA 8 PHE B2220 ASP B2225 -1 O LEU B2221 N GLY B2286 SHEET 6 BA 8 VAL B2129 ALA B2135 1 O GLY B2130 N PHE B2222 SHEET 7 BA 8 VAL B2161 VAL B2167 1 O ILE B2162 N LEU B2131 SHEET 8 BA 8 ARG B2182 LYS B2188 1 O SER B2183 N PHE B2163 SHEET 1 BB 2 VAL B2229 PHE B2230 0 SHEET 2 BB 2 MET B2354 SER B2355 -1 O SER B2355 N VAL B2229 CISPEP 1 GLU A 1192 LYS A 1193 0 -22.80 SITE 1 AC1 3 GLN A1247 TRP A1249 GLU B2192 SITE 1 AC2 5 ARG B2202 ILE B2206 ASP B2225 ALA B2281 SITE 2 AC2 5 PHE B2284 SITE 1 AC3 4 GLU B2297 CYS B2298 HIS B2319 TYR B2323 SITE 1 AC4 2 VAL B2211 HIS B2216 SITE 1 AC5 8 MET B2166 LYS B2188 ILE B2189 LYS B2190 SITE 2 AC5 8 LYS B2193 THR B2205 GLU B2208 HIS B2209 CRYST1 95.930 103.260 121.490 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 0.010424 0.000000 0.000000 0.00000 SCALE2 0.000000 0.009684 0.000000 0.00000 SCALE3 0.000000 0.000000 0.008231 0.00000 MTRIX1 1 -0.966600 0.003080 0.256270 86.46831 1 MTRIX2 1 -0.027830 -0.995280 -0.093000 18.47139 1 MTRIX3 1 0.254770 -0.097020 0.962120 -10.08132 1