HEADER TRANSFERASE 09-JUL-09 2WNF TITLE CRYSTAL STRUCTURE OF A MAMMALIAN SIALYLTRANSFERASE IN COMPLEX WITH TITLE 2 GAL-BETA-1-3GALNAC-ORTHO-NITROPHENOL COMPND MOL_ID: 1; COMPND 2 MOLECULE: CMP-N-ACETYLNEURAMINATE-BETA-GALACTOSAMIDE-ALPHA-2,3- COMPND 3 SIALYLTRANSFERASE; COMPND 4 CHAIN: A; COMPND 5 FRAGMENT: RESIDUES 46-343 COMPND 12; COMPND 6 SYNONYM: GAL-NAC6S, GAL-BETA-1\,ST3GALA.1,ST3GALIA, ST3GAL I, 3- COMPND 7 GALNAC-ALPHA-2,3-SIALYLTRANSFERASE, ST3O, SIAT4-A, BETA-GALACTOSIDE COMPND 8 ALPHA-2\,3-SIALYLTRANSFERASE, ALPHA 2\,3-ST; COMPND 9 EC: 2.4.99.4; COMPND 10 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: SUS SCROFA; SOURCE 3 ORGANISM_COMMON: PIG; SOURCE 4 ORGANISM_TAXID: 9823; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 7 EXPRESSION_SYSTEM_STRAIN: ORIGAMI2; SOURCE 8 EXPRESSION_SYSTEM_PLASMID: PCWIN2-MBP KEYWDS GLYCOSYLTRANSFERASE, DISULFIDE BOND, GOLGI APPARATUS, KEYWDS 2 SIALYLTRANSFERASE, GLYCOPROTEIN, SIGNAL-ANCHOR, TRANSMEMBRANE, KEYWDS 3 MEMBRANE, SECRETED, TRANSFERASE, SIALIC ACID EXPDTA X-RAY DIFFRACTION AUTHOR F.V.RAO,J.R.RICH,B.RAIKIC,W.W.WAKARCHUK,S.G.WITHERS,N.C.J.STRYNADKA REVDAT 8 23-OCT-24 2WNF 1 REMARK REVDAT 7 13-DEC-23 2WNF 1 HETSYN REVDAT 6 29-JUL-20 2WNF 1 COMPND REMARK HETNAM LINK REVDAT 6 2 1 SITE ATOM REVDAT 5 20-MAY-15 2WNF 1 REMARK REVDAT 4 16-NOV-11 2WNF 1 JRNL REMARK REVDAT 3 13-JUL-11 2WNF 1 VERSN REVDAT 2 20-OCT-09 2WNF 1 JRNL REVDAT 1 13-OCT-09 2WNF 0 JRNL AUTH F.V.RAO,J.R.RICH,B.RAKIC,S.BUDDAI,M.F.SCHWARTZ,K.JOHNSON, JRNL AUTH 2 C.BOWE,W.W.WAKARCHUK,S.DEFREES,S.G.WITHERS,N.C.J.STRYNADKA JRNL TITL STRUCTURAL INSIGHT INTO MAMMALIAN SIALYLTRANSFERASES. JRNL REF NAT.STRUCT.MOL.BIOL. V. 16 1186 2009 JRNL REFN ISSN 1545-9993 JRNL PMID 19820709 JRNL DOI 10.1038/NSMB.1685 REMARK 2 REMARK 2 RESOLUTION. 1.25 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.5.0088 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) : 1.25 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 33.11 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 99.8 REMARK 3 NUMBER OF REFLECTIONS : 80958 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) : 0.181 REMARK 3 R VALUE (WORKING SET) : 0.180 REMARK 3 FREE R VALUE : 0.195 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 4261 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) : 1.25 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.28 REMARK 3 REFLECTION IN BIN (WORKING SET) : 5785 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 97.32 REMARK 3 BIN R VALUE (WORKING SET) : 0.2370 REMARK 3 BIN FREE R VALUE SET COUNT : 290 REMARK 3 BIN FREE R VALUE : 0.2540 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 2221 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 35 REMARK 3 SOLVENT ATOMS : 321 REMARK 3 REMARK 3 B VALUES. REMARK 3 B VALUE TYPE : LIKELY RESIDUAL REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 14.45 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 0.26000 REMARK 3 B22 (A**2) : 0.10000 REMARK 3 B33 (A**2) : -0.35000 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): 0.044 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.045 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.027 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 1.324 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.961 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.955 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 2463 ; 0.026 ; 0.022 REMARK 3 BOND LENGTHS OTHERS (A): NULL ; NULL ; NULL REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 3366 ; 2.039 ; 1.953 REMARK 3 BOND ANGLES OTHERS (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 303 ; 6.472 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 121 ;33.447 ;23.058 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 420 ;13.319 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 20 ;13.206 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 359 ; 0.147 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 1911 ; 0.015 ; 0.021 REMARK 3 GENERAL PLANES OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED CONTACTS OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION OTHERS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): NULL ; NULL ; NULL 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): NULL ; NULL ; NULL 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): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): NULL ; NULL ; NULL 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 : 1 REMARK 3 REMARK 3 TLS GROUP : 1 REMARK 3 NUMBER OF COMPONENTS GROUP : 2 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : A 61 A 305 REMARK 3 RESIDUE RANGE : A 317 A 343 REMARK 3 ORIGIN FOR THE GROUP (A): 17.5510 22.7370 37.3940 REMARK 3 T TENSOR REMARK 3 T11: 0.0076 T22: 0.0046 REMARK 3 T33: 0.0048 T12: 0.0011 REMARK 3 T13: 0.0005 T23: -0.0039 REMARK 3 L TENSOR REMARK 3 L11: 0.3556 L22: 0.4714 REMARK 3 L33: 0.8658 L12: -0.0562 REMARK 3 L13: 0.0579 L23: -0.0680 REMARK 3 S TENSOR REMARK 3 S11: 0.0034 S12: 0.0144 S13: -0.0152 REMARK 3 S21: 0.0029 S22: -0.0136 S23: -0.0087 REMARK 3 S31: 0.0323 S32: 0.0124 S33: 0.0102 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : NULL 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. REMARK 4 REMARK 4 2WNF COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 09-JUL-09. REMARK 100 THE DEPOSITION ID IS D_1290040330. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 09-SEP-08 REMARK 200 TEMPERATURE (KELVIN) : 173 REMARK 200 PH : NULL REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : CLSI REMARK 200 BEAMLINE : 08ID-1 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.000 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : MARMOSAIC 225 MM CCD REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 85229 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.250 REMARK 200 RESOLUTION RANGE LOW (A) : 33.110 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 2.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.8 REMARK 200 DATA REDUNDANCY : 6.900 REMARK 200 R MERGE (I) : 0.06000 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 23.4000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.25 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.29 REMARK 200 COMPLETENESS FOR SHELL (%) : 98.3 REMARK 200 DATA REDUNDANCY IN SHELL : 4.90 REMARK 200 R MERGE FOR SHELL (I) : 0.40000 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 2.800 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: PHASER REMARK 200 STARTING MODEL: PDB ENTRY 2WML REMARK 200 REMARK 200 REMARK: NONE REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 38.00 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.00 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 30% PEG 4000 AND 0.1 M MES, PH 6.8 REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: I 2 2 2 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,Y,-Z REMARK 290 4555 X,-Y,-Z REMARK 290 5555 X+1/2,Y+1/2,Z+1/2 REMARK 290 6555 -X+1/2,-Y+1/2,Z+1/2 REMARK 290 7555 -X+1/2,Y+1/2,-Z+1/2 REMARK 290 8555 X+1/2,-Y+1/2,-Z+1/2 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 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 5 1.000000 0.000000 0.000000 38.99350 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 39.17350 REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 49.59550 REMARK 290 SMTRY1 6 -1.000000 0.000000 0.000000 38.99350 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 39.17350 REMARK 290 SMTRY3 6 0.000000 0.000000 1.000000 49.59550 REMARK 290 SMTRY1 7 -1.000000 0.000000 0.000000 38.99350 REMARK 290 SMTRY2 7 0.000000 1.000000 0.000000 39.17350 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 49.59550 REMARK 290 SMTRY1 8 1.000000 0.000000 0.000000 38.99350 REMARK 290 SMTRY2 8 0.000000 -1.000000 0.000000 39.17350 REMARK 290 SMTRY3 8 0.000000 0.000000 -1.000000 49.59550 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: PISA 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 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 A2086 LIES ON A SPECIAL POSITION. 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 46 REMARK 465 LEU A 47 REMARK 465 SER A 48 REMARK 465 GLU A 49 REMARK 465 ASN A 50 REMARK 465 PHE A 51 REMARK 465 LYS A 52 REMARK 465 LYS A 53 REMARK 465 LEU A 54 REMARK 465 MSE A 55 REMARK 465 LYS A 56 REMARK 465 TYR A 57 REMARK 465 PRO A 58 REMARK 465 TYR A 59 REMARK 465 ARG A 60 REMARK 465 ASN A 306 REMARK 465 ASN A 307 REMARK 465 PRO A 308 REMARK 465 SER A 309 REMARK 465 ALA A 310 REMARK 465 GLY A 311 REMARK 465 ALA A 312 REMARK 465 PHE A 313 REMARK 465 ARG A 314 REMARK 465 LYS A 315 REMARK 465 THR A 316 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 2037 O HOH A 2091 2.14 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 GLU A 69 CB GLU A 69 CG -0.116 REMARK 500 GLU A 69 CD GLU A 69 OE2 -0.071 REMARK 500 GLU A 98 CD GLU A 98 OE1 0.068 REMARK 500 GLU A 110 CB GLU A 110 CG -0.129 REMARK 500 GLU A 245 CB GLU A 245 CG -0.116 REMARK 500 GLU A 245 CD GLU A 245 OE1 0.092 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 A 80 NE - CZ - NH2 ANGL. DEV. = -3.3 DEGREES REMARK 500 ASP A 99 CB - CG - OD1 ANGL. DEV. = 6.0 DEGREES REMARK 500 ARG A 121 NE - CZ - NH2 ANGL. DEV. = -3.6 DEGREES REMARK 500 ARG A 143 NE - CZ - NH2 ANGL. DEV. = -4.1 DEGREES REMARK 500 CYS A 145 CA - CB - SG ANGL. DEV. = 10.4 DEGREES REMARK 500 ARG A 228 NE - CZ - NH1 ANGL. DEV. = -4.0 DEGREES REMARK 500 ARG A 343 NE - CZ - NH1 ANGL. DEV. = 5.2 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 ASN A 173 -142.36 63.55 REMARK 500 THR A 225 -101.24 -136.96 REMARK 500 THR A 232 -105.50 -115.23 REMARK 500 THR A 232 -105.50 -122.02 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 A2037 DISTANCE = 6.06 ANGSTROMS REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 2WNB RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF A MAMMALIAN SIALYLTRANSFERASE IN COMPLEX WITH REMARK 900 DISACCHARIDE AND CMP REMARK 900 RELATED ID: 2WML RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF A MAMMALIAN SIALYLTRANSFERASE DBREF 2WNF A 46 343 UNP Q02745 SIA4A_PIG 46 343 SEQRES 1 A 298 GLU LEU SER GLU ASN PHE LYS LYS LEU MSE LYS TYR PRO SEQRES 2 A 298 TYR ARG PRO CYS THR CYS THR ARG CYS ILE GLU GLU GLN SEQRES 3 A 298 ARG VAL SER ALA TRP PHE ASP GLU ARG PHE ASN ARG SER SEQRES 4 A 298 MSE GLN PRO LEU LEU THR ALA LYS ASN ALA HIS LEU GLU SEQRES 5 A 298 GLU ASP THR TYR LYS TRP TRP LEU ARG LEU GLN ARG GLU SEQRES 6 A 298 LYS GLN PRO ASN ASN LEU ASN ASP THR ILE ARG GLU LEU SEQRES 7 A 298 PHE GLN VAL VAL PRO GLY ASN VAL ASP PRO LEU LEU GLU SEQRES 8 A 298 LYS ARG LEU VAL SER CYS ARG ARG CYS ALA VAL VAL GLY SEQRES 9 A 298 ASN SER GLY ASN LEU LYS GLU SER TYR TYR GLY PRO GLN SEQRES 10 A 298 ILE ASP SER HIS ASP PHE VAL LEU ARG MSE ASN LYS ALA SEQRES 11 A 298 PRO THR GLU GLY PHE GLU ALA ASP VAL GLY SER LYS THR SEQRES 12 A 298 THR HIS HIS PHE VAL TYR PRO GLU SER PHE ARG GLU LEU SEQRES 13 A 298 ALA GLN GLU VAL SER MSE ILE LEU VAL PRO PHE LYS THR SEQRES 14 A 298 THR ASP LEU GLU TRP VAL ILE SER ALA THR THR THR GLY SEQRES 15 A 298 ARG ILE SER HIS THR TYR VAL PRO VAL PRO ALA LYS ILE SEQRES 16 A 298 LYS VAL LYS LYS GLU LYS ILE LEU ILE TYR HIS PRO ALA SEQRES 17 A 298 PHE ILE LYS TYR VAL PHE ASP ARG TRP LEU GLN GLY HIS SEQRES 18 A 298 GLY ARG TYR PRO SER THR GLY ILE LEU SER VAL ILE PHE SEQRES 19 A 298 SER LEU HIS ILE CYS ASP GLU VAL ASP LEU TYR GLY PHE SEQRES 20 A 298 GLY ALA ASP SER LYS GLY ASN TRP HIS HIS TYR TRP GLU SEQRES 21 A 298 ASN ASN PRO SER ALA GLY ALA PHE ARG LYS THR GLY VAL SEQRES 22 A 298 HIS ASP GLY ASP PHE GLU SER ASN VAL THR THR ILE LEU SEQRES 23 A 298 ALA SER ILE ASN LYS ILE ARG ILE PHE LYS GLY ARG MODRES 2WNF MSE A 85 MET SELENOMETHIONINE MODRES 2WNF MSE A 172 MET SELENOMETHIONINE MODRES 2WNF MSE A 207 MET SELENOMETHIONINE HET MSE A 85 8 HET MSE A 172 8 HET MSE A 207 8 HET A2G B 1 14 HET GAL B 2 11 HET CG3 A1344 10 HETNAM MSE SELENOMETHIONINE HETNAM A2G 2-ACETAMIDO-2-DEOXY-ALPHA-D-GALACTOPYRANOSE HETNAM GAL BETA-D-GALACTOPYRANOSE HETNAM CG3 HYDROXY(2-HYDROXYPHENYL)OXOAMMONIUM HETSYN A2G N-ACETYL-ALPHA-D-GALACTOSAMINE; 2-ACETAMIDO-2-DEOXY- HETSYN 2 A2G ALPHA-D-GALACTOSE; 2-ACETAMIDO-2-DEOXY-D-GALACTOSE; 2- HETSYN 3 A2G ACETAMIDO-2-DEOXY-GALACTOSE; N-ACETYL-2-DEOXY-2-AMINO- HETSYN 4 A2G GALACTOSE HETSYN GAL BETA-D-GALACTOSE; D-GALACTOSE; GALACTOSE FORMUL 1 MSE 3(C5 H11 N O2 SE) FORMUL 2 A2G C8 H15 N O6 FORMUL 2 GAL C6 H12 O6 FORMUL 3 CG3 C6 H6 N O3 1+ FORMUL 4 HOH *321(H2 O) HELIX 1 1 SER A 74 PHE A 81 1 8 HELIX 2 2 GLU A 97 ARG A 106 1 10 HELIX 3 3 ASN A 115 PHE A 124 1 10 HELIX 4 4 GLU A 136 VAL A 140 5 5 HELIX 5 5 LYS A 213 THR A 224 1 12 HELIX 6 6 LYS A 243 GLU A 245 5 3 HELIX 7 7 HIS A 251 TRP A 262 1 12 HELIX 8 8 ILE A 274 CYS A 284 1 11 HELIX 9 9 ASP A 322 ILE A 334 1 13 SHEET 1 AA 7 ILE A 247 ILE A 249 0 SHEET 2 AA 7 SER A 206 LEU A 209 1 O MSE A 207 N LEU A 248 SHEET 3 AA 7 HIS A 190 VAL A 193 1 O HIS A 191 N ILE A 208 SHEET 4 AA 7 PHE A 168 MSE A 172 1 O ARG A 171 N PHE A 192 SHEET 5 AA 7 ARG A 144 VAL A 147 1 O ARG A 144 N PHE A 168 SHEET 6 AA 7 GLU A 286 LEU A 289 1 O GLU A 286 N CYS A 145 SHEET 7 AA 7 ARG A 338 ILE A 339 1 O ARG A 338 N LEU A 289 SSBOND 1 CYS A 62 CYS A 67 1555 1555 2.06 SSBOND 2 CYS A 64 CYS A 142 1555 1555 2.04 SSBOND 3 CYS A 145 CYS A 284 1555 1555 2.04 LINK C SER A 84 N MSE A 85 1555 1555 1.33 LINK C MSE A 85 N GLN A 86 1555 1555 1.32 LINK C ARG A 171 N MSE A 172 1555 1555 1.34 LINK C MSE A 172 N ASN A 173 1555 1555 1.33 LINK C SER A 206 N MSE A 207 1555 1555 1.33 LINK C MSE A 207 N ILE A 208 1555 1555 1.33 LINK OAO CG3 A1344 C1 A2G B 1 1555 1555 1.43 LINK O3 A2G B 1 C1 GAL B 2 1555 1555 1.41 CRYST1 77.987 78.347 99.191 90.00 90.00 90.00 I 2 2 2 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 0.012823 0.000000 0.000000 0.00000 SCALE2 0.000000 0.012764 0.000000 0.00000 SCALE3 0.000000 0.000000 0.010082 0.00000