HEADER TRANSFERASE 25-JUN-07 2Z4T TITLE CRYSTAL STRUCTURE OF VIBRIONACEAE PHOTOBACTERIUM SP. JT-ISH-224 2,6- TITLE 2 SIALYLTRANSFERASE IN A TERNARY COMPLEX WITH DONOR PRODUCT CMP AND TITLE 3 ACCEPTER SUBSTRATE LACTOSE COMPND MOL_ID: 1; COMPND 2 MOLECULE: BETA-GALACTOSIDE ALPHA-2,6-SIALYLTRANSFERASE; COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: PHOTOBACTERIUM SP.; SOURCE 3 ORGANISM_TAXID: 426532; SOURCE 4 STRAIN: JT-ISH-224; SOURCE 5 GENE: PST6-224; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 8 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 9 EXPRESSION_SYSTEM_PLASMID: PTRC99A KEYWDS GT-B FOLD, IMMUNOGLOBULIN-LIKE BETA-SANDWICH FOLD, KEYWDS 2 GLYCOSYLTRANSFERASE, TRANSFERASE EXPDTA X-RAY DIFFRACTION AUTHOR Y.KAKUTA,N.OKINO,H.KAJIWARA,M.ICHIKAWA,Y.TAKAKURA,M.ITO,T.YAMAMOTO REVDAT 6 16-OCT-24 2Z4T 1 REMARK REVDAT 5 01-NOV-23 2Z4T 1 REMARK HETSYN REVDAT 4 29-JUL-20 2Z4T 1 COMPND REMARK HET HETNAM REVDAT 4 2 1 HETSYN FORMUL LINK SITE REVDAT 4 3 1 ATOM REVDAT 3 13-JUL-11 2Z4T 1 VERSN REVDAT 2 24-FEB-09 2Z4T 1 VERSN REVDAT 1 08-APR-08 2Z4T 0 JRNL AUTH Y.KAKUTA,N.OKINO,H.KAJIWARA,M.ICHIKAWA,Y.TAKAKURA,M.ITO, JRNL AUTH 2 T.YAMAMOTO JRNL TITL CRYSTAL STRUCTURE OF VIBRIONACEAE PHOTOBACTERIUM SP. JRNL TITL 2 JT-ISH-224 ALPHA2,6-SIALYLTRANSFERASE IN A TERNARY COMPLEX JRNL TITL 3 WITH DONOR PRODUCT CMP AND ACCEPTOR SUBSTRATE LACTOSE: JRNL TITL 4 CATALYTIC MECHANISM AND SUBSTRATE RECOGNITION JRNL REF GLYCOBIOLOGY V. 18 66 2008 JRNL REFN ISSN 0959-6658 JRNL PMID 17962295 JRNL DOI 10.1093/GLYCOB/CWM119 REMARK 2 REMARK 2 RESOLUTION. 2.50 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) : 2.50 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 41.31 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.8 REMARK 3 NUMBER OF REFLECTIONS : 32443 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) : 0.195 REMARK 3 R VALUE (WORKING SET) : 0.192 REMARK 3 FREE R VALUE : 0.243 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.100 REMARK 3 FREE R VALUE TEST SET COUNT : 1727 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) : 2.50 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.56 REMARK 3 REFLECTION IN BIN (WORKING SET) : 2349 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 99.84 REMARK 3 BIN R VALUE (WORKING SET) : 0.2620 REMARK 3 BIN FREE R VALUE SET COUNT : 132 REMARK 3 BIN FREE R VALUE : 0.3020 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 3955 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 87 REMARK 3 SOLVENT ATOMS : 281 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) : 44.65 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -0.20000 REMARK 3 B22 (A**2) : -0.20000 REMARK 3 B33 (A**2) : 0.30000 REMARK 3 B12 (A**2) : -0.10000 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): 0.266 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.227 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.150 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 12.178 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.946 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.910 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 4198 ; 0.013 ; 0.022 REMARK 3 BOND LENGTHS OTHERS (A): NULL ; NULL ; NULL REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 5717 ; 1.882 ; 1.964 REMARK 3 BOND ANGLES OTHERS (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 510 ;14.288 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 205 ;40.912 ;26.000 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 725 ;18.120 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 11 ;26.286 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 649 ; 0.180 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 3142 ; 0.006 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): 2178 ; 0.231 ; 0.200 REMARK 3 NON-BONDED CONTACTS OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): 2836 ; 0.316 ; 0.200 REMARK 3 NON-BONDED TORSION OTHERS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): 326 ; 0.157 ; 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): 59 ; 0.230 ; 0.200 REMARK 3 SYMMETRY VDW OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): 12 ; 0.159 ; 0.200 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): 2554 ; 0.657 ; 1.500 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 4088 ; 1.196 ; 2.000 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 1848 ; 1.626 ; 3.000 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 1621 ; 2.648 ; 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 : 1 REMARK 3 REMARK 3 TLS GROUP : 1 REMARK 3 NUMBER OF COMPONENTS GROUP : 3 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : A 22 A 98 REMARK 3 RESIDUE RANGE : A 99 A 302 REMARK 3 RESIDUE RANGE : A 303 A 498 REMARK 3 ORIGIN FOR THE GROUP (A): 22.8010 -36.1020 -20.5710 REMARK 3 T TENSOR REMARK 3 T11: -0.0385 T22: -0.2049 REMARK 3 T33: -0.2810 T12: -0.0063 REMARK 3 T13: -0.0007 T23: 0.0051 REMARK 3 L TENSOR REMARK 3 L11: 1.1437 L22: 0.9091 REMARK 3 L33: 0.4668 L12: 0.8178 REMARK 3 L13: 0.3862 L23: 0.3454 REMARK 3 S TENSOR REMARK 3 S11: 0.1307 S12: 0.0380 S13: -0.0551 REMARK 3 S21: 0.0919 S22: -0.0036 S23: -0.0341 REMARK 3 S31: 0.0447 S32: 0.0004 S33: -0.1271 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : MASK REMARK 3 PARAMETERS FOR MASK CALCULATION REMARK 3 VDW PROBE RADIUS : 1.20 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 2Z4T COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 27-JUN-07. REMARK 100 THE DEPOSITION ID IS D_1000027521. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : NULL REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 8.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : SPRING-8 REMARK 200 BEAMLINE : BL38B1 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 : SI 111 CHANNEL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : RIGAKU JUPITER 210 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 34277 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.500 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 : 5.400 REMARK 200 R MERGE (I) : 0.08200 REMARK 200 R SYM (I) : 0.08200 REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 20.0000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.50 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.59 REMARK 200 COMPLETENESS FOR SHELL (%) : 100.0 REMARK 200 DATA REDUNDANCY IN SHELL : 5.50 REMARK 200 R MERGE FOR SHELL (I) : 0.43200 REMARK 200 R SYM FOR SHELL (I) : 0.43200 REMARK 200 <I/SIGMA(I)> FOR SHELL : 3.700 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 2EX1 REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 70.04 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 4.11 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.2M LITHIUM SULFATE, 30% PEG4000, REMARK 280 0.1M TRIS-HCL (PH8.5), VAPOR DIFFUSION, TEMPERATURE 298.0K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 31 2 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -Y,X-Y,Z+1/3 REMARK 290 3555 -X+Y,-X,Z+2/3 REMARK 290 4555 Y,X,-Z REMARK 290 5555 X-Y,-Y,-Z+2/3 REMARK 290 6555 -X,-X+Y,-Z+1/3 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 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 2 0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 68.11000 REMARK 290 SMTRY1 3 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 3 -0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 136.22000 REMARK 290 SMTRY1 4 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 4 0.866025 0.500000 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 0.00000 REMARK 290 SMTRY2 5 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 136.22000 REMARK 290 SMTRY1 6 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 6 -0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 6 0.000000 0.000000 -1.000000 68.11000 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 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 MET A 1 REMARK 465 LYS A 2 REMARK 465 ASN A 3 REMARK 465 PHE A 4 REMARK 465 LEU A 5 REMARK 465 LEU A 6 REMARK 465 LEU A 7 REMARK 465 THR A 8 REMARK 465 LEU A 9 REMARK 465 ILE A 10 REMARK 465 LEU A 11 REMARK 465 LEU A 12 REMARK 465 THR A 13 REMARK 465 ALA A 14 REMARK 465 CYS A 15 REMARK 465 ASN A 16 REMARK 465 ASN A 17 REMARK 465 SER A 18 REMARK 465 GLU A 19 REMARK 465 GLU A 20 REMARK 465 ASN A 21 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 THR A 22 OG1 CG2 REMARK 480 REMARK 480 ZERO OCCUPANCY ATOM REMARK 480 THE FOLLOWING RESIDUES HAVE ATOMS MODELED WITH ZERO REMARK 480 OCCUPANCY. THE LOCATION AND PROPERTIES OF THESE ATOMS REMARK 480 MAY NOT BE RELIABLE. (M=MODEL NUMBER; RES=RESIDUE NAME; REMARK 480 C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE): REMARK 480 M RES C SSEQI ATOMS REMARK 480 TYR A 104 CD1 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 OD2 ASP A 502 O HOH A 5227 2.09 REMARK 500 O GLU A 458 O HOH A 5240 2.18 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 TYR A 104 CD1 TYR A 104 CE1 -0.275 REMARK 500 HIS A 192 CG HIS A 192 CD2 -0.214 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 ILE A 34 C - N - CA ANGL. DEV. = 17.2 DEGREES REMARK 500 ASN A 49 N - CA - C ANGL. DEV. = 16.3 DEGREES REMARK 500 TYR A 104 CD1 - CG - CD2 ANGL. DEV. = -13.6 DEGREES REMARK 500 TYR A 104 CB - CG - CD1 ANGL. DEV. = 14.6 DEGREES REMARK 500 TYR A 104 CG - CD1 - CE1 ANGL. DEV. = 24.5 DEGREES REMARK 500 TYR A 104 CD1 - CE1 - CZ ANGL. DEV. = -11.7 DEGREES REMARK 500 HIS A 192 CG - CD2 - NE2 ANGL. DEV. = 12.1 DEGREES REMARK 500 PHE A 206 N - CA - C ANGL. DEV. = -22.9 DEGREES REMARK 500 ASN A 350 N - CA - C ANGL. DEV. = 21.1 DEGREES REMARK 500 SER A 351 C - N - CA ANGL. DEV. = 16.0 DEGREES REMARK 500 GLY A 404 N - CA - C ANGL. DEV. = -15.3 DEGREES REMARK 500 MET A 486 N - CA - C ANGL. DEV. = -21.2 DEGREES REMARK 500 ALA A 501 N - CA - C ANGL. DEV. = 18.6 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 A 34 111.13 139.36 REMARK 500 SER A 48 -93.70 147.92 REMARK 500 ILE A 50 110.01 78.51 REMARK 500 THR A 68 36.67 -97.58 REMARK 500 GLU A 69 -46.25 75.12 REMARK 500 ALA A 124 -144.29 -95.13 REMARK 500 THR A 176 117.41 -29.38 REMARK 500 ASN A 201 125.84 -37.89 REMARK 500 ASP A 270 99.69 -65.80 REMARK 500 THR A 271 30.21 -97.17 REMARK 500 SER A 351 -64.95 132.28 REMARK 500 HIS A 405 107.18 -16.35 REMARK 500 SER A 421 -66.64 95.67 REMARK 500 ILE A 425 82.85 -9.19 REMARK 500 THR A 470 -75.80 -105.74 REMARK 500 ILE A 471 -89.60 -18.70 REMARK 500 ASP A 473 132.24 -26.50 REMARK 500 TRP A 500 -22.97 -36.50 REMARK 500 ALA A 501 -116.30 24.87 REMARK 500 ASP A 502 -56.35 68.16 REMARK 500 ASP A 502 -54.64 120.73 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 THR A 33 ILE A 34 -70.08 REMARK 500 SER A 48 ASN A 49 31.08 REMARK 500 LYS A 54 HIS A 55 109.72 REMARK 500 LYS A 100 GLY A 101 -32.81 REMARK 500 SER A 205 PHE A 206 -132.43 REMARK 500 LYS A 403 GLY A 404 70.96 REMARK 500 GLY A 404 HIS A 405 110.42 REMARK 500 PRO A 420 SER A 421 38.40 REMARK 500 ASP A 424 ILE A 425 81.36 REMARK 500 VAL A 485 MET A 486 -127.18 REMARK 500 ALA A 501 ASP A 502 34.03 REMARK 500 REMARK 500 REMARK: NULL DBREF 2Z4T A 1 514 UNP A8QYL1 A8QYL1_9GAMM 1 514 SEQRES 1 A 514 MET LYS ASN PHE LEU LEU LEU THR LEU ILE LEU LEU THR SEQRES 2 A 514 ALA CYS ASN ASN SER GLU GLU ASN THR GLN SER ILE ILE SEQRES 3 A 514 LYS ASN ASP ILE ASN LYS THR ILE ILE ASP GLU GLU TYR SEQRES 4 A 514 VAL ASN LEU GLU PRO ILE ASN GLN SER ASN ILE SER PHE SEQRES 5 A 514 THR LYS HIS SER TRP VAL GLN THR CYS GLY THR GLN GLN SEQRES 6 A 514 LEU LEU THR GLU GLN ASN LYS GLU SER ILE SER LEU SER SEQRES 7 A 514 VAL VAL ALA PRO ARG LEU ASP ASP ASP GLU LYS TYR CYS SEQRES 8 A 514 PHE ASP PHE ASN GLY VAL SER ASN LYS GLY GLU LYS TYR SEQRES 9 A 514 ILE THR LYS VAL THR LEU ASN VAL VAL ALA PRO SER LEU SEQRES 10 A 514 GLU VAL TYR VAL ASP HIS ALA SER LEU PRO THR LEU GLN SEQRES 11 A 514 GLN LEU MET ASP ILE ILE LYS SER GLU GLU GLU ASN PRO SEQRES 12 A 514 THR ALA GLN ARG TYR ILE ALA TRP GLY ARG ILE VAL PRO SEQRES 13 A 514 THR ASP GLU GLN MET LYS GLU LEU ASN ILE THR SER PHE SEQRES 14 A 514 ALA LEU ILE ASN ASN HIS THR PRO ALA ASP LEU VAL GLN SEQRES 15 A 514 GLU ILE VAL LYS GLN ALA GLN THR LYS HIS ARG LEU ASN SEQRES 16 A 514 VAL LYS LEU SER SER ASN THR ALA HIS SER PHE ASP ASN SEQRES 17 A 514 LEU VAL PRO ILE LEU LYS GLU LEU ASN SER PHE ASN ASN SEQRES 18 A 514 VAL THR VAL THR ASN ILE ASP LEU TYR ASP ASP GLY SER SEQRES 19 A 514 ALA GLU TYR VAL ASN LEU TYR ASN TRP ARG ASP THR LEU SEQRES 20 A 514 ASN LYS THR ASP ASN LEU LYS ILE GLY LYS ASP TYR LEU SEQRES 21 A 514 GLU ASP VAL ILE ASN GLY ILE ASN GLU ASP THR SER ASN SEQRES 22 A 514 THR GLY THR SER SER VAL TYR ASN TRP GLN LYS LEU TYR SEQRES 23 A 514 PRO ALA ASN TYR HIS PHE LEU ARG LYS ASP TYR LEU THR SEQRES 24 A 514 LEU GLU PRO SER LEU HIS GLU LEU ARG ASP TYR ILE GLY SEQRES 25 A 514 ASP SER LEU LYS GLN MET GLN TRP ASP GLY PHE LYS LYS SEQRES 26 A 514 PHE ASN SER LYS GLN GLN GLU LEU PHE LEU SER ILE VAL SEQRES 27 A 514 ASN PHE ASP LYS GLN LYS LEU GLN ASN GLU TYR ASN SER SEQRES 28 A 514 SER ASN LEU PRO ASN PHE VAL PHE THR GLY THR THR VAL SEQRES 29 A 514 TRP ALA GLY ASN HIS GLU ARG GLU TYR TYR ALA LYS GLN SEQRES 30 A 514 GLN ILE ASN VAL ILE ASN ASN ALA ILE ASN GLU SER SER SEQRES 31 A 514 PRO HIS TYR LEU GLY ASN SER TYR ASP LEU PHE PHE LYS SEQRES 32 A 514 GLY HIS PRO GLY GLY GLY ILE ILE ASN THR LEU ILE MET SEQRES 33 A 514 GLN ASN TYR PRO SER MET VAL ASP ILE PRO SER LYS ILE SEQRES 34 A 514 SER PHE GLU VAL LEU MET MET THR ASP MET LEU PRO ASP SEQRES 35 A 514 ALA VAL ALA GLY ILE ALA SER SER LEU TYR PHE THR ILE SEQRES 36 A 514 PRO ALA GLU LYS ILE LYS PHE ILE VAL PHE THR SER THR SEQRES 37 A 514 GLU THR ILE THR ASP ARG GLU THR ALA LEU ARG SER PRO SEQRES 38 A 514 LEU VAL GLN VAL MET ILE LYS LEU GLY ILE VAL LYS GLU SEQRES 39 A 514 GLU ASN VAL LEU PHE TRP ALA ASP LEU PRO ASN CYS GLU SEQRES 40 A 514 THR GLY VAL CYS ILE ALA VAL HET GLC B 1 12 HET GAL B 2 11 HET C5P A1427 21 HET GOL A3000 6 HET GOL A3001 6 HET GOL A3002 6 HET GOL A3003 6 HET GOL A3004 6 HET PO4 A4000 5 HET PO4 A4001 5 HET MG A5000 1 HET MG A5001 1 HET MG A5002 1 HETNAM GLC ALPHA-D-GLUCOPYRANOSE HETNAM GAL BETA-D-GALACTOPYRANOSE HETNAM C5P CYTIDINE-5'-MONOPHOSPHATE HETNAM GOL GLYCEROL HETNAM PO4 PHOSPHATE ION HETNAM MG MAGNESIUM ION HETSYN GLC ALPHA-D-GLUCOSE; D-GLUCOSE; GLUCOSE HETSYN GAL BETA-D-GALACTOSE; D-GALACTOSE; GALACTOSE HETSYN GOL GLYCERIN; PROPANE-1,2,3-TRIOL FORMUL 2 GLC C6 H12 O6 FORMUL 2 GAL C6 H12 O6 FORMUL 3 C5P C9 H14 N3 O8 P FORMUL 4 GOL 5(C3 H8 O3) FORMUL 9 PO4 2(O4 P 3-) FORMUL 11 MG 3(MG 2+) FORMUL 14 HOH *281(H2 O) HELIX 1 1 SER A 125 ASN A 142 1 18 HELIX 2 2 THR A 157 LEU A 164 1 8 HELIX 3 3 PRO A 177 LYS A 191 1 15 HELIX 4 4 HIS A 204 ASN A 217 1 14 HELIX 5 5 GLY A 233 ARG A 244 1 12 HELIX 6 6 ASN A 248 ASN A 265 1 18 HELIX 7 7 GLY A 275 TYR A 280 1 6 HELIX 8 8 ASN A 281 TYR A 286 1 6 HELIX 9 9 ASP A 296 GLU A 301 1 6 HELIX 10 10 LEU A 304 GLY A 312 1 9 HELIX 11 11 ASP A 321 PHE A 326 1 6 HELIX 12 12 ASN A 327 ASN A 339 1 13 HELIX 13 13 ASP A 341 ASN A 350 1 10 HELIX 14 14 GLY A 367 HIS A 369 5 3 HELIX 15 15 GLU A 370 ASN A 387 1 18 HELIX 16 16 GLY A 409 ASN A 418 1 10 HELIX 17 17 SER A 430 THR A 437 1 8 HELIX 18 18 SER A 449 THR A 454 5 6 HELIX 19 19 PRO A 456 GLU A 458 5 3 HELIX 20 20 SER A 480 LEU A 489 1 10 HELIX 21 21 LYS A 493 VAL A 497 5 5 HELIX 22 22 ALA A 501 LEU A 503 5 3 SHEET 1 A 4 ILE A 26 ILE A 35 0 SHEET 2 A 4 LYS A 103 VAL A 113 1 O ASN A 111 N LYS A 32 SHEET 3 A 4 GLU A 88 SER A 98 -1 N TYR A 90 O LEU A 110 SHEET 4 A 4 PHE A 52 CYS A 61 -1 N THR A 53 O VAL A 97 SHEET 1 B 2 TYR A 39 LEU A 42 0 SHEET 2 B 2 LEU A 77 VAL A 80 -1 O LEU A 77 N LEU A 42 SHEET 1 C 7 ILE A 166 SER A 168 0 SHEET 2 C 7 GLN A 146 TRP A 151 1 N ARG A 147 O THR A 167 SHEET 3 C 7 SER A 116 ASP A 122 1 N TYR A 120 O TYR A 148 SHEET 4 C 7 LEU A 194 ASN A 201 1 O ASN A 195 N LEU A 117 SHEET 5 C 7 VAL A 222 TYR A 230 1 O THR A 223 N LEU A 194 SHEET 6 C 7 ALA A 288 PHE A 292 1 O HIS A 291 N LEU A 229 SHEET 7 C 7 LEU A 315 GLN A 317 1 O LYS A 316 N TYR A 290 SHEET 1 D 6 VAL A 423 ASP A 424 0 SHEET 2 D 6 ASP A 399 LYS A 403 1 N PHE A 402 O VAL A 423 SHEET 3 D 6 ASN A 356 THR A 360 1 N PHE A 359 O PHE A 401 SHEET 4 D 6 ALA A 443 ILE A 447 1 O ALA A 443 N VAL A 358 SHEET 5 D 6 ILE A 460 PHE A 465 1 O LYS A 461 N VAL A 444 SHEET 6 D 6 LEU A 498 PHE A 499 1 O LEU A 498 N PHE A 465 SSBOND 1 CYS A 61 CYS A 91 1555 1555 2.07 SSBOND 2 CYS A 506 CYS A 511 1555 1555 2.09 LINK O4 GLC B 1 C1 GAL B 2 1555 1555 1.41 LINK OE1 GLU A 301 MG MG A5002 1555 1555 2.50 LINK O TYR A 349 MG MG A5000 1555 1555 2.47 CISPEP 1 THR A 22 GLN A 23 0 -16.93 CISPEP 2 ASN A 49 ILE A 50 0 -27.38 CISPEP 3 ASN A 350 SER A 351 0 -6.05 CISPEP 4 ILE A 471 THR A 472 0 -8.72 CISPEP 5 ALA A 501 ASP A 502 0 5.92 CRYST1 90.292 90.292 204.330 90.00 90.00 120.00 P 31 2 1 6 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 0.011075 0.006394 0.000000 0.00000 SCALE2 0.000000 0.012789 0.000000 0.00000 SCALE3 0.000000 0.000000 0.004894 0.00000