HEADER HYDROLASE 05-MAR-12 3VPL TITLE CRYSTAL STRUCTURE OF A 2-FLUOROXYLOTRIOSYL COMPLEX OF THE VIBRIO SP. TITLE 2 AX-4 BETA-1,3-XYLANASE CAVEAT 3VPL BXF B 1 HAS WRONG CHIRALITY AT ATOM C1 COMPND MOL_ID: 1; COMPND 2 MOLECULE: BETA-1,3-XYLANASE XYL4; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: UNP RESIDUES 23-349; COMPND 5 SYNONYM: BETA-1,3-XYLANASE; COMPND 6 EC: 3.2.1.32; COMPND 7 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: VIBRIO; SOURCE 3 ORGANISM_TAXID: 678; SOURCE 4 STRAIN: AX-4; SOURCE 5 GENE: XYL4; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: BL21(DE3)PLYSS; SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 10 EXPRESSION_SYSTEM_PLASMID: PET23A KEYWDS BETA-1, 3-XYLANASE, GLYCOSIDE HYDROLASE, TIM BARREL, HYDROLASE EXPDTA X-RAY DIFFRACTION AUTHOR N.WATANABE,K.SAKAGUCHI REVDAT 3 08-NOV-23 3VPL 1 REMARK HETSYN REVDAT 2 29-JUL-20 3VPL 1 CAVEAT COMPND REMARK SEQADV REVDAT 2 2 1 HETNAM LINK SITE ATOM REVDAT 1 06-MAR-13 3VPL 0 JRNL AUTH K.SAKAGUCHI,E.D.GODDARD-BORGER,T.KAWAMURA,M.KIYOHARA, JRNL AUTH 2 I.TANAKA,M.ITO,S.G.WITHERS,N.WATANABE JRNL TITL THE CRYSTAL STRUCTURE OF A 2-FLUOROXYLOTRIOSYL COMPLEX OF JRNL TITL 2 THE VIBRIO SP. AX-4 BETA-1,3-XYLANASE AT 1.2 A RESOLUTION JRNL REF TO BE PUBLISHED JRNL REFN REMARK 1 REMARK 1 REFERENCE 1 REMARK 1 AUTH E.D.GODDARD-BORGER,K.SAKAGUCHI,S.REITINGER,N.WATANABE,M.ITO, REMARK 1 AUTH 2 S.G.WITHERS REMARK 1 TITL MECHANISTIC INSIGHTS INTO THE 1,3-XYLANASES: USEFUL ENZYMES REMARK 1 TITL 2 FOR MANIPULATION OF ALGAL BIOMASS REMARK 1 REF J.AM.CHEM.SOC. V. 134 3895 2012 REMARK 1 REFN ISSN 0002-7863 REMARK 1 PMID 22296113 REMARK 1 DOI 10.1021/JA211836T REMARK 2 REMARK 2 RESOLUTION. 1.20 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.6.0117 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) : 1.20 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 29.61 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 96.9 REMARK 3 NUMBER OF REFLECTIONS : 98433 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) : 0.142 REMARK 3 R VALUE (WORKING SET) : 0.141 REMARK 3 FREE R VALUE : 0.156 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 4931 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) : 1.20 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.23 REMARK 3 REFLECTION IN BIN (WORKING SET) : 6375 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 94.25 REMARK 3 BIN R VALUE (WORKING SET) : 0.1710 REMARK 3 BIN FREE R VALUE SET COUNT : 331 REMARK 3 BIN FREE R VALUE : 0.2030 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 2540 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 67 REMARK 3 SOLVENT ATOMS : 511 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 12.57 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 0.03000 REMARK 3 B22 (A**2) : -0.04000 REMARK 3 B33 (A**2) : 0.01000 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): 0.035 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.036 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.020 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 0.426 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.976 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.971 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 2879 ; 0.028 ; 0.020 REMARK 3 BOND LENGTHS OTHERS (A): NULL ; NULL ; NULL REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 3999 ; 2.434 ; 1.947 REMARK 3 BOND ANGLES OTHERS (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 386 ; 6.093 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 146 ;37.063 ;25.000 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 415 ;11.957 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 13 ;15.130 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 434 ; 0.258 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 2307 ; 0.017 ; 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 : NULL REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : MASK REMARK 3 PARAMETERS FOR MASK CALCULATION REMARK 3 VDW PROBE RADIUS : 1.20 REMARK 3 ION PROBE RADIUS : 0.80 REMARK 3 SHRINKAGE RADIUS : 0.80 REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: HYDROGENS HAVE BEEN USED IF PRESENT IN REMARK 3 THE INPUT U VALUES: REFINED INDIVIDUALLY REMARK 4 REMARK 4 3VPL COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 13-MAR-12. REMARK 100 THE DEPOSITION ID IS D_1000095341. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 13-FEB-11 REMARK 200 TEMPERATURE (KELVIN) : 95 REMARK 200 PH : 6.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : PHOTON FACTORY REMARK 200 BEAMLINE : BL-17A REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : NULL REMARK 200 WAVELENGTH OR RANGE (A) : 1.0 REMARK 200 MONOCHROMATOR : SI(111) REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 315R REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 98695 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.200 REMARK 200 RESOLUTION RANGE LOW (A) : 50.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : -3.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 97.1 REMARK 200 DATA REDUNDANCY : 7.300 REMARK 200 R MERGE (I) : 0.04400 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 14.1000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.20 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.22 REMARK 200 COMPLETENESS FOR SHELL (%) : 94.6 REMARK 200 DATA REDUNDANCY IN SHELL : 7.20 REMARK 200 R MERGE FOR SHELL (I) : 0.25700 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : NULL 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: 2DDX REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 43.63 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.18 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 1.0M SODIUM CITRATE, 0.1M MES, PH 6.5, REMARK 280 VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 293K 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 26.17150 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 40.82300 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 37.71850 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 40.82300 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 26.17150 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 37.71850 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: PISA REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B, C 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 GLY A 325 REMARK 465 SER A 326 REMARK 465 THR A 327 REMARK 465 HIS A 328 REMARK 465 HIS A 329 REMARK 465 HIS A 330 REMARK 465 HIS A 331 REMARK 465 HIS A 332 REMARK 465 HIS A 333 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 SER A 203 CB OG 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 ND1 HIS A 137 O HOH A 1214 1.48 REMARK 500 O HOH A 1579 O HOH A 1592 1.66 REMARK 500 O HOH A 1514 O HOH A 1535 1.85 REMARK 500 O HOH A 1220 O HOH A 1604 1.90 REMARK 500 OE1 GLN A 199 O HOH A 1322 1.91 REMARK 500 O HOH A 1324 O HOH A 1571 1.92 REMARK 500 OG SER A 240 O HOH A 1411 1.99 REMARK 500 O HOH A 1506 O HOH A 1567 2.01 REMARK 500 O HOH A 1154 O HOH A 1533 2.01 REMARK 500 O HOH A 1237 O HOH A 1544 2.01 REMARK 500 CD1 LEU A 1 O HOH A 1557 2.02 REMARK 500 CE1 HIS A 137 O HOH A 1214 2.05 REMARK 500 OD1 ASN A 66 O HOH A 1611 2.10 REMARK 500 O HOH A 1289 O HOH A 1578 2.12 REMARK 500 O HOH A 1520 O HOH A 1571 2.14 REMARK 500 O HOH A 1408 O HOH A 1568 2.16 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 O42 DNX A 1004 O HOH A 1604 4445 1.75 REMARK 500 O1 DNX A 1004 O HOH A 1451 4445 1.80 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 A 90 CD ARG A 90 NE 0.119 REMARK 500 GLU A 174 CD GLU A 174 OE2 0.097 REMARK 500 GLU A 212 CD GLU A 212 OE1 0.083 REMARK 500 TYR A 251 CE1 TYR A 251 CZ -0.090 REMARK 500 ASP A 273 C ASP A 273 O 0.117 REMARK 500 TRP A 276 CG TRP A 276 CD2 0.102 REMARK 500 TRP A 276 CE2 TRP A 276 CD2 0.096 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 LEU A 1 CA - CB - CG ANGL. DEV. = 17.9 DEGREES REMARK 500 LEU A 1 CB - CG - CD2 ANGL. DEV. = 11.4 DEGREES REMARK 500 ASP A 51 CB - CG - OD1 ANGL. DEV. = 7.3 DEGREES REMARK 500 ASP A 84 CB - CG - OD2 ANGL. DEV. = -5.8 DEGREES REMARK 500 ASP A 96 CB - CG - OD1 ANGL. DEV. = 6.7 DEGREES REMARK 500 ARG A 202 NE - CZ - NH2 ANGL. DEV. = -4.6 DEGREES REMARK 500 ASP A 245 CB - CG - OD1 ANGL. DEV. = 7.1 DEGREES REMARK 500 GLU A 246 OE1 - CD - OE2 ANGL. DEV. = -7.5 DEGREES REMARK 500 LYS A 263 CD - CE - NZ ANGL. DEV. = 14.8 DEGREES REMARK 500 ASP A 273 CB - CG - OD1 ANGL. DEV. = 13.9 DEGREES REMARK 500 ASP A 273 CB - CG - OD2 ANGL. DEV. = -10.4 DEGREES REMARK 500 ARG A 277 NE - CZ - NH2 ANGL. DEV. = -3.2 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 LEU A 5 14.71 52.61 REMARK 500 GLN A 17 31.19 -142.46 REMARK 500 ASN A 60 92.85 -164.04 REMARK 500 SER A 157 62.62 35.39 REMARK 500 PHE A 184 -74.12 -126.44 REMARK 500 ARG A 217 -1.05 79.44 REMARK 500 TYR A 282 73.92 76.46 REMARK 500 TRP A 287 -56.27 -120.09 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 LEU A 1 ASP A 2 147.99 REMARK 500 REMARK 500 REMARK: NULL REMARK 600 REMARK 600 HETEROGEN REMARK 600 REMARK 600 THE GLU212 ATTACKS AND BREAKS THE BOND BETWEEN BXF-DNX AND A NEW REMARK 600 BOND BETWEEN BXF(A1001)-GLU212 IS FORMED, AND THE ENZYME REACTION REMARK 600 WAS STOPPED AT A GLYCOSYL-ENZYME INTERMEDIATE STATE. DBREF 3VPL A 1 327 UNP D5MP61 3XYN1_VIBSX 23 349 SEQADV 3VPL HIS A 328 UNP D5MP61 EXPRESSION TAG SEQADV 3VPL HIS A 329 UNP D5MP61 EXPRESSION TAG SEQADV 3VPL HIS A 330 UNP D5MP61 EXPRESSION TAG SEQADV 3VPL HIS A 331 UNP D5MP61 EXPRESSION TAG SEQADV 3VPL HIS A 332 UNP D5MP61 EXPRESSION TAG SEQADV 3VPL HIS A 333 UNP D5MP61 EXPRESSION TAG SEQRES 1 A 333 LEU ASP GLY VAL LEU VAL PRO GLU SER GLY ILE LEU VAL SEQRES 2 A 333 SER VAL GLY GLN ASP VAL ASP SER VAL ASN ASP TYR ALA SEQRES 3 A 333 SER ALA LEU GLY THR ILE PRO ALA GLY VAL THR ASN TYR SEQRES 4 A 333 VAL GLY ILE VAL ASN LEU ASP GLY LEU ASN SER ASP ALA SEQRES 5 A 333 ASP ALA GLY ALA GLY ARG ASN ASN ILE ALA GLU LEU ALA SEQRES 6 A 333 ASN ALA TYR PRO THR SER ALA LEU VAL VAL GLY VAL SER SEQRES 7 A 333 MET ASN GLY GLU VAL ASP ALA VAL ALA SER GLY ARG TYR SEQRES 8 A 333 ASN ALA ASN ILE ASP THR LEU LEU ASN THR LEU ALA GLY SEQRES 9 A 333 TYR ASP ARG PRO VAL TYR LEU ARG TRP ALA TYR GLU VAL SEQRES 10 A 333 ASP GLY PRO TRP ASN GLY HIS SER PRO SER GLY ILE VAL SEQRES 11 A 333 THR SER PHE GLN TYR VAL HIS ASP ARG ILE ILE ALA LEU SEQRES 12 A 333 GLY HIS GLN ALA LYS ILE SER LEU VAL TRP GLN VAL ALA SEQRES 13 A 333 SER TYR CYS PRO THR PRO GLY GLY GLN LEU ASP GLN TRP SEQRES 14 A 333 TRP PRO GLY SER GLU TYR VAL ASP TRP VAL GLY LEU SER SEQRES 15 A 333 TYR PHE ALA PRO GLN ASP CYS ASN TRP ASP ARG VAL ASN SEQRES 16 A 333 GLU ALA ALA GLN PHE ALA ARG SER LYS GLY LYS PRO LEU SEQRES 17 A 333 PHE LEU ASN GLU SER THR PRO GLN ARG TYR GLN VAL ALA SEQRES 18 A 333 ASP LEU THR TYR SER ALA ASP PRO ALA LYS GLY THR ASN SEQRES 19 A 333 ARG GLN SER LYS THR SER GLN GLN LEU TRP ASP GLU TRP SEQRES 20 A 333 PHE ALA PRO TYR PHE GLN PHE MET SER ASP ASN SER ASP SEQRES 21 A 333 ILE VAL LYS GLY PHE THR TYR ILE ASN ALA ASP TRP ASP SEQRES 22 A 333 SER GLN TRP ARG TRP ALA ALA PRO TYR ASN GLU GLY TYR SEQRES 23 A 333 TRP GLY ASP SER ARG VAL GLN ALA ASN ALA LEU ILE LYS SEQRES 24 A 333 SER ASN TRP GLN GLN GLU ILE ALA LYS GLY GLN TYR ILE SEQRES 25 A 333 ASN HIS SER GLU THR LEU PHE GLU THR LEU GLY TYR GLY SEQRES 26 A 333 SER THR HIS HIS HIS HIS HIS HIS HET BXF B 1 9 HET XYP B 2 9 HET XYP B 3 9 HET BXF C 1 9 HET XYP C 2 9 HET XYP C 3 9 HET DNX A1004 13 HETNAM BXF 2-DEOXY-2-FLUORO-BETA-D-XYLOPYRANOSE HETNAM XYP BETA-D-XYLOPYRANOSE HETNAM DNX 3,4-DINITROPHENOL HETSYN BXF 2-DEOXY-2-FLUORO-BETA-D-XYLOSE; 2-DEOXY-2-FLUORO-D- HETSYN 2 BXF XYLOSE; 2-DEOXY-2-FLUORO-XYLOSE HETSYN XYP BETA-D-XYLOSE; D-XYLOSE; XYLOSE FORMUL 2 BXF 2(C5 H9 F O4) FORMUL 2 XYP 4(C5 H10 O5) FORMUL 4 DNX C6 H4 N2 O5 FORMUL 5 HOH *511(H2 O) HELIX 1 1 ASP A 18 GLY A 30 1 13 HELIX 2 2 ASN A 60 TYR A 68 1 9 HELIX 3 3 GLU A 82 SER A 88 1 7 HELIX 4 4 TYR A 91 TYR A 105 1 15 HELIX 5 5 GLY A 119 GLY A 123 5 5 HELIX 6 6 SER A 125 LEU A 143 1 19 HELIX 7 7 LEU A 166 TRP A 170 5 5 HELIX 8 8 GLY A 172 VAL A 176 5 5 HELIX 9 9 ALA A 185 ASN A 190 5 6 HELIX 10 10 TRP A 191 GLY A 205 1 15 HELIX 11 11 THR A 239 TRP A 247 1 9 HELIX 12 12 TRP A 247 ASN A 258 1 12 HELIX 13 13 ASP A 271 ALA A 279 5 9 HELIX 14 14 ARG A 291 ALA A 294 5 4 HELIX 15 15 ASN A 295 ALA A 307 1 13 HELIX 16 16 THR A 317 LEU A 322 1 6 SHEET 1 A10 TYR A 311 ILE A 312 0 SHEET 2 A10 ILE A 11 GLY A 16 1 N ILE A 11 O ILE A 312 SHEET 3 A10 VAL A 262 ILE A 268 1 O LYS A 263 N LEU A 12 SHEET 4 A10 LEU A 208 SER A 213 1 N LEU A 210 O THR A 266 SHEET 5 A10 TRP A 178 TYR A 183 1 N TYR A 183 O GLU A 212 SHEET 6 A10 ILE A 149 GLN A 154 1 N TRP A 153 O TRP A 178 SHEET 7 A10 VAL A 109 TRP A 113 1 N LEU A 111 O SER A 150 SHEET 8 A10 ALA A 72 SER A 78 1 N VAL A 75 O ARG A 112 SHEET 9 A10 GLY A 35 GLY A 41 1 N VAL A 40 O SER A 78 SHEET 10 A10 ILE A 11 GLY A 16 1 N VAL A 15 O GLY A 35 SHEET 1 B 4 GLN A 236 SER A 237 0 SHEET 2 B 4 THR A 224 TYR A 225 -1 N TYR A 225 O GLN A 236 SHEET 3 B 4 TYR A 218 GLN A 219 -1 N GLN A 219 O THR A 224 SHEET 4 B 4 GLY A 288 ASP A 289 1 O ASP A 289 N TYR A 218 SSBOND 1 CYS A 159 CYS A 189 1555 1555 2.04 LINK OE1 GLU A 212 C1 BXF B 1 1555 1555 1.45 LINK O1 DNX A1004 C1 BXF C 1 1555 1555 1.41 LINK O3 BXF B 1 C1 XYP B 2 1555 1555 1.42 LINK O3 XYP B 2 C1 XYP B 3 1555 1555 1.42 LINK O3 BXF C 1 C1 XYP C 2 1555 1555 1.43 LINK O4 XYP C 2 C1 XYP C 3 1555 1555 1.45 CISPEP 1 GLY A 16 GLN A 17 0 7.12 CISPEP 2 ALA A 280 PRO A 281 0 7.60 CRYST1 52.343 75.437 81.646 90.00 90.00 90.00 P 21 21 21 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 0.019105 0.000000 0.000000 0.00000 SCALE2 0.000000 0.013256 0.000000 0.00000 SCALE3 0.000000 0.000000 0.012248 0.00000