PDB Short entry for 2WVT HEADER HYDROLASE 20-OCT-09 2WVT TITLE CRYSTAL STRUCTURE OF AN ALPHA-L-FUCOSIDASE GH29 FROM BACTEROIDES TITLE 2 THETAIOTAOMICRON IN COMPLEX WITH A NOVEL IMINOSUGAR FUCOSIDASE TITLE 3 INHIBITOR COMPND MOL_ID: 1; COMPND 2 MOLECULE: ALPHA-L-FUCOSIDASE; COMPND 3 CHAIN: A, B; COMPND 4 FRAGMENT: RESIDUES 31-473; COMPND 5 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: BACTEROIDES THETAIOTAOMICRON; SOURCE 3 ORGANISM_TAXID: 226186; SOURCE 4 STRAIN: VPI-5482; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 511693; SOURCE 7 EXPRESSION_SYSTEM_STRAIN: BL21; SOURCE 8 EXPRESSION_SYSTEM_PLASMID: PET28 KEYWDS HYDROLASE, ALPHA-L-FUCOSE, GLYCOSIDE HYDROLASE FAMILY 29 EXPDTA X-RAY DIFFRACTION AUTHOR A.LAMMERTS VAN BUEREN,A.ARDEVOL,J.FAYERS-KERR,B.LUO,Y.ZHANG, AUTHOR 2 M.SOLLOGOUB,Y.BLERIOT,C.ROVIRA,G.J.DAVIES REVDAT 4 20-DEC-23 2WVT 1 REMARK REVDAT 3 15-JUN-11 2WVT 1 REMARK HETSYN REVDAT 2 07-JUL-10 2WVT 1 JRNL REMARK SITE CRYST1 REVDAT 2 2 1 HETATM MASTER REVDAT 1 02-FEB-10 2WVT 0 JRNL AUTH A.LAMMERTS VAN BUEREN,A.ARDEVOL,J.FAYERS-KERR,B.LUO,Y.ZHANG, JRNL AUTH 2 M.SOLLOGOUB,Y.BLERIOT,C.ROVIRA,G.J.DAVIES JRNL TITL ANALYSIS OF THE REACTION COORDINATE OF ALPHA-L-FUCOSIDASES: JRNL TITL 2 A COMBINED STRUCTURAL AND QUANTUM MECHANICAL APPROACH. JRNL REF J.AM.CHEM.SOC. V. 132 1804 2010 JRNL REFN ISSN 0002-7863 JRNL PMID 20092273 JRNL DOI 10.1021/JA908908Q REMARK 2 REMARK 2 RESOLUTION. 1.80 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.5.0102 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) : 1.80 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 90.93 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 99.9 REMARK 3 NUMBER OF REFLECTIONS : 88765 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) : 0.209 REMARK 3 R VALUE (WORKING SET) : 0.207 REMARK 3 FREE R VALUE : 0.245 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 4690 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) : 1.80 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.85 REMARK 3 REFLECTION IN BIN (WORKING SET) : 6518 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 99.74 REMARK 3 BIN R VALUE (WORKING SET) : 0.3050 REMARK 3 BIN FREE R VALUE SET COUNT : 354 REMARK 3 BIN FREE R VALUE : 0.3490 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 7163 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 76 REMARK 3 SOLVENT ATOMS : 455 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 19.16 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -1.10000 REMARK 3 B22 (A**2) : 2.37000 REMARK 3 B33 (A**2) : -2.01000 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : -1.16000 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED OVERALL COORDINATE ERROR. REMARK 3 ESU BASED ON R VALUE (A): 0.138 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.132 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.105 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 3.471 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.948 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.926 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 7429 ; 0.013 ; 0.022 REMARK 3 BOND LENGTHS OTHERS (A): 5153 ; 0.001 ; 0.020 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 10058 ; 1.349 ; 1.938 REMARK 3 BOND ANGLES OTHERS (DEGREES): 12445 ; 0.861 ; 3.001 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 875 ; 5.976 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 356 ;32.872 ;24.045 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 1246 ;14.947 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 38 ;20.742 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 1016 ; 0.082 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 8198 ; 0.006 ; 0.021 REMARK 3 GENERAL PLANES OTHERS (A): 1586 ; 0.001 ; 0.020 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): 4356 ; 0.700 ; 1.500 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): 1777 ; 0.186 ; 1.500 REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 7019 ; 1.247 ; 2.000 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 3073 ; 1.936 ; 3.000 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 3038 ; 3.024 ; 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. U VALUES REFINED INDIVIDUALLY REMARK 4 REMARK 4 2WVT COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 20-OCT-09. REMARK 100 THE DEPOSITION ID IS D_1290041438. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 18-APR-09 REMARK 200 TEMPERATURE (KELVIN) : 120 REMARK 200 PH : NULL REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : ESRF REMARK 200 BEAMLINE : ID23-1 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.99 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC CCD REMARK 200 INTENSITY-INTEGRATION SOFTWARE : NULL REMARK 200 DATA SCALING SOFTWARE : NULL REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 93456 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.800 REMARK 200 RESOLUTION RANGE LOW (A) : 48.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 2.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.9 REMARK 200 DATA REDUNDANCY : 3.700 REMARK 200 R MERGE (I) : 0.10000 REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 8.7000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : NULL REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : NULL REMARK 200 COMPLETENESS FOR SHELL (%) : NULL REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 <I/SIGMA(I)> 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: NULL REMARK 200 STARTING MODEL: PDB ENTRY 2WVV REMARK 200 REMARK 200 REMARK: NONE REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 47.87 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.38 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: NULL REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: I 1 2 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,Y,-Z REMARK 290 3555 X+1/2,Y+1/2,Z+1/2 REMARK 290 4555 -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 32.94215 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 42.58000 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 57.43101 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 32.94215 REMARK 290 SMTRY2 4 0.000000 1.000000 0.000000 42.58000 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 57.43101 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: DIMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 4120 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 35230 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: 2.8 KCAL/MOL 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 GLU A 31 REMARK 465 ALA A 32 REMARK 465 LYS A 33 REMARK 465 LYS A 34 REMARK 465 LYS A 473 REMARK 465 GLU B 31 REMARK 465 ALA B 32 REMARK 465 LYS B 33 REMARK 465 LYS B 34 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 LYS A 424 CG CD CE NZ REMARK 470 LYS B 424 CG CD CE NZ 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 OD1 ASN B 78 O HOH B 2024 1.82 REMARK 500 OE1 GLU B 45 O HOH B 2002 1.85 REMARK 500 CD2 LEU A 433 NZ LYS A 457 2.09 REMARK 500 O HOH B 2028 O HOH B 2155 2.18 REMARK 500 O LEU A 434 O HOH A 2194 2.19 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 264 NE - CZ - NH2 ANGL. DEV. = -3.2 DEGREES REMARK 500 ARG B 264 NE - CZ - NH1 ANGL. DEV. = 4.0 DEGREES REMARK 500 ARG B 264 NE - CZ - NH2 ANGL. DEV. = -4.9 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 ARG A 60 -50.93 56.74 REMARK 500 ASN A 108 78.10 -152.69 REMARK 500 THR A 132 99.56 -68.01 REMARK 500 LYS A 157 -32.13 69.35 REMARK 500 ASN A 239 53.86 -116.64 REMARK 500 HIS A 272 -63.73 67.81 REMARK 500 ASN A 314 78.84 -157.40 REMARK 500 VAL A 381 -60.90 -120.04 REMARK 500 ASN A 402 45.48 -107.71 REMARK 500 ARG B 60 -46.09 62.96 REMARK 500 ASN B 153 46.82 -101.18 REMARK 500 LYS B 157 -36.23 66.93 REMARK 500 HIS B 272 -69.56 70.74 REMARK 500 SER B 285 35.09 -145.91 REMARK 500 ASN B 314 79.24 -160.41 REMARK 500 ASN B 448 18.16 59.77 REMARK 500 ALA B 472 -161.98 -75.54 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 B2036 DISTANCE = 5.82 ANGSTROMS REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE FHN A 1473 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE FHN B 1474 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GOL A 1474 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GOL A 1475 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GOL B 1475 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GOL B 1476 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC7 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GOL B 1477 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC8 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE IMD A 1477 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC9 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE IMD B 1479 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 2WVS RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF AN ALPHA-L-FUCOSIDASE GH29 TRAPPED COVALENT REMARK 900 INTERMEDIATE FROM BACTEROIDES THETAIOTAOMICRON IN COMPLEX WITH 2 - REMARK 900 FLUORO-FUCOSYL FLUORIDE USING AN E288Q MUTANT REMARK 900 RELATED ID: 2WVU RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF A MICHAELIS COMPLEX OF ALPHA-L-FUCOSIDASE GH29 REMARK 900 FROM BACTEROIDES THETAIOTAOMICRON WITH THE SYNTHETIC SUBSTRATE 4- REMARK 900 NITROPHENYL-ALPHA-L-FUCOSE REMARK 900 RELATED ID: 2WVV RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF AN ALPHA-L-FUCOSIDASE GH29 FROM BACTEROIDES REMARK 900 THETAIOTAOMICRON DBREF 2WVT A 31 473 UNP Q8A3I4 Q8A3I4_BACTN 31 473 DBREF 2WVT B 31 473 UNP Q8A3I4 Q8A3I4_BACTN 31 473 SEQRES 1 A 443 GLU ALA LYS LYS GLU ILE PRO LEU LYS TYR GLY ALA THR SEQRES 2 A 443 ASN GLU GLY LYS ARG GLN ASP PRO ALA MET GLN LYS PHE SEQRES 3 A 443 ARG ASP ASN ARG LEU GLY ALA PHE ILE HIS TRP GLY LEU SEQRES 4 A 443 TYR ALA ILE PRO GLY GLY GLU TRP ASN GLY LYS VAL TYR SEQRES 5 A 443 GLY GLY ALA ALA GLU TRP LEU LYS SER TRP ALA LYS VAL SEQRES 6 A 443 PRO ALA ASP GLU TRP LEU LYS LEU MET ASP GLN TRP ASN SEQRES 7 A 443 PRO THR LYS PHE ASP ALA LYS LYS TRP ALA LYS MET ALA SEQRES 8 A 443 LYS GLU MET GLY THR LYS TYR VAL LYS ILE THR THR LYS SEQRES 9 A 443 HIS HIS GLU GLY PHE CYS LEU TRP PRO SER LYS TYR THR SEQRES 10 A 443 LYS TYR THR VAL ALA ASN THR PRO TYR LYS ARG ASP ILE SEQRES 11 A 443 LEU GLY GLU LEU VAL LYS ALA TYR ASN ASP GLU GLY ILE SEQRES 12 A 443 ASP VAL HIS PHE TYR PHE SER VAL MET ASP TRP SER ASN SEQRES 13 A 443 PRO ASP TYR ARG TYR ASP ILE LYS SER LYS GLU ASP SER SEQRES 14 A 443 ILE ALA PHE SER ARG PHE LEU GLU PHE THR ASP ASN GLN SEQRES 15 A 443 LEU LYS GLU LEU ALA THR ARG TYR PRO THR VAL LYS ASP SEQRES 16 A 443 PHE TRP PHE ASP GLY THR TRP ASP ALA SER VAL LYS LYS SEQRES 17 A 443 ASN GLY TRP TRP THR ALA HIS ALA GLU GLN MET LEU LYS SEQRES 18 A 443 GLU LEU VAL PRO GLY VAL ALA ILE ASN SER ARG LEU ARG SEQRES 19 A 443 ALA ASP ASP LYS GLY LYS ARG HIS PHE ASP SER ASN GLY SEQRES 20 A 443 ARG LEU MET GLY ASP TYR GLU SER GLY TYR GLU ARG ARG SEQRES 21 A 443 LEU PRO ASP PRO VAL LYS ASP LEU LYS VAL THR GLN TRP SEQRES 22 A 443 ASP TRP GLU ALA CYS MET THR ILE PRO GLU ASN GLN TRP SEQRES 23 A 443 GLY TYR HIS LYS ASP TRP SER LEU SER TYR VAL LYS THR SEQRES 24 A 443 PRO ILE GLU VAL ILE ASP ARG ILE VAL HIS ALA VAL SER SEQRES 25 A 443 MET GLY GLY ASN MET VAL VAL ASN PHE GLY PRO GLN ALA SEQRES 26 A 443 ASP GLY ASP PHE ARG PRO GLU GLU LYS ALA MET ALA THR SEQRES 27 A 443 ALA ILE GLY LYS TRP MET ASN ARG TYR GLY LYS ALA VAL SEQRES 28 A 443 TYR ALA CYS ASP TYR ALA GLY PHE GLU LYS GLN ASP TRP SEQRES 29 A 443 GLY TYR TYR THR ARG GLY LYS ASN ASP GLU VAL TYR MET SEQRES 30 A 443 VAL VAL PHE ASN GLN PRO TYR SER GLU ARG LEU ILE VAL SEQRES 31 A 443 LYS THR PRO LYS GLY ILE THR VAL GLU LYS ALA THR LEU SEQRES 32 A 443 LEU THR THR GLY GLU ASP ILE THR VAL VAL GLU THR THR SEQRES 33 A 443 ARG ASN GLU TYR ASN VAL SER VAL PRO LYS LYS ASN PRO SEQRES 34 A 443 GLY GLU PRO TYR VAL ILE GLN LEU LYS VAL ARG ALA ALA SEQRES 35 A 443 LYS SEQRES 1 B 443 GLU ALA LYS LYS GLU ILE PRO LEU LYS TYR GLY ALA THR SEQRES 2 B 443 ASN GLU GLY LYS ARG GLN ASP PRO ALA MET GLN LYS PHE SEQRES 3 B 443 ARG ASP ASN ARG LEU GLY ALA PHE ILE HIS TRP GLY LEU SEQRES 4 B 443 TYR ALA ILE PRO GLY GLY GLU TRP ASN GLY LYS VAL TYR SEQRES 5 B 443 GLY GLY ALA ALA GLU TRP LEU LYS SER TRP ALA LYS VAL SEQRES 6 B 443 PRO ALA ASP GLU TRP LEU LYS LEU MET ASP GLN TRP ASN SEQRES 7 B 443 PRO THR LYS PHE ASP ALA LYS LYS TRP ALA LYS MET ALA SEQRES 8 B 443 LYS GLU MET GLY THR LYS TYR VAL LYS ILE THR THR LYS SEQRES 9 B 443 HIS HIS GLU GLY PHE CYS LEU TRP PRO SER LYS TYR THR SEQRES 10 B 443 LYS TYR THR VAL ALA ASN THR PRO TYR LYS ARG ASP ILE SEQRES 11 B 443 LEU GLY GLU LEU VAL LYS ALA TYR ASN ASP GLU GLY ILE SEQRES 12 B 443 ASP VAL HIS PHE TYR PHE SER VAL MET ASP TRP SER ASN SEQRES 13 B 443 PRO ASP TYR ARG TYR ASP ILE LYS SER LYS GLU ASP SER SEQRES 14 B 443 ILE ALA PHE SER ARG PHE LEU GLU PHE THR ASP ASN GLN SEQRES 15 B 443 LEU LYS GLU LEU ALA THR ARG TYR PRO THR VAL LYS ASP SEQRES 16 B 443 PHE TRP PHE ASP GLY THR TRP ASP ALA SER VAL LYS LYS SEQRES 17 B 443 ASN GLY TRP TRP THR ALA HIS ALA GLU GLN MET LEU LYS SEQRES 18 B 443 GLU LEU VAL PRO GLY VAL ALA ILE ASN SER ARG LEU ARG SEQRES 19 B 443 ALA ASP ASP LYS GLY LYS ARG HIS PHE ASP SER ASN GLY SEQRES 20 B 443 ARG LEU MET GLY ASP TYR GLU SER GLY TYR GLU ARG ARG SEQRES 21 B 443 LEU PRO ASP PRO VAL LYS ASP LEU LYS VAL THR GLN TRP SEQRES 22 B 443 ASP TRP GLU ALA CYS MET THR ILE PRO GLU ASN GLN TRP SEQRES 23 B 443 GLY TYR HIS LYS ASP TRP SER LEU SER TYR VAL LYS THR SEQRES 24 B 443 PRO ILE GLU VAL ILE ASP ARG ILE VAL HIS ALA VAL SER SEQRES 25 B 443 MET GLY GLY ASN MET VAL VAL ASN PHE GLY PRO GLN ALA SEQRES 26 B 443 ASP GLY ASP PHE ARG PRO GLU GLU LYS ALA MET ALA THR SEQRES 27 B 443 ALA ILE GLY LYS TRP MET ASN ARG TYR GLY LYS ALA VAL SEQRES 28 B 443 TYR ALA CYS ASP TYR ALA GLY PHE GLU LYS GLN ASP TRP SEQRES 29 B 443 GLY TYR TYR THR ARG GLY LYS ASN ASP GLU VAL TYR MET SEQRES 30 B 443 VAL VAL PHE ASN GLN PRO TYR SER GLU ARG LEU ILE VAL SEQRES 31 B 443 LYS THR PRO LYS GLY ILE THR VAL GLU LYS ALA THR LEU SEQRES 32 B 443 LEU THR THR GLY GLU ASP ILE THR VAL VAL GLU THR THR SEQRES 33 B 443 ARG ASN GLU TYR ASN VAL SER VAL PRO LYS LYS ASN PRO SEQRES 34 B 443 GLY GLU PRO TYR VAL ILE GLN LEU LYS VAL ARG ALA ALA SEQRES 35 B 443 LYS HET FHN A1473 13 HET GOL A1474 6 HET GOL A1475 6 HET IMD A1476 5 HET IMD A1477 5 HET FHN B1474 13 HET GOL B1475 6 HET GOL B1476 6 HET GOL B1477 6 HET IMD B1478 5 HET IMD B1479 5 HETNAM FHN (2S,3R,5R,6S)-3,4,5-TRIHYDROXY-2,6-BIS(HYDROXYMETHYL) HETNAM 2 FHN PIPERIDINIUM HETNAM GOL GLYCEROL HETNAM IMD IMIDAZOLE HETSYN GOL GLYCERIN; PROPANE-1,2,3-TRIOL FORMUL 3 FHN 2(C7 H16 N O5 1+) FORMUL 4 GOL 5(C3 H8 O3) FORMUL 6 IMD 4(C3 H5 N2 1+) FORMUL 14 HOH *455(H2 O) HELIX 1 1 ASP A 50 ARG A 60 1 11 HELIX 2 2 GLY A 68 ILE A 72 5 5 HELIX 3 3 ALA A 85 GLU A 87 5 3 HELIX 4 4 TRP A 88 ALA A 93 1 6 HELIX 5 5 PRO A 96 LYS A 102 1 7 HELIX 6 6 LEU A 103 TRP A 107 5 5 HELIX 7 7 ASP A 113 GLY A 125 1 13 HELIX 8 8 VAL A 151 THR A 154 5 4 HELIX 9 9 ASP A 159 GLU A 171 1 13 HELIX 10 10 SER A 195 TYR A 220 1 26 HELIX 11 11 ASP A 233 LYS A 238 1 6 HELIX 12 12 ASN A 239 VAL A 254 1 16 HELIX 13 13 SER A 261 ARG A 264 5 4 HELIX 14 14 ASP A 297 TRP A 303 5 7 HELIX 15 15 ASP A 321 SER A 325 5 5 HELIX 16 16 THR A 329 MET A 343 1 15 HELIX 17 17 ARG A 360 GLY A 378 1 19 HELIX 18 18 LYS A 379 VAL A 381 5 3 HELIX 19 19 ASP B 50 ARG B 60 1 11 HELIX 20 20 GLY B 68 ILE B 72 5 5 HELIX 21 21 ALA B 85 GLU B 87 5 3 HELIX 22 22 TRP B 88 ALA B 93 1 6 HELIX 23 23 PRO B 96 LYS B 102 1 7 HELIX 24 24 LEU B 103 TRP B 107 5 5 HELIX 25 25 ASP B 113 GLY B 125 1 13 HELIX 26 26 VAL B 151 THR B 154 5 4 HELIX 27 27 ASP B 159 GLU B 171 1 13 HELIX 28 28 SER B 195 TYR B 220 1 26 HELIX 29 29 ASP B 233 LYS B 238 1 6 HELIX 30 30 ASN B 239 VAL B 254 1 16 HELIX 31 31 SER B 261 ARG B 264 5 4 HELIX 32 32 ASP B 297 TRP B 303 5 7 HELIX 33 33 ASP B 321 SER B 325 5 5 HELIX 34 34 THR B 329 MET B 343 1 15 HELIX 35 35 ARG B 360 GLY B 378 1 19 HELIX 36 36 LYS B 379 VAL B 381 5 3 SHEET 1 AA 7 ALA A 258 ILE A 259 0 SHEET 2 AA 7 ASP A 225 ASP A 229 1 N PHE A 226 O ALA A 258 SHEET 3 AA 7 ASP A 174 SER A 180 1 O PHE A 177 N TRP A 227 SHEET 4 AA 7 TYR A 128 LYS A 134 1 O VAL A 129 N HIS A 176 SHEET 5 AA 7 LEU A 61 ILE A 65 1 O ALA A 63 N LYS A 130 SHEET 6 AA 7 GLY A 345 PHE A 351 1 O MET A 347 N GLY A 62 SHEET 7 AA 7 TRP A 305 MET A 309 1 O TRP A 305 N ASN A 346 SHEET 1 AB 2 GLU A 76 TRP A 77 0 SHEET 2 AB 2 LYS A 80 VAL A 81 -1 O LYS A 80 N TRP A 77 SHEET 1 AC 4 GLY A 395 ARG A 399 0 SHEET 2 AC 4 VAL A 405 VAL A 409 -1 O TYR A 406 N THR A 398 SHEET 3 AC 4 TYR A 463 ARG A 470 -1 O TYR A 463 N VAL A 409 SHEET 4 AC 4 THR A 427 LEU A 433 -1 O THR A 427 N ARG A 470 SHEET 1 AD 2 ASN A 411 PRO A 413 0 SHEET 2 AD 2 ASN B 411 PRO B 413 -1 O GLN B 412 N GLN A 412 SHEET 1 AE 3 ARG A 417 LYS A 421 0 SHEET 2 AE 3 GLU A 449 SER A 453 -1 O TYR A 450 N VAL A 420 SHEET 3 AE 3 VAL A 442 THR A 446 -1 O VAL A 443 N ASN A 451 SHEET 1 BA 7 ALA B 258 ILE B 259 0 SHEET 2 BA 7 VAL B 223 ASP B 229 1 O LYS B 224 N ALA B 258 SHEET 3 BA 7 ASP B 174 SER B 180 1 O VAL B 175 N LYS B 224 SHEET 4 BA 7 TYR B 128 THR B 132 1 O VAL B 129 N HIS B 176 SHEET 5 BA 7 LEU B 61 ILE B 65 1 O ALA B 63 N LYS B 130 SHEET 6 BA 7 GLY B 345 PHE B 351 1 O MET B 347 N GLY B 62 SHEET 7 BA 7 TRP B 305 MET B 309 1 O TRP B 305 N ASN B 346 SHEET 1 BB 2 GLU B 76 TRP B 77 0 SHEET 2 BB 2 LYS B 80 VAL B 81 -1 O LYS B 80 N TRP B 77 SHEET 1 BC 4 GLY B 395 ARG B 399 0 SHEET 2 BC 4 VAL B 405 VAL B 409 -1 O TYR B 406 N THR B 398 SHEET 3 BC 4 TYR B 463 ALA B 471 -1 O TYR B 463 N VAL B 409 SHEET 4 BC 4 ILE B 426 LEU B 433 -1 O THR B 427 N ARG B 470 SHEET 1 BD 3 ARG B 417 LYS B 421 0 SHEET 2 BD 3 GLU B 449 SER B 453 -1 O TYR B 450 N VAL B 420 SHEET 3 BD 3 VAL B 442 THR B 446 -1 O VAL B 443 N ASN B 451 SITE 1 AC1 12 HIS A 66 GLU A 87 TRP A 88 HIS A 135 SITE 2 AC1 12 HIS A 136 TYR A 178 TRP A 227 ASP A 229 SITE 3 AC1 12 ARG A 262 GLU A 288 CYS A 308 TRP A 316 SITE 1 AC2 12 HIS B 66 GLU B 87 TRP B 88 HIS B 135 SITE 2 AC2 12 HIS B 136 TYR B 178 TRP B 227 ASP B 229 SITE 3 AC2 12 ARG B 262 GLU B 288 CYS B 308 TRP B 316 SITE 1 AC3 6 TRP A 232 ARG A 262 ARG A 271 HIS A 272 SITE 2 AC3 6 GLY A 286 HOH A2214 SITE 1 AC4 3 GLU A 284 GLY A 286 TYR A 287 SITE 1 AC5 6 ALA B 85 GLU B 87 TRP B 88 ASN B 314 SITE 2 AC5 6 TRP B 316 HOH B2131 SITE 1 AC6 6 ASP A 393 VAL B 295 LYS B 391 GLN B 392 SITE 2 AC6 6 ASP B 393 HOH B2241 SITE 1 AC7 7 ASP A 393 ASP B 335 LYS B 391 GLY B 395 SITE 2 AC7 7 TYR B 396 ASN B 411 HOH B2211 SITE 1 AC8 4 LYS A 456 LYS A 457 ASN A 458 HOH A2208 SITE 1 AC9 3 LYS B 90 SER B 91 TYR B 191 CRYST1 104.830 85.160 121.285 90.00 108.73 90.00 I 1 2 1 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 0.009539 0.000000 0.003234 0.00000 SCALE2 0.000000 0.011743 0.000000 0.00000 SCALE3 0.000000 0.000000 0.008706 0.00000