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- PDB-1v0k: Xylanase Xyn10A from Streptomyces lividans in complex with xylobi... -

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Basic information

Entry
Database: PDB / ID: 1v0k
TitleXylanase Xyn10A from Streptomyces lividans in complex with xylobio-deoxynojirimycin at pH 5.8
ComponentsENDO-1,4-BETA-XYLANASE A
KeywordsHYDROLASE / GLYCOSIDE HYDROLASE FAMILY 10 / XYLANASE / XYLAN DEGRADATION / DEOXYNOJIRIMYCIN
Function / homology
Function and homology information


endo-1,4-beta-xylanase activity / endo-1,4-beta-xylanase / xylan catabolic process / carbohydrate binding / extracellular region
Similarity search - Function
Glycosyl hydrolases family 10, active site / Glycosyl hydrolases family 10 (GH10) active site. / Glycoside hydrolase family 10 / Glycosyl hydrolases family 10 (GH10) domain profile. / Glycoside hydrolase family 10 domain / Glycosyl hydrolase family 10 / Glycosyl hydrolase family 10 / Ricin-type beta-trefoil lectin domain / Ricin-type beta-trefoil / Lectin domain of ricin B chain profile. ...Glycosyl hydrolases family 10, active site / Glycosyl hydrolases family 10 (GH10) active site. / Glycoside hydrolase family 10 / Glycosyl hydrolases family 10 (GH10) domain profile. / Glycoside hydrolase family 10 domain / Glycosyl hydrolase family 10 / Glycosyl hydrolase family 10 / Ricin-type beta-trefoil lectin domain / Ricin-type beta-trefoil / Lectin domain of ricin B chain profile. / Ricin B, lectin domain / Ricin B-like lectins / Glycosidases / Glycoside hydrolase superfamily / TIM Barrel / Alpha-Beta Barrel / Alpha Beta
Similarity search - Domain/homology
PIPERIDINE-3,4,5-TRIOL / beta-D-xylopyranose / Endo-1,4-beta-xylanase A
Similarity search - Component
Biological speciesSTREPTOMYCES LIVIDANS (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.03 Å
AuthorsGloster, T.M. / Williams, S.J. / Roberts, S. / Tarling, C.A. / Wicki S, J. / Withers, G. / Davies, G.J.
CitationJournal: Chem.Commun.(Camb.) / Year: 2004
Title: Atomic Resolution Analyses of the Binding of Xylobiose-Derived Deoxynojirimycin and Isofagomine to Xylanase Xyn10A
Authors: Gloster, T.M. / Williams, S.J. / Roberts, S. / Tarling, C.A. / Wicki, J. / Withers, S.G. / Davies, G.J.
History
DepositionMar 31, 2004Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 16, 2004Provider: repository / Type: Initial release
Revision 1.1May 7, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 2.0Jul 29, 2020Group: Atomic model / Data collection ...Atomic model / Data collection / Derived calculations / Other / Structure summary
Category: atom_site / atom_site_anisotrop ...atom_site / atom_site_anisotrop / chem_comp / entity / pdbx_chem_comp_identifier / pdbx_database_status / pdbx_entity_nonpoly / struct_conn / struct_site / struct_site_gen
Item: _atom_site.auth_atom_id / _atom_site.label_atom_id ..._atom_site.auth_atom_id / _atom_site.label_atom_id / _atom_site_anisotrop.pdbx_auth_atom_id / _atom_site_anisotrop.pdbx_label_atom_id / _chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_database_status.status_code_sf / _pdbx_entity_nonpoly.name / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_label_atom_id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Dec 13, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI ..._chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag
Remark 700 SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "AA" IN EACH CHAIN ON SHEET RECORDS BELOW ... SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "AA" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 10-STRANDED BARREL THIS IS REPRESENTED BY A 11-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: ENDO-1,4-BETA-XYLANASE A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,4133
Polymers34,1291
Non-polymers2832
Water12,665703
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)67.080, 46.204, 86.071
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein ENDO-1,4-BETA-XYLANASE A / XYLANASE A / 1 / 4-BETA-D-XYLAN XYLANOHYDROLASE A


Mass: 34129.457 Da / Num. of mol.: 1 / Fragment: CATALYTIC MODULE, RESIDUES 42-354
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) STREPTOMYCES LIVIDANS (bacteria) / Production host: STREPTOMYCES LIVIDANS (bacteria) / Strain (production host): IAF 19 / References: UniProt: P26514, endo-1,4-beta-xylanase
#2: Sugar ChemComp-XYP / beta-D-xylopyranose / beta-D-xylose / D-xylose / xylose / Xylose


Type: D-saccharide, beta linking / Mass: 150.130 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Formula: C5H10O5
IdentifierTypeProgram
DXylpbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
b-D-xylopyranoseCOMMON NAMEGMML 1.0
b-D-XylpIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
XylSNFG CARBOHYDRATE SYMBOLGMML 1.0
#3: Chemical ChemComp-XDN / PIPERIDINE-3,4,5-TRIOL / XYLOSE-DERIVED 1-DEOXY-NOJIRIMYCIN


Mass: 133.146 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C5H11NO3
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 703 / Source method: isolated from a natural source / Formula: H2O
Compound detailsCONTRIBUTES TO THE HYDROLYSIS OF HEMICELLULOSE, WHICH IS THE MAJOR COMPONENT OF PLANT CELL-WALLS. ...CONTRIBUTES TO THE HYDROLYSIS OF HEMICELLULOSE, WHICH IS THE MAJOR COMPONENT OF PLANT CELL-WALLS. XLNA AND XLNB SEEM TO ACT SEQUENTIALLY ON THE SUBSTRATE TO YIELD XYLOBIOSE AND XYLOSE AS CARBON SOURCES.
Sequence detailsTHE FIRST 41 RESIDUES IN THE DATABASE CORRESPOND TO THE SIGNAL PEPTIDE. THE NUMBERING USED IN THE ...THE FIRST 41 RESIDUES IN THE DATABASE CORRESPOND TO THE SIGNAL PEPTIDE. THE NUMBERING USED IN THE PDB FILE IS AFTER CLEAVAGE OF THE SIGNAL PEPTIDE. RESIDUE 1 AND THE LAST 11 RESIDUES ARE TOO DISORDERED TO BE BUILT IN DENSITY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 1.9 Å3/Da / Density % sol: 35.3 % / Description: STRUCTURE ISOMORPHOUS WITH STARTING MODEL
Crystal growpH: 5.8
Details: 20 MG/ML PROTEIN, 0.1 M MES, PH 5.8, 18% PEG 5K MME, 7.5% ISOPROPANOL

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-1 / Wavelength: 0.934
DetectorType: ADSC CCD / Detector: CCD / Date: Oct 15, 2003 / Details: SAGITALLY FOCUSING GE(220) AND A MULTILAYER
RadiationMonochromator: DIAMOND (111), GE(220) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.934 Å / Relative weight: 1
ReflectionResolution: 1.03→30 Å / Num. obs: 128937 / % possible obs: 97.1 % / Redundancy: 4.2 % / Rmerge(I) obs: 0.047 / Net I/σ(I): 23.8
Reflection shellResolution: 1.03→1.05 Å / Redundancy: 3.5 % / Rmerge(I) obs: 0.415 / Mean I/σ(I) obs: 2.31 / % possible all: 93.7

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Processing

Software
NameVersionClassification
REFMAC5.2.0000refinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1OD8

1od8


Resolution: 1.03→27.15 Å / Cor.coef. Fo:Fc: 0.985 / Cor.coef. Fo:Fc free: 0.978 / SU B: 0.712 / SU ML: 0.016 / Cross valid method: THROUGHOUT / ESU R: 0.022 / ESU R Free: 0.024 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. RESIDUE 1 AND THE LAST 11 RESIDUES ARE TOO DISORDERED TO BE BUILT IN DENSITY A CIS-PEPTIDE BOND BETWEEN RESIDUES 89 AND 90 IS MANIFESTED ...Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. RESIDUE 1 AND THE LAST 11 RESIDUES ARE TOO DISORDERED TO BE BUILT IN DENSITY A CIS-PEPTIDE BOND BETWEEN RESIDUES 89 AND 90 IS MANIFESTED BECAUSE THE MAIN CHAIN IS BUILT IN DOUBLE CONFORMATION.
RfactorNum. reflection% reflectionSelection details
Rfree0.137 6421 5 %RANDOM
Rwork0.114 ---
obs0.115 122389 96.9 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 7.54 Å2
Baniso -1Baniso -2Baniso -3
1-0.82 Å20 Å20 Å2
2---0.44 Å20 Å2
3----0.38 Å2
Refinement stepCycle: LAST / Resolution: 1.03→27.15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2328 0 18 703 3049
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0212602
X-RAY DIFFRACTIONr_bond_other_d0.0010.022237
X-RAY DIFFRACTIONr_angle_refined_deg1.5721.9083560
X-RAY DIFFRACTIONr_angle_other_deg0.82235233
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.5555325
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.34324.436133
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.2215422
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.3921519
X-RAY DIFFRACTIONr_chiral_restr0.1090.2394
X-RAY DIFFRACTIONr_gen_planes_refined0.010.022970
X-RAY DIFFRACTIONr_gen_planes_other0.0040.02546
X-RAY DIFFRACTIONr_nbd_refined0.3170.2598
X-RAY DIFFRACTIONr_nbd_other0.2360.22347
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other0.1130.21278
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1770.2390
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.0880.214
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2810.243
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1980.2106
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.4041.52054
X-RAY DIFFRACTIONr_mcbond_other0.5461.5650
X-RAY DIFFRACTIONr_mcangle_it1.68322603
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it2.28231187
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it2.8734.5956
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.03→1.06 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.301 452
Rwork0.283 8441

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