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- PDB-1e0v: Xylanase 10A from Sreptomyces lividans. cellobiosyl-enzyme interm... -

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Basic information

Entry
Database: PDB / ID: 1e0v
TitleXylanase 10A from Sreptomyces lividans. cellobiosyl-enzyme intermediate at 1.7 A
ComponentsENDO-1,4-BETA-XYLANASE A
KeywordsHYDROLASE / XYLANASE / XYLAN DEGRADATION / GLYCOSYL-ENZYME INTERMEDIATE
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. / Ricin-type beta-trefoil lectin domain / Glycosyl hydrolases family 10 (GH10) domain profile. / Glycoside hydrolase family 10 / Glycoside hydrolase family 10 domain / Glycosyl hydrolase family 10 / Glycosyl hydrolase family 10 / Ricin-type beta-trefoil / Lectin domain of ricin B chain profile. ...Glycosyl hydrolases family 10, active site / Glycosyl hydrolases family 10 (GH10) active site. / Ricin-type beta-trefoil lectin domain / Glycosyl hydrolases family 10 (GH10) domain profile. / Glycoside hydrolase family 10 / Glycoside hydrolase family 10 domain / Glycosyl hydrolase family 10 / Glycosyl hydrolase family 10 / 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
2-deoxy-2-fluoro-beta-cellobiose / Endo-1,4-beta-xylanase A
Similarity search - Component
Biological speciesSTREPTOMYCES LIVIDANS (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.7 Å
AuthorsDucros, V. / Charnock, S.J. / Derewenda, U. / Derewenda, Z.S. / Dauter, Z. / Dupont, C. / Shareck, F. / Morosoli, R. / Kluepfel, D. / Davies, G.J.
Citation
Journal: J.Biol.Chem. / Year: 2000
Title: Substrate Specificity in Glycoside Hydrolase Family 10. Structural and Kinetic Analysis of the Streptomyces Lividans Xylanase 10A
Authors: Ducros, V. / Charnock, S.J. / Derewenda, U. / Derewenda, Z.S. / Dauter, Z. / Dupont, C. / Shareck, F. / Morosoli, R. / Kluepfel, D. / Davies, G.J.
#1: Journal: J.Biol.Chem. / Year: 2000
Title: Substrate Specificity in Glycoside Hydrolase Family 10. Tyrosine 87 and Leucine 314 Play a Pivotal Role in Discriminating between Glucose and Xylose Binding in the Proximal Active Site of ...Title: Substrate Specificity in Glycoside Hydrolase Family 10. Tyrosine 87 and Leucine 314 Play a Pivotal Role in Discriminating between Glucose and Xylose Binding in the Proximal Active Site of Pseudomonas Cellulosa Xylanase 10A.
Authors: Andrews, S.R. / Charnock, S.J. / Lakey, J.H. / Davies, G.J. / Claeyssens, M. / Nerinckx, W. / Underwood, M. / Sinnott, M.L. / Warren, R.A. / Gilbert, H.J.
#2: Journal: J.Biol.Chem. / Year: 1994
Title: Crystal Structure, at 2.6 A Resolution, of the Streptomyces Lividans Xylanase A, a Member of the F Family of B-1,4-D-Glycanases
Authors: Derewenda, U. / Swenson, L. / Green, R. / Wei, Y. / Morosoli, R. / Shareck, F. / Kluepfel, D. / Derewenda, Z.S.
History
DepositionApr 10, 2000Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 5, 2001Provider: repository / Type: Initial release
Revision 1.1Feb 5, 2014Group: Database references / Derived calculations ...Database references / Derived calculations / Non-polymer description / Other / Structure summary / Version format compliance
Revision 2.0Jul 29, 2020Group: Atomic model / Data collection ...Atomic model / Data collection / Derived calculations / Non-polymer description / Other / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / entity / entity_name_com / pdbx_branch_scheme / pdbx_chem_comp_identifier / pdbx_database_status / pdbx_entity_branch / pdbx_entity_branch_descriptor / pdbx_entity_branch_link / pdbx_entity_branch_list / pdbx_entity_nonpoly / pdbx_molecule_features / pdbx_nonpoly_scheme / struct_conn / struct_site / struct_site_gen
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_asym_id / _atom_site.auth_atom_id / _atom_site.auth_comp_id / _atom_site.auth_seq_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.type_symbol / _chem_comp.formula / _chem_comp.formula_weight / _chem_comp.id / _chem_comp.mon_nstd_flag / _chem_comp.name / _chem_comp.type / _entity.pdbx_description / _entity.src_method / _entity.type / _pdbx_database_status.status_code_sf
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1May 1, 2024Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 2.2Nov 13, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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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)34,4302
Polymers34,0851
Non-polymers3441
Water9,098505
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)67.870, 46.270, 87.070
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 / XYLANASE A


Mass: 34085.449 Da / Num. of mol.: 1 / Fragment: CATALYTIC MODULE, RESIDUES 42-343
Source method: isolated from a genetically manipulated source
Details: GLYCOSYL ENXYME INTERMEDIATE. COVALENT LINK BETWEEN GLU 236 AND THE SUBSTRATE
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: Polysaccharide beta-D-glucopyranose-(1-4)-2-deoxy-2-fluoro-alpha-D-glucopyranose / 2-deoxy-2-fluoro-beta-cellobiose


Type: oligosaccharide, Oligosaccharide / Class: Substrate analog / Mass: 344.288 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: oligosaccharide / References: 2-deoxy-2-fluoro-beta-cellobiose
DescriptorTypeProgram
WURCS=2.0/2,2,1/[a2122h-1a_1-5_2*F][a2122h-1b_1-5]/1-2/a4-b1WURCSPDB2Glycan 1.1.0
[][D-1-deoxy-Glcp2fluoro]{[(4+1)][b-D-Glcp]{}}LINUCSPDB-CARE
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 505 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY
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 IF AFTER CLEAVAGE OF THE SIGNAL PEPTIDE. THE LAST 10 RESIDUES ARE INVISIBLE 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: 2.2 Å3/Da / Density % sol: 44.3 %
Crystal growpH: 7.5
Details: PROTEIN WAS CRYSTALLISED WITH 16 % PEG 4000 AS PRECIPITANT,100MM HEPES PH 7.5 AS BUFFER, 10% ISOPROPANOL, CRYSTAL WERE SOAKED IN PRESENCE OF POWDERED SUBSTR
Crystal grow
*PLUS
Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
10.1 Msodium HEPES1reservoir
216 %(w/v)PEG40001reservoir
310 %(v/v)isopropanol1drop
430 mg/mlprotein1drop

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Sep 15, 1999
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.7→15 Å / Num. obs: 29439 / % possible obs: 97 % / Observed criterion σ(I): 2 / Redundancy: 4.3 % / Biso Wilson estimate: 17.5 Å2 / Rmerge(I) obs: 0.032 / Net I/σ(I): 36.5
Reflection shellResolution: 1.7→1.76 Å / Redundancy: 4.9 % / Rmerge(I) obs: 0.121 / Mean I/σ(I) obs: 9.4 / % possible all: 82
Reflection
*PLUS
Lowest resolution: 15 Å / % possible obs: 97 %
Reflection shell
*PLUS
% possible obs: 82 %

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Processing

Software
NameClassification
REFMACrefinement
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: NATIVE STRUCTURE AT 1.2

Resolution: 1.7→15 Å / Cross valid method: THROUGHOUT / σ(F): 0
Details: DOUBLY CONFIGURATED DISULPHIDE BOND BETWEEN CYS168 AND CYS201 THE SIDE CHAIN OF GLN 88, TRP 274 AND ARG 275 ARE MISSING SINCE THEY ARE TOO DISORDERED TO BE BUILT INTO DENSITY
RfactorNum. reflection% reflectionSelection details
Rfree0.199 1538 5 %RANDOM
Rwork0.158 ---
obs-28774 97 %-
Refinement stepCycle: LAST / Resolution: 1.7→15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2314 0 22 505 2841
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONp_bond_d0.0070.02
X-RAY DIFFRACTIONp_angle_d0.0220.04
X-RAY DIFFRACTIONp_angle_deg
X-RAY DIFFRACTIONp_planar_d0.0220.05
X-RAY DIFFRACTIONp_hb_or_metal_coord
X-RAY DIFFRACTIONp_mcbond_it2.0593
X-RAY DIFFRACTIONp_mcangle_it2.7495
X-RAY DIFFRACTIONp_scbond_it3.224
X-RAY DIFFRACTIONp_scangle_it4.0216
X-RAY DIFFRACTIONp_plane_restr0.0180.03
X-RAY DIFFRACTIONp_chiral_restr0.0930.15
X-RAY DIFFRACTIONp_singtor_nbd0.160.3
X-RAY DIFFRACTIONp_multtor_nbd0.240.3
X-RAY DIFFRACTIONp_xhyhbond_nbd
X-RAY DIFFRACTIONp_xyhbond_nbd0.150.3
X-RAY DIFFRACTIONp_planar_tor3.27
X-RAY DIFFRACTIONp_staggered_tor12.415
X-RAY DIFFRACTIONp_orthonormal_tor
X-RAY DIFFRACTIONp_transverse_tor26.320
X-RAY DIFFRACTIONp_special_tor
Software
*PLUS
Name: REFMAC / Classification: refinement
Refinement
*PLUS
Lowest resolution: 15 Å / Rfactor obs: 0.15
Solvent computation
*PLUS
Displacement parameters
*PLUS

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