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- PDB-1e0w: Xylanase 10A from Sreptomyces lividans. native structure at 1.2 a... -

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Basic information

Entry
Database: PDB / ID: 1e0w
TitleXylanase 10A from Sreptomyces lividans. native structure at 1.2 angstrom resolution
ComponentsENDO-1,4-BETA-XYLANASE A
KeywordsHYDROLASE / XYLAN DEGRADATION
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
Endo-1,4-beta-xylanase A
Similarity search - Component
Biological speciesSTREPTOMYCES LIVIDANS (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / OTHER / Resolution: 1.2 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 1.2Nov 13, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / diffrn_source / pdbx_entry_details / pdbx_modification_feature
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _diffrn_source.pdbx_synchrotron_site / _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


Theoretical massNumber of molelcules
Total (without water)34,1291
Polymers34,1291
Non-polymers00
Water7,891438
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)70.250, 46.930, 86.390
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: 34129.457 Da / Num. of mol.: 1 / Fragment: CATALYTIC MODULE, RESIDUES 42-343
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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 438 / 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 11 AMINO ACIDS 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: 2.2 Å3/Da / Density % sol: 44.3 %
Crystal growpH: 4.6
Details: PROTEIN 60MG/ML WAS CRYSTALLISED WITH 5% PEG 4000, 100MM SODIUM ACETATE PH 4.6
Crystal grow
*PLUS
Method: vapor diffusion, hanging drop / Details: Derewenda, U., (1994) J.Biol.Chem., 269, 20811.
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
160 mg/mlprotein1drop
25 %PEG40001drop
3100 mMsodium acetate1drop
45 %PEG40001reservoir
5100 mMsodium acetate1reservoir

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Data collection

DiffractionMean temperature: 297 K
Diffraction sourceSource: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: X31 / Wavelength: 0.87
DetectorDate: Nov 15, 1997
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.87 Å / Relative weight: 1
ReflectionResolution: 1.2→15 Å / Num. obs: 84936 / % possible obs: 96 % / Observed criterion σ(I): 2 / Redundancy: 4.3 % / Rmerge(I) obs: 0.051 / Net I/σ(I): 23.6
Reflection shellResolution: 1.2→1.22 Å / Redundancy: 3.4 % / Rmerge(I) obs: 0.35 / Mean I/σ(I) obs: 3.4 / % possible all: 91
Reflection
*PLUS
Lowest resolution: 15 Å / % possible obs: 96 %
Reflection shell
*PLUS
Highest resolution: 1.2 Å / % possible obs: 91 %

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Processing

Software
NameClassification
REFMACrefinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: OTHER / Resolution: 1.2→15 Å / Cross valid method: THROUGHOUT / σ(F): 0
Details: DOUBLY CONFIGURATED DISULPHIDE BOND BETWEEN CYS168 AND CYS201
RfactorNum. reflection% reflectionSelection details
Rfree0.124 4292 5 %RANDOM
Rwork0.098 ---
obs-81581 96 %-
Refinement stepCycle: LAST / Resolution: 1.2→15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2333 0 0 438 2771
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONp_bond_d0.010.02
X-RAY DIFFRACTIONp_angle_d0.0250.04
X-RAY DIFFRACTIONp_angle_deg
X-RAY DIFFRACTIONp_planar_d0.0310.05
X-RAY DIFFRACTIONp_hb_or_metal_coord
X-RAY DIFFRACTIONp_mcbond_it2.4523
X-RAY DIFFRACTIONp_mcangle_it3.275
X-RAY DIFFRACTIONp_scbond_it4.4994
X-RAY DIFFRACTIONp_scangle_it5.7416
X-RAY DIFFRACTIONp_plane_restr0.0280.03
X-RAY DIFFRACTIONp_chiral_restr0.0980.15
X-RAY DIFFRACTIONp_singtor_nbd0.150.3
X-RAY DIFFRACTIONp_multtor_nbd0.240.3
X-RAY DIFFRACTIONp_xhyhbond_nbd
X-RAY DIFFRACTIONp_xyhbond_nbd0.130.3
X-RAY DIFFRACTIONp_planar_tor5.27
X-RAY DIFFRACTIONp_staggered_tor11.915
X-RAY DIFFRACTIONp_orthonormal_tor
X-RAY DIFFRACTIONp_transverse_tor27.320
X-RAY DIFFRACTIONp_special_tor
Software
*PLUS
Name: REFMAC / Classification: refinement
Refinement
*PLUS
Lowest resolution: 15 Å / Rfactor obs: 0.09
Solvent computation
*PLUS
Displacement parameters
*PLUS

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