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- PDB-3w25: The high-resolution crystal structure of TsXylA, intracellular xy... -

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Basic information

Entry
Database: PDB / ID: 3w25
TitleThe high-resolution crystal structure of TsXylA, intracellular xylanase from /Thermoanaerobacterium saccharolyticum JW/SL-YS485/: the complex of the E146A mutant with xylobiose
ComponentsGlycoside hydrolase family 10
KeywordsHYDROLASE / glycoside hydrolase / xylanase / thermophilic / xylobiose
Function / homology
Function and homology information


endo-1,4-beta-xylanase activity / endo-1,4-beta-xylanase / xylan catabolic process / carbohydrate binding
Similarity search - Function
Carbohydrate family 9 binding domain-like / Carbohydrate-binding domain, family 9 / S-layer homology domain / S-layer homology domain / Carbohydrate-binding, CenC-like / Carbohydrate binding domain / S-layer homology (SLH) domain profile. / Glycoside hydrolase, family 5, conserved site / Glycosyl hydrolases family 5 signature. / Glycosyl hydrolases family 10, active site ...Carbohydrate family 9 binding domain-like / Carbohydrate-binding domain, family 9 / S-layer homology domain / S-layer homology domain / Carbohydrate-binding, CenC-like / Carbohydrate binding domain / S-layer homology (SLH) domain profile. / Glycoside hydrolase, family 5, conserved site / Glycosyl hydrolases family 5 signature. / Glycosyl hydrolases family 10, active site / Glycosyl hydrolases family 10 (GH10) active site. / Glycosyl hydrolases family 10 (GH10) domain profile. / Glycoside hydrolase family 10 / Glycoside hydrolase family 10 domain / Glycosyl hydrolase family 10 / Glycosyl hydrolase family 10 / Galactose-binding-like domain superfamily / Glycosidases / Glycoside hydrolase superfamily / TIM Barrel / Alpha-Beta Barrel / Alpha Beta
Similarity search - Domain/homology
4beta-beta-xylobiose / Beta-xylanase
Similarity search - Component
Biological speciesThermoanaerobacterium saccharolyticum (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.32 Å
AuthorsHan, X. / Gao, J. / Shang, N. / Huang, C.-H. / Ko, T.-P. / Zhu, Z. / Wiegel, J. / Shao, W. / Guo, R.-T.
CitationJournal: Proteins / Year: 2013
Title: Structural and functional analyses of catalytic domain of GH10 xylanase from Thermoanaerobacterium saccharolyticum JW/SL-YS485
Authors: Han, X. / Gao, J. / Shang, N. / Huang, C.-H. / Ko, T.-P. / Chen, C.C. / Chan, H.C. / Cheng, Y.S. / Zhu, Z. / Wiegel, J. / Luo, W. / Guo, R.-T. / Ma, Y.
History
DepositionNov 27, 2012Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Apr 3, 2013Provider: repository / Type: Initial release
Revision 1.1Jul 31, 2013Group: Database references
Revision 2.0Jul 29, 2020Group: Atomic model / Data collection ...Atomic model / Data collection / Database references / Derived calculations / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / entity / entity_name_com / pdbx_branch_scheme / pdbx_chem_comp_identifier / pdbx_entity_branch / pdbx_entity_branch_descriptor / pdbx_entity_branch_link / pdbx_entity_branch_list / pdbx_entity_nonpoly / pdbx_molecule_features / pdbx_nonpoly_scheme / pdbx_struct_assembly_gen / struct_asym / struct_conn / struct_ref_seq_dif / 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_seq_id / _atom_site.label_asym_id / _atom_site.label_atom_id / _atom_site.type_symbol / _chem_comp.name / _chem_comp.type / _entity.formula_weight / _entity.pdbx_description / _entity.pdbx_number_of_molecules / _entity.type / _pdbx_struct_assembly_gen.asym_id_list / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_ref_seq_dif.details
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Nov 8, 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Glycoside hydrolase family 10
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,2872
Polymers38,0051
Non-polymers2821
Water12,340685
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)77.112, 118.607, 45.362
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212

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Components

#1: Protein Glycoside hydrolase family 10


Mass: 38005.020 Da / Num. of mol.: 1 / Fragment: UNP residues 349-684 / Mutation: E146A,P326L
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermoanaerobacterium saccharolyticum (bacteria)
Strain: JW/SL-YS485 / Gene: Tsac_1459 / Plasmid: pET46 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: I3VVC1, endo-1,4-beta-xylanase
#2: Polysaccharide beta-D-xylopyranose-(1-4)-beta-D-xylopyranose / 4beta-beta-xylobiose


Type: oligosaccharide, Oligosaccharide / Class: Metabolism / Mass: 282.245 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: oligosaccharide / References: 4beta-beta-xylobiose
DescriptorTypeProgram
DXylpb1-4DXylpb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/1,2,1/[a212h-1b_1-5]/1-1/a4-b1WURCSPDB2Glycan 1.1.0
[][b-D-Xylp]{[(4+1)][b-D-Xylp]{}}LINUCSPDB-CARE
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 685 / Source method: isolated from a natural source / Formula: H2O

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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: 2.73 Å3/Da / Density % sol: 54.93 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / pH: 8
Details: 0.1M Tris, 25% PEG 6000, 0.8M LiCl, pH 8.0, VAPOR DIFFUSION, SITTING DROP, temperature 295K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSRRC / Beamline: BL13B1 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Jun 6, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.32→25 Å / Num. all: 98337 / Num. obs: 98337 / % possible obs: 99.8 % / Redundancy: 7 % / Rmerge(I) obs: 0.103 / Net I/σ(I): 20.6
Reflection shellResolution: 1.32→1.37 Å / Rmerge(I) obs: 0.466 / Mean I/σ(I) obs: 3.3 / Rsym value: 0.068 / % possible all: 99.9

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Processing

Software
NameVersionClassification
HKL-2000data collection
PHASESphasing
CNS1.1refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3W24

3w24


Resolution: 1.32→25 Å / Occupancy max: 1 / Occupancy min: 1 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.1836 4751 4.8 %RANDOM
Rwork0.1616 ---
all-98337 --
obs-94867 96.3 %-
Solvent computationBsol: 45.9114 Å2
Displacement parametersBiso max: 53.68 Å2 / Biso mean: 15.4165 Å2 / Biso min: 4.38 Å2
Baniso -1Baniso -2Baniso -3
1--0.135 Å20 Å20 Å2
2---1.549 Å20 Å2
3---1.684 Å2
Refinement stepCycle: LAST / Resolution: 1.32→25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2593 0 19 685 3297
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_mcbond_it1.0261.5
X-RAY DIFFRACTIONc_scbond_it2.012
X-RAY DIFFRACTIONc_mcangle_it1.4582
X-RAY DIFFRACTIONc_scangle_it2.8372.5
LS refinement shellResolution: 1.32→1.37 Å

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