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- PDB-3w24: The high-resolution crystal structure of TsXylA, intracellular xy... -

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Basic information

Entry
Database: PDB / ID: 3w24
TitleThe high-resolution crystal structure of TsXylA, intracellular xylanase from Thermoanaerobacterium saccharolyticum JW/SL-YS485
ComponentsGlycoside hydrolase family 10
KeywordsHYDROLASE / glycoside hydrolase / xylanase / thermophilic
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
Biological speciesThermoanaerobacterium saccharolyticum (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.35 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 1.2Nov 8, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Glycoside hydrolase family 10


Theoretical massNumber of molelcules
Total (without water)38,0631
Polymers38,0631
Non-polymers00
Water10,899605
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)76.944, 118.781, 45.290
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212
Components on special symmetry positions
IDModelComponents
11A-448-

HOH

21A-518-

HOH

31A-707-

HOH

41A-720-

HOH

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Components

#1: Protein Glycoside hydrolase family 10 / xylanase


Mass: 38063.055 Da / Num. of mol.: 1 / Fragment: UNP residues 349-684 / Mutation: P326L
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermoanaerobacterium saccharolyticum (bacteria)
Strain: JW/SL-YS485 / Gene: Tsac_1459 / Plasmid: pET46a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: I3VVC1, endo-1,4-beta-xylanase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 605 / 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: 2.67 Å3/Da / Density % sol: 54 %
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
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Jun 6, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthRelative weight: 1
ReflectionResolution: 1.35→25 Å / Num. obs: 90031 / % possible obs: 97.6 % / Redundancy: 3.6 % / Rmerge(I) obs: 0.062 / Net I/σ(I): 21.8
Reflection shellResolution: 1.35→1.4 Å / Redundancy: 3.6 % / Rmerge(I) obs: 0.481 / Mean I/σ(I) obs: 3.8 / % possible all: 100

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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: 2Q8X

2q8x


Resolution: 1.35→23.63 Å / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.198 --RANDOM
Rwork0.175 ---
obs-87122 94.8 %-
Solvent computationBsol: 53.6594 Å2
Displacement parametersBiso mean: 15.9421 Å2
Baniso -1Baniso -2Baniso -3
1--0.769 Å20 Å20 Å2
2---2.85 Å20 Å2
3---3.619 Å2
Refinement stepCycle: LAST / Resolution: 1.35→23.63 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2597 0 0 605 3202
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_mcbond_it1.0981.5
X-RAY DIFFRACTIONc_scbond_it2.132
X-RAY DIFFRACTIONc_mcangle_it1.5332
X-RAY DIFFRACTIONc_scangle_it3.1042.5

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