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- PDB-4xv0: Crystal structure of an endo-beta-1,4-xylanase (glycoside hydrola... -

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Basic information

Entry
Database: PDB / ID: 4xv0
TitleCrystal structure of an endo-beta-1,4-xylanase (glycoside hydrolase family 10/GH10) enzyme from Trichoderma reesei
ComponentsBeta-xylanaseXylanase
KeywordsHYDROLASE / xylanase / fungus / TIM barrel / alpha8/beta8 fold / glycoside hydrolase family 10 / GH10
Function / homology
Function and homology information


endo-1,4-beta-xylanase activity / endo-1,4-beta-xylanase / xylan catabolic process / extracellular region
Similarity search - Function
Glycosyl hydrolases family 10 (GH10) domain profile. / Glycoside hydrolase family 10 domain / Glycosyl hydrolase family 10 / Glycosyl hydrolase family 10 / Glycosidases / Glycoside hydrolase superfamily / TIM Barrel / Alpha-Beta Barrel / Alpha Beta
Similarity search - Domain/homology
Endo-1,4-beta-xylanase 3
Similarity search - Component
Biological speciesHypocrea jecorina (fungus)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.9697 Å
AuthorsStogios, P.J. / Xu, X. / Cui, H. / Savchenko, A.
CitationJournal: To Be Published
Title: Crystal structure of an endo-beta-1,4-xylanase (glycoside hydrolase family 10/GH10) enzyme from Trichoderma reesei
Authors: Stogios, P.J. / Xu, X. / Cui, H. / Savchenko, A.
History
DepositionJan 26, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 11, 2015Provider: repository / Type: Initial release
Revision 2.0Sep 27, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Polymer sequence / Refinement description / Source and taxonomy
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / entity_poly / entity_src_gen / pdbx_initial_refinement_model / pdbx_prerelease_seq / pdbx_struct_oper_list
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _entity_poly.pdbx_seq_one_letter_code_can / _entity_src_gen.pdbx_alt_source_flag / _pdbx_struct_oper_list.symmetry_operation

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Beta-xylanase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,96212
Polymers33,1561
Non-polymers80611
Water8,161453
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)41.708, 47.490, 136.403
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 Beta-xylanase / Xylanase


Mass: 33156.086 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Hypocrea jecorina (fungus) / Strain: QM6a / Gene: TRIREDRAFT_120229 / Plasmid: ANIp7G / Production host: Aspergillus niger (mold) / References: UniProt: G0RA32, endo-1,4-beta-xylanase
#2: Chemical
ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: SO4
#3: Chemical
ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Cl
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 453 / 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: 2.04 Å3/Da / Density % sol: 39.6 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 6.5 / Details: 0.1 M Bis-tris pH 6.5, 1.5 M ammonium sulphate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS HTC / Detector: IMAGE PLATE / Date: May 22, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.9697→30 Å / Num. obs: 19529 / % possible obs: 81.8 % / Redundancy: 5 % / Rmerge(I) obs: 0.037 / Net I/σ(I): 65.43
Reflection shellResolution: 1.9697→2 Å / Redundancy: 3.1 % / Rmerge(I) obs: 0.057 / Mean I/σ(I) obs: 36.08 / % possible all: 81.8

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Processing

Software
NameVersionClassification
PHENIX(phenix.refine: 1.9_1692)refinement
HKL-3000data reduction
HKL-3000data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1TUX

1tux


Resolution: 1.9697→28.476 Å / SU ML: 0.18 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 16.31 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.1851 974 5 %Random selection
Rwork0.122 ---
obs0.1251 19478 97.85 %-
Solvent computationShrinkage radii: 1.2 Å / VDW probe radii: 1.3 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.9697→28.476 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2340 0 41 453 2834
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0072441
X-RAY DIFFRACTIONf_angle_d1.1133323
X-RAY DIFFRACTIONf_dihedral_angle_d13.187878
X-RAY DIFFRACTIONf_chiral_restr0.075367
X-RAY DIFFRACTIONf_plane_restr0.004431
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.9697-2.07350.21611220.12492326X-RAY DIFFRACTION88
2.0735-2.20340.21911390.12152632X-RAY DIFFRACTION99
2.2034-2.37340.22271400.12652644X-RAY DIFFRACTION100
2.3734-2.61210.18341410.13052683X-RAY DIFFRACTION100
2.6121-2.98980.19071400.12832675X-RAY DIFFRACTION99
2.9898-3.76540.17611420.11152692X-RAY DIFFRACTION99
3.7654-28.47870.15761500.1212852X-RAY DIFFRACTION99
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
11.6970.36350.39741.3280.27951.7735-0.030.10150.0844-0.04410.0189-0.0448-0.14460.13230.00970.09350.00510.01240.08440.00260.1175-1.04564.187917.4056
20.81340.28910.25791.3210.40911.52250.0004-0.0252-0.03380.02470.0150.02290.1025-0.0744-0.01810.08220.00070.00560.09460.00320.0974-13.5254-6.236630.4644
33.27950.1004-1.32460.64310.15091.2149-0.01290.0949-0.0972-0.02150.0468-0.02460.08960.0226-0.02520.11710.0061-0.01710.0887-0.01220.0961-5.7081-10.073611.4359
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain A and resi 47:125
2X-RAY DIFFRACTION2chain A and resi 126:239
3X-RAY DIFFRACTION3chain A and resi 240:346

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