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- PDB-8yjj: Crystal structure of xylanase from Trichoderma longibrachiatum -

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Basic information

Entry
Database: PDB / ID: 8yjj
TitleCrystal structure of xylanase from Trichoderma longibrachiatum
ComponentsEndo-1,4-beta-xylanaseXylanase
KeywordsHYDROLASE / room temperature / xylanase / Trichoderma longibrachiatum
Function / homology
Function and homology information


endo-1,4-beta-xylanase activity / endo-1,4-beta-xylanase / xylan catabolic process
Similarity search - Function
Glycoside hydrolase family 11, active site 2 / Glycosyl hydrolases family 11 (GH11) active site signature 2. / Glycoside hydrolase family 11, active site 1 / Glycosyl hydrolases family 11 (GH11) active site signature 1. / Glycoside hydrolase family 11 / Glycosyl hydrolases family 11 (GH11) domain / Glycosyl hydrolases family 11 / Glycosyl hydrolases family 11 (GH11) domain profile. / Glycoside hydrolase family 11/12 / Concanavalin A-like lectin/glucanase domain superfamily
Similarity search - Domain/homology
Endo-1,4-beta-xylanase
Similarity search - Component
Biological speciesTrichoderma longibrachiatum (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsNam, K.H.
Funding support Korea, Republic Of, 1items
OrganizationGrant numberCountry
National Research Foundation (NRF, Korea)NRF-2021R1I1A1A01050838 Korea, Republic Of
CitationJournal: To Be Published
Title: Crystal structure of xylanase from Trichoderma longibrachiatum
Authors: Nam, K.H.
History
DepositionMar 2, 2024Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Mar 13, 2024Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Endo-1,4-beta-xylanase


Theoretical massNumber of molelcules
Total (without water)20,8381
Polymers20,8381
Non-polymers00
Water4,053225
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)40.476, 39.085, 56.640
Angle α, β, γ (deg.)90.00, 110.33, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Endo-1,4-beta-xylanase / Xylanase


Mass: 20838.436 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Trichoderma longibrachiatum (fungus) / References: UniProt: A0A2T4BZZ5, endo-1,4-beta-xylanase
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 225 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 2.02 Å3/Da / Density % sol: 38.99 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, hanging drop / Details: MES, ammonium sulfate, magnesium chloride

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: PAL/PLS / Beamline: 7A (6B, 6C1) / Wavelength: 0.9794 Å
DetectorType: ADSC QUANTUM 270 / Detector: CCD / Date: May 17, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9794 Å / Relative weight: 1
ReflectionResolution: 1.9→30 Å / Num. obs: 22849 / % possible obs: 96 % / Redundancy: 2.7 % / Rmerge(I) obs: 0.123 / Net I/σ(I): 16.23
Reflection shellResolution: 1.9→1.93 Å / Rmerge(I) obs: 0.262 / Num. unique obs: 644

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Processing

Software
NameVersionClassification
PHENIX(1.20.1_4487: ???)refinement
HKL-2000data scaling
HKL-2000data reduction
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1XYP

1xyp


Resolution: 1.9→27.23 Å / SU ML: 0.15 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 18.88 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1957 2323 10.17 %
Rwork0.1774 --
obs0.1793 22849 89.07 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.9→27.23 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1436 0 0 225 1661
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0021487
X-RAY DIFFRACTIONf_angle_d0.6672029
X-RAY DIFFRACTIONf_dihedral_angle_d7.123211
X-RAY DIFFRACTIONf_chiral_restr0.047202
X-RAY DIFFRACTIONf_plane_restr0.004267
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.9-1.940.22591410.20831229X-RAY DIFFRACTION90
1.94-1.980.20261540.19451217X-RAY DIFFRACTION92
1.98-2.030.20251340.19031254X-RAY DIFFRACTION91
2.03-2.080.24131450.17491225X-RAY DIFFRACTION92
2.08-2.130.19661260.18651264X-RAY DIFFRACTION92
2.13-2.20.18821410.18041241X-RAY DIFFRACTION92
2.2-2.270.19221410.18721232X-RAY DIFFRACTION91
2.27-2.350.2291330.17431234X-RAY DIFFRACTION91
2.35-2.440.24551380.19441250X-RAY DIFFRACTION91
2.44-2.550.22861500.18961227X-RAY DIFFRACTION90
2.55-2.690.22191280.18961190X-RAY DIFFRACTION89
2.69-2.860.20611330.18711182X-RAY DIFFRACTION88
2.86-3.080.19871360.17481181X-RAY DIFFRACTION87
3.08-3.390.16551370.16271170X-RAY DIFFRACTION87
3.39-3.870.15191250.15611191X-RAY DIFFRACTION86
3.87-4.870.15471330.14771132X-RAY DIFFRACTION84
4.88-27.230.21621280.19491107X-RAY DIFFRACTION81

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