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- PDB-6k9w: Crystal Structures of Endo-beta-1,4-xylanase II Complexed with Xy... -

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Basic information

Entry
Database: PDB / ID: 6k9w
TitleCrystal Structures of Endo-beta-1,4-xylanase II Complexed with Xylotriose
ComponentsEndo-1,4-beta-xylanase 2
KeywordsHYDROLASE / xylanase II / complex / Co-crystallization / Xylotriose
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
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
IODIDE ION / Endo-1,4-beta-xylanase 2
Similarity search - Component
Biological speciesTrichoderma reesei RUT C-30 (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.1 Å
AuthorsLi, C. / Wan, Q.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China31670790 China
CitationJournal: Protein J. / Year: 2020
Title: Studying the Role of a Single Mutation of a Family 11 Glycoside Hydrolase Using High-Resolution X-ray Crystallography.
Authors: Li, Z. / Zhang, X. / Li, C. / Kovalevsky, A. / Wan, Q.
History
DepositionJun 18, 2019Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jan 27, 2021Provider: repository / Type: Initial release
Revision 1.1Nov 22, 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
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Endo-1,4-beta-xylanase 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,1084
Polymers20,7271
Non-polymers3813
Water5,711317
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration, molecular weight of 20 KDa shown in gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area130 Å2
ΔGint-1 kcal/mol
Surface area7930 Å2
MethodPISA
Unit cell
Length a, b, c (Å)48.192, 59.526, 69.856
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Endo-1,4-beta-xylanase 2 / Xylanase 2 / 1 / 4-beta-D-xylan xylanohydrolase 2 / Alkaline endo-beta-1 / 4-xylanase


Mass: 20727.338 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Trichoderma reesei RUT C-30 (fungus) / Gene: xyn2 / Production host: Escherichia coli (E. coli) / References: UniProt: P36217, endo-1,4-beta-xylanase
#2: Chemical ChemComp-IOD / IODIDE ION


Mass: 126.904 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: I / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 317 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.42 Å3/Da / Density % sol: 49.11 %
Crystal growTemperature: 277 K / Method: evaporation / Details: 20% PEG 8000, 0.2M NaI, 0.1M MES

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Data collection

DiffractionMean temperature: 80 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL18U1 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Nov 7, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.1→30.125 Å / Num. obs: 81794 / % possible obs: 99.54 % / Redundancy: 6.5 % / Biso Wilson estimate: 8.4 Å2 / Rmerge(I) obs: 0.0295 / Net I/σ(I): 16.37
Reflection shellResolution: 1.1→1.139 Å / Rmerge(I) obs: 0.0295 / Num. unique obs: 8002

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Processing

Software
NameVersionClassification
XDSdata reduction
SCALEPACKdata scaling
PHENIX1.11.1_2575refinement
PDB_EXTRACT3.25data extraction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2DFC

2dfc


Resolution: 1.1→30.125 Å / SU ML: 0.08 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 11.91
RfactorNum. reflection% reflection
Rfree0.1439 4137 5.06 %
Rwork0.1357 --
obs0.1361 81794 99.54 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 64.06 Å2 / Biso mean: 12.8218 Å2 / Biso min: 4.65 Å2
Refinement stepCycle: final / Resolution: 1.1→30.125 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1472 0 3 317 1792
Biso mean--15.17 28.8 -
Num. residues----188
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0141652
X-RAY DIFFRACTIONf_angle_d1.8182283
X-RAY DIFFRACTIONf_chiral_restr0.519230
X-RAY DIFFRACTIONf_plane_restr0.012309
X-RAY DIFFRACTIONf_dihedral_angle_d12.575568
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.1-1.11250.16461320.1558252799
1.1125-1.12560.16021420.1448253498
1.1256-1.13930.15771360.14112531100
1.1393-1.15370.15941430.1327253299
1.1537-1.16890.14591400.1287253199
1.1689-1.18490.15541380.13212552100
1.1849-1.20190.14331350.1323256199
1.2019-1.21980.16021350.1323254999
1.2198-1.23890.12781390.1358256999
1.2389-1.25920.15261430.13072552100
1.2592-1.28090.15161180.131256699
1.2809-1.30420.13251190.1322259399
1.3042-1.32930.16161380.13012572100
1.3293-1.35640.14461350.12952554100
1.3564-1.38590.13411330.1332607100
1.3859-1.41810.1231520.13692578100
1.4181-1.45360.1371350.13092562100
1.4536-1.49290.15521330.12662583100
1.4929-1.53680.13391320.12232595100
1.5368-1.58640.12931460.11952586100
1.5864-1.64310.12581500.11732599100
1.6431-1.70890.13761470.11762577100
1.7089-1.78670.14221430.12222617100
1.7867-1.88090.12631380.12662597100
1.8809-1.99870.13621230.12512646100
1.9987-2.1530.1361490.1262595100
2.153-2.36950.13131430.12822647100
2.3695-2.71220.14991440.13572660100
2.7122-3.41640.14221340.14012677100
3.4164-30.1250.16851420.17442808100

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