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- PDB-6kwc: Crystal Structure Analysis of Endo-beta-1,4-xylanase II -

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Basic information

Entry
Database: PDB / ID: 6kwc
TitleCrystal Structure Analysis of Endo-beta-1,4-xylanase II
ComponentsEndo-1,4-beta-xylanase 2
KeywordsHYDROLASE / Xylanase II / 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: 1.3 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
DepositionSep 6, 2019Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jan 27, 2021Provider: repository / Type: Initial release
Revision 1.1Nov 22, 2023Group: Advisory / Data collection ...Advisory / 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 / pdbx_unobs_or_zero_occ_atoms
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)21,4856
Polymers20,8851
Non-polymers6005
Water4,684260
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 area800 Å2
ΔGint-1 kcal/mol
Surface area7990 Å2
MethodPISA
Unit cell
Length a, b, c (Å)48.495, 59.185, 69.841
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 Endo-1,4-beta-xylanase 2 / Xylanase 2 / 1 / 4-beta-D-xylan xylanohydrolase 2 / Alkaline endo-beta-1 / 4-xylanase


Mass: 20885.494 Da / Num. of mol.: 1 / Mutation: N44E/E177Q
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Trichoderma reesei RUT C-30 (fungus) / Gene: xyn2, M419DRAFT_124931 / Production host: Escherichia coli (E. coli) / References: UniProt: P36217, endo-1,4-beta-xylanase
#2: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#3: Chemical
ChemComp-IOD / IODIDE ION


Mass: 126.904 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: I
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 260 / 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: 2.4 Å3/Da / Density % sol: 48.74 %
Crystal growTemperature: 291 K / Method: evaporation / pH: 4.5 / Details: PEG 8000, NaI, NaAc-HAc

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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: Jun 2, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.297→19.92 Å / Num. obs: 49236 / % possible obs: 97.5 % / Redundancy: 2.65 % / Biso Wilson estimate: 19.7 Å2 / Rmerge(I) obs: 0.19 / Net I/σ(I): 7.5
Reflection shellResolution: 1.3→1.34 Å / Rmerge(I) obs: 0.19

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Processing

Software
NameVersionClassification
PHENIX1.12_2829refinement
XDSdata reduction
SCALEPACKdata scaling
PDB_EXTRACT3.25data extraction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2DFC

2dfc


Resolution: 1.3→19.92 Å / SU ML: 0.12 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 16.85
RfactorNum. reflection% reflection
Rfree0.172 2479 5.04 %
Rwork0.157 --
obs0.158 49218 97.5 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 24.51 Å2
Refinement stepCycle: LAST / Resolution: 1.3→19.92 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1483 0 10 260 1753
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0071581
X-RAY DIFFRACTIONf_angle_d1.0142164
X-RAY DIFFRACTIONf_dihedral_angle_d12.732538
X-RAY DIFFRACTIONf_chiral_restr0.089215
X-RAY DIFFRACTIONf_plane_restr0.007287
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.2971-1.3220.2791160.23082418X-RAY DIFFRACTION92
1.322-1.3490.2471520.21132615X-RAY DIFFRACTION100
1.349-1.37830.21671250.20552623X-RAY DIFFRACTION100
1.3783-1.41040.23131630.18762597X-RAY DIFFRACTION100
1.4104-1.44560.21731290.17352640X-RAY DIFFRACTION100
1.4456-1.48470.19431430.16582616X-RAY DIFFRACTION100
1.4847-1.52840.19911300.14832652X-RAY DIFFRACTION100
1.5284-1.57770.17371500.1482629X-RAY DIFFRACTION100
1.5777-1.63410.18511480.14292634X-RAY DIFFRACTION100
1.6341-1.69950.19211490.14122649X-RAY DIFFRACTION100
1.6995-1.77680.23871490.17512623X-RAY DIFFRACTION100
1.7768-1.87040.19791400.16672661X-RAY DIFFRACTION100
1.8704-1.98750.14851170.12442647X-RAY DIFFRACTION99
1.9875-2.14080.17011510.12142624X-RAY DIFFRACTION99
2.1408-2.35590.1451470.12422616X-RAY DIFFRACTION98
2.3559-2.69610.13191340.13312585X-RAY DIFFRACTION95
2.6961-3.3940.15061210.15342448X-RAY DIFFRACTION90
3.394-19.9170.19041150.19512462X-RAY DIFFRACTION86

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