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- PDB-6kwf: Crystal Structure Analysis of Endo-beta-1,4-xylanase II Complexed... -

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Basic information

Entry
Database: PDB / ID: 6kwf
TitleCrystal Structure Analysis of Endo-beta-1,4-xylanase II Complexed with Xylotriose
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
4beta-beta-xylotriose / IODIDE ION / beta-D-xylopyranose / Endo-1,4-beta-xylanase 2
Similarity search - Component
Biological speciesTrichoderma reesei RUT C-30 (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.22 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 1.0Dec 30, 2020Provider: 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)22,0729
Polymers20,8151
Non-polymers1,2568
Water4,882271
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 area940 Å2
ΔGint-9 kcal/mol
Surface area7670 Å2
MethodPISA
Unit cell
Length a, b, c (Å)66.679, 67.931, 78.810
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number23
Space group name H-MI222
Components on special symmetry positions
IDModelComponents
11A-328-

HOH

21A-525-

HOH

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Components

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Protein , 1 types, 1 molecules A

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


Mass: 20815.400 Da / Num. of mol.: 1 / Mutation: N44D
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

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Sugars , 2 types, 2 molecules

#2: Polysaccharide beta-D-xylopyranose-(1-4)-beta-D-xylopyranose-(1-4)-beta-D-xylopyranose / 4beta-beta-xylotriose


Type: oligosaccharide, Oligosaccharide / Class: Metabolism / Mass: 414.360 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: oligosaccharide / References: 4beta-beta-xylotriose
DescriptorTypeProgram
DXylpb1-4DXylpb1-4DXylpb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/1,3,2/[a212h-1b_1-5]/1-1-1/a4-b1_b4-c1WURCSPDB2Glycan 1.1.0
[][b-D-Xylp]{[(4+1)][b-D-Xylp]{[(4+1)][b-D-Xylp]{}}}LINUCSPDB-CARE
#3: Sugar ChemComp-XYP / beta-D-xylopyranose / beta-D-xylose / D-xylose / xylose


Type: D-saccharide, beta linking / Mass: 150.130 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Formula: C5H10O5 / Feature type: SUBJECT OF INVESTIGATION
IdentifierTypeProgram
DXylpbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
b-D-xylopyranoseCOMMON NAMEGMML 1.0
b-D-XylpIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
XylSNFG CARBOHYDRATE SYMBOLGMML 1.0

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Non-polymers , 3 types, 277 molecules

#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3 / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical
ChemComp-IOD / IODIDE ION


Mass: 126.904 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: I / Feature type: SUBJECT OF INVESTIGATION
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 271 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 2.14 Å3/Da / Density % sol: 42.62 %
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: 1.22→19.84 Å / Num. obs: 52630 / % possible obs: 98.3 % / Redundancy: 1.6 % / Biso Wilson estimate: 11.68 Å2 / Rmerge(I) obs: 0.91 / Net I/σ(I): 8.24
Reflection shellResolution: 1.22→1.264 Å / Rmerge(I) obs: 0.91 / Num. unique obs: 5303

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Processing

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

2dfc


Resolution: 1.22→19.839 Å / SU ML: 0.1 / Cross valid method: THROUGHOUT / σ(F): 1.71 / Phase error: 15.19
RfactorNum. reflection% reflection
Rfree0.1559 1464 2.78 %
Rwork0.145 --
obs0.1453 52619 98.39 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 91.52 Å2 / Biso mean: 15.7247 Å2 / Biso min: 4.98 Å2
Refinement stepCycle: final / Resolution: 1.22→19.839 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1478 0 103 271 1852
Biso mean--31.45 29.8 -
Num. residues----190
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0151730
X-RAY DIFFRACTIONf_angle_d2.2122391
X-RAY DIFFRACTIONf_chiral_restr0.089246
X-RAY DIFFRACTIONf_plane_restr0.007317
X-RAY DIFFRACTIONf_dihedral_angle_d12.665581
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.22-1.26360.20511490.20535153100
1.2636-1.31420.22741410.19435157100
1.3142-1.3740.18821500.18225119100
1.374-1.44640.1811510.16885119100
1.4464-1.5370.16731440.1559510099
1.537-1.65560.16471460.1438512599
1.6556-1.82210.17031470.1418511398
1.8221-2.08550.14081480.129506898
2.0855-2.62660.15671440.1351507097
2.6266-19.8390.13681440.1382513194

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