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

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Basic information

Entry
Database: PDB / ID: 6kwd
TitleCrystal Structure Analysis 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
4beta-beta-xylotriose / 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: 1.298 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)21,3624
Polymers20,7281
Non-polymers6333
Water4,125229
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 area1080 Å2
ΔGint-2 kcal/mol
Surface area7850 Å2
MethodPISA
Unit cell
Length a, b, c (Å)47.598, 59.161, 69.604
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: 20728.322 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 / Production host: Escherichia coli (E. coli) / References: UniProt: P36217, endo-1,4-beta-xylanase
#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: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-IOD / IODIDE ION


Mass: 126.904 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: I / Feature type: SUBJECT OF INVESTIGATION
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 229 / 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: 2.36 Å3/Da / Density % sol: 47.97 %
Crystal growTemperature: 291 K / Method: evaporation / pH: 6 / Details: PEG 8000, NaI, 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: 1.298→32.73 Å / Num. obs: 49040 / % possible obs: 99.5 % / Redundancy: 2.17 % / Biso Wilson estimate: 15.95 Å2 / Rmerge(I) obs: 0.108 / Net I/σ(I): 15.25
Reflection shellResolution: 1.298→1.344 Å / Rmerge(I) obs: 0.108 / Num. unique obs: 4713

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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: 1.298→32.73 Å / SU ML: 0.12 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 16.4
RfactorNum. reflection% reflection
Rfree0.1628 2484 5.07 %
Rwork0.1505 --
obs0.1511 49040 99.4 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 96.52 Å2 / Biso mean: 23.1254 Å2 / Biso min: 11.46 Å2
Refinement stepCycle: final / Resolution: 1.298→32.73 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1472 0 63 229 1764
Biso mean--51.51 37.45 -
Num. residues----189
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0091607
X-RAY DIFFRACTIONf_angle_d1.3342206
X-RAY DIFFRACTIONf_chiral_restr0.085225
X-RAY DIFFRACTIONf_plane_restr0.006288
X-RAY DIFFRACTIONf_dihedral_angle_d13.167536
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.298-1.32260.23071210.1962240993
1.3226-1.34960.23351410.19042532100
1.3496-1.3790.23431290.1822579100
1.379-1.41110.19791520.17522550100
1.4111-1.44640.22491330.16822582100
1.4464-1.48550.1681300.15352586100
1.4855-1.52920.20731350.14932562100
1.5292-1.57850.15851470.12942579100
1.5785-1.63490.13891460.12762571100
1.6349-1.70040.16641450.12622571100
1.7004-1.77780.16451400.12412572100
1.7778-1.87150.14791380.12512595100
1.8715-1.98870.15711210.12972631100
1.9887-2.14230.15231500.12822568100
2.1423-2.35780.15111390.13762612100
2.3578-2.69880.15981410.14032630100
2.6988-3.39970.14431340.1542266199
3.3997-32.730.16861420.1745276699

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