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Basic information

Entry
Database: PDB / ID: 6k9x
TitleCrystal Structure Analysis of Protein
ComponentsEndo-1,4-beta-xylanase 2
KeywordsHYDROLASE / Xylanase
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 speciesHypocrea jecorina RUT C-30 (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.2 Å
AuthorsLi, C. / Wan, Q.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China31670790 China
CitationJournal: Acta Crystallographica Section D-Biological Crystallography
Year: 2014
Title: X-ray crystallographic studies of family 11 xylanase Michaelis and product complexes: implications for the catalytic mechanism
Authors: Wan, Q.
History
DepositionJun 18, 2019Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Apr 28, 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)21,5225
Polymers20,7271
Non-polymers7954
Water3,999222
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 area950 Å2
ΔGint-10 kcal/mol
Surface area7650 Å2
MethodPISA
Unit cell
Length a, b, c (Å)48.597, 58.268, 70.239
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: 20727.336 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Hypocrea jecorina RUT C-30 (fungus) / Gene: xyn2, M419DRAFT_124931 / 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


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-IOD / IODIDE ION


Mass: 126.904 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: I
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 222 / 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: 2.4 Å3/Da / Density % sol: 48.73 %
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: BL19U1 / 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: 1.2→39.964 Å / Num. obs: 62650 / % possible obs: 99.17 % / Redundancy: 5.7 % / Biso Wilson estimate: 12.19 Å2 / Net I/σ(I): 18.32
Reflection shellResolution: 1.2→1.243 Å / Num. unique obs: 6177

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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: 1.2→39.964 Å / SU ML: 0.08 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 12.52
RfactorNum. reflection% reflection
Rfree0.1412 3144 5.03 %
Rwork0.1298 --
obs0.1304 62517 99.12 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 73.09 Å2 / Biso mean: 16.275 Å2 / Biso min: 7.54 Å2
Refinement stepCycle: final / Resolution: 1.2→39.964 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1472 0 59 222 1753
Biso mean--17.4 29.96 -
Num. residues----189
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0091617
X-RAY DIFFRACTIONf_angle_d1.112226
X-RAY DIFFRACTIONf_chiral_restr0.082230
X-RAY DIFFRACTIONf_plane_restr0.006291
X-RAY DIFFRACTIONf_dihedral_angle_d12.934539
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 22

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.2-1.21880.18521340.15752679281398
1.2188-1.23870.19611580.140426462804100
1.2387-1.26010.17531370.141826872824100
1.2601-1.2830.13951190.135726872806100
1.283-1.30770.1541350.12827142849100
1.3077-1.33440.16351490.12426652814100
1.3344-1.36340.14831430.12242657280099
1.3634-1.39510.14991400.121126902830100
1.3951-1.430.15961490.12832694284399
1.43-1.46870.15041380.11922666280499
1.4687-1.51190.1381340.113426882822100
1.5119-1.56070.12291450.113726972842100
1.5607-1.61650.11541540.1112704285899
1.6165-1.68120.13051540.11562661281599
1.6812-1.75770.11881570.11972689284699
1.7577-1.85040.13391460.12032690283699
1.8504-1.96630.14031110.12692662277397
1.9663-2.11810.16111580.12032704286299
2.1181-2.33130.13051570.12422724288199
2.3313-2.66860.13381410.12742752289399
2.6686-3.36190.12741410.13042754289599
3.3619-39.98620.15341440.1512863300797

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