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

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Basic information

Entry
Database: PDB / ID: 6jug
TitleCrystal Structures of Endo-beta-1,4-xylanase II Complexed with Xylotriose
ComponentsEndo-1,4-beta-xylanase 2
KeywordsHYDROLASE / xylanase II / complex / Xylotriose
Function / homology
Function and homology information


endo-1,4-beta-xylanase / endo-1,4-beta-xylanase activity / xylan catabolic process / extracellular region
Similarity search - Function
Glycoside hydrolase family 11/12, catalytic domain / 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 ...Glycoside hydrolase family 11/12, catalytic domain / 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 / Jelly Rolls / Sandwich / Mainly Beta
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: 1.19 Å
AuthorsLi, C. / Wan, Q.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China31670790 China
Citation
Journal: 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.
#1: Journal: 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: Qun, W. / Qiu, Z.
#2: Journal: PNAS / Year: 2015
Title: Direct determination of protonation states and visualization of hydrogen bonding in a glycoside hydrolase with neutron crystallography.
Authors: Wan, Q. / Jerry, M.P.
History
DepositionApr 13, 2019Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Apr 15, 2020Provider: repository / Type: Initial release
Revision 1.1Dec 23, 2020Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.id ..._citation.country / _citation.id / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Nov 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

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)21,1224
Polymers20,7411
Non-polymers3813
Water4,522251
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 area7900 Å2
MethodPISA
Unit cell
Length a, b, c (Å)48.379, 59.140, 69.851
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: 20741.363 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) / Strain: Rut C-30 / 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
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 251 / Source method: isolated from a natural source / Formula: H2O

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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: 2.41 Å3/Da / Density % sol: 48.94 %
Crystal growTemperature: 291 K / Method: evaporation / pH: 6 / Details: 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: 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: 1.19→37.45 Å / Num. obs: 63593 / % possible obs: 97.94 % / Redundancy: 6 % / Biso Wilson estimate: 9.93 Å2 / Net I/σ(I): 19.6
Reflection shellResolution: 1.19→1.233 Å / Num. unique obs: 5906 / % possible all: 91.91

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Processing

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

2dfc


Resolution: 1.19→37.446 Å / SU ML: 0.09 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 12.58
RfactorNum. reflection% reflection
Rfree0.1441 3204 5.04 %
Rwork0.1338 --
obs0.1343 63593 97.94 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 52.32 Å2 / Biso mean: 13.8832 Å2 / Biso min: 5.41 Å2
Refinement stepCycle: final / Resolution: 1.19→37.446 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1473 0 3 251 1727
Biso mean--18.86 28.56 -
Num. residues----189
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0111566
X-RAY DIFFRACTIONf_angle_d1.3752147
X-RAY DIFFRACTIONf_chiral_restr0.111214
X-RAY DIFFRACTIONf_plane_restr0.009286
X-RAY DIFFRACTIONf_dihedral_angle_d12.451532
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 23

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.19-1.20780.18521140.1592257237185
1.2078-1.22660.18731320.15222524265697
1.2266-1.24680.15511430.14752639278299
1.2468-1.26830.15261420.146526482790100
1.2683-1.29130.14691320.13782627275999
1.2913-1.31620.17161160.14142658277499
1.3162-1.3430.1811520.13812650280299
1.343-1.37220.15291300.13872613274399
1.3722-1.40420.15391510.142578272999
1.4042-1.43930.15791420.13382573271596
1.4393-1.47820.13071330.1332601273497
1.4782-1.52170.15561330.12622622275599
1.5217-1.57080.15281500.12582650280099
1.5708-1.62690.13761430.12292640278399
1.6269-1.69210.14491540.12062627278199
1.6921-1.76910.15031520.12222655280799
1.7691-1.86240.13161380.11882646278499
1.8624-1.9790.12131150.11652605272096
1.979-2.13180.13221520.11542651280398
2.1318-2.34630.12611540.12272684283899
2.3463-2.68580.13441440.13272715285999
2.6858-3.38340.14611370.13312727286499
3.3834-37.46440.15071450.15942799294497

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