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- PDB-5ziw: Crystal Structures of Mutant Endo-beta-1,4-xylanase(Y77F) -

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Basic information

Entry
Database: PDB / ID: 5ziw
TitleCrystal Structures of Mutant Endo-beta-1,4-xylanase(Y77F)
ComponentsEndo-1,4-beta-xylanase 2
KeywordsHYDROLASE / Mutant 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 11/12, catalytic domain / 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, active site 2 / Glycosyl hydrolases family 11 (GH11) active site signature 2. / Glycoside hydrolase family 11/12, catalytic domain / 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 speciesHypocrea jecorina (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.3 Å
AuthorsZhang, X. / Wan, Q.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China31670790 China
Citation
Journal: to be published
Title: Crystal Structures of Endo-beta-1,4-xylanase II
Authors: Wan, Q. / Zhang, X.
#1: Journal: Proc. Natl. Acad. Sci. U.S.A. / Year: 2015
Title: Direct determination of protonation states and visualization of hydrogen bonding in a glycoside hydrolase with neutron crystallography.
Authors: Wan, Q. / Parks, J.M. / Hanson, B.L. / Fisher, S.Z. / Ostermann, A. / Schrader, T.E. / Graham, D.E. / Coates, L. / Langan, P. / Kovalevsky, A.
#2: Journal: Acta Crystallogr. D Biol. Crystallogr. / Year: 2014
Title: X-ray crystallographic studies of family 11 xylanase Michaelis and product complexes: implications for the catalytic mechanism.
Authors: Wan, Q. / Zhang, Q. / Hamilton-Brehm, S. / Weiss, K. / Mustyakimov, M. / Coates, L. / Langan, P. / Graham, D. / Kovalevsky, A.
History
DepositionMar 17, 2018Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Mar 20, 2019Provider: 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)21,0924
Polymers20,7111
Non-polymers3813
Water4,936274
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 area7910 Å2
MethodPISA
Unit cell
Length a, b, c (Å)48.424, 59.378, 70.046
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: 20711.338 Da / Num. of mol.: 1 / Mutation: Y77F
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Hypocrea jecorina (strain ATCC 56765 / BCRC 32924 / NRRL 11460 / Rut C-30) (fungus)
Strain: ATCC 56765 / BCRC 32924 / NRRL 11460 / Rut C-30 / Gene: xyn2, M419DRAFT_124931 / 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.: 274 / 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: 2.43 Å3/Da / Density % sol: 49.41 %
Crystal growTemperature: 291 K / Method: evaporation / pH: 5 / Details: 20% PEG 8000, 0.2M NaI, 0.1M PBS

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Data collection

DiffractionMean temperature: 80 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jan 20, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.3→45.294 Å / Num. obs: 49041 / % possible obs: 97.29 % / Redundancy: 6.5 % / Biso Wilson estimate: 10.24 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.02897 / Rsym value: 0.02897 / Net I/σ(I): 18.78
Reflection shellResolution: 1.3→1.346 Å / Redundancy: 6 % / Rmerge(I) obs: 0.204 / Mean I/σ(I) obs: 4.2 / Num. unique obs: 4906 / % possible all: 98.73

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Processing

Software
NameVersionClassification
SCALEPACKdata scaling
PHENIX1.11.1_2575refinement
PDB_EXTRACT3.24data extraction
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2DFC

2dfc


Resolution: 1.3→45.294 Å / SU ML: 0.11 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 14.67
RfactorNum. reflection% reflection
Rfree0.1617 2481 5.06 %
Rwork0.1432 --
obs0.1441 49005 97.29 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 54.69 Å2 / Biso mean: 14.0013 Å2 / Biso min: 5.86 Å2
Refinement stepCycle: final / Resolution: 1.3→45.294 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1471 0 3 274 1748
Biso mean--22.14 29.5 -
Num. residues----189
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.011563
X-RAY DIFFRACTIONf_angle_d1.0792142
X-RAY DIFFRACTIONf_chiral_restr0.094213
X-RAY DIFFRACTIONf_plane_restr0.008286
X-RAY DIFFRACTIONf_dihedral_angle_d12.982530
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 18

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.3-1.3250.28261230.20272556267998
1.325-1.35210.22381520.185226222774100
1.3521-1.38150.20551260.180526152741100
1.3815-1.41360.21491550.171126002755100
1.4136-1.4490.18111360.162326302766100
1.449-1.48810.19631370.145926162753100
1.4881-1.53190.15911310.134426652796100
1.5319-1.58140.1641500.126326062756100
1.5814-1.63790.15391490.12426272776100
1.6379-1.70350.14621490.117426362785100
1.7035-1.7810.16141470.120826302777100
1.781-1.87490.1291400.12272633277399
1.8749-1.99240.1478930.12482119221279
1.9924-2.14620.13691550.119426522807100
2.1462-2.36220.14091290.12662374250389
2.3622-2.7040.14411350.14112562269794
2.704-3.40650.15291370.14472706284399
3.4065-45.32130.17421370.16742675281293

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