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- PDB-7ayp: Structure of a GH11 domain refined from the X-ray diffraction dat... -

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Basic information

Entry
Database: PDB / ID: 7ayp
TitleStructure of a GH11 domain refined from the X-ray diffraction data of a GH11-CBM36-1 crystal.
ComponentsEndo-1,4-beta-xylanase
KeywordsHYDROLASE / Multidomain protein / carbohydrate binding domains / GH11 / interdomain interactions / carbohydrate esterases / Isothermal titration calorimetry
Function / homology
Function and homology information


hydrolase activity, acting on carbon-nitrogen (but not peptide) bonds / endo-1,4-beta-xylanase activity / endo-1,4-beta-xylanase / xylan catabolic process / carbohydrate binding / metal ion binding
Similarity search - Function
NodB homology domain profile. / NodB homology domain / Polysaccharide deacetylase / CBM6 (carbohydrate binding type-6) domain profile. / Carbohydrate binding module family 6 / 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 ...NodB homology domain profile. / NodB homology domain / Polysaccharide deacetylase / CBM6 (carbohydrate binding type-6) domain profile. / Carbohydrate binding module family 6 / 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/deacetylase, beta/alpha-barrel / Glycoside hydrolase family 11/12 / Galactose-binding-like domain superfamily / Concanavalin A-like lectin/glucanase domain superfamily
Similarity search - Domain/homology
endo-1,4-beta-xylanase
Similarity search - Component
Biological speciesuncultured bacterium (environmental samples)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.70001286876 Å
AuthorsAnye, V. / Schubert, W.D.
Funding support South Africa, 1items
OrganizationGrant numberCountry
National Research Foundation in South Africa South Africa
CitationJournal: Plos One / Year: 2022
Title: Structural and biophysical characterization of the multidomain xylanase Xyl.
Authors: Anye, V. / Kruger, R.F. / Schubert, W.D.
History
DepositionNov 12, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 25, 2020Provider: repository / Type: Initial release
Revision 1.1Jun 29, 2022Group: Database references / Category: citation / citation_author / database_2
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _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 / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.2Jan 31, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Endo-1,4-beta-xylanase


Theoretical massNumber of molelcules
Total (without water)46,5901
Polymers46,5901
Non-polymers00
Water2,450136
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: homology
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area8920 Å2
MethodPISA
Unit cell
Length a, b, c (Å)108.216, 108.216, 54.228
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number173
Space group name H-MP63
Space group name HallP6c
Symmetry operation#1: x,y,z
#2: x-y,x,z+1/2
#3: y,-x+y,z+1/2
#4: -y,x-y,z
#5: -x+y,-x,z
#6: -x,-y,z+1/2
Components on special symmetry positions
IDModelComponents
11A-630-

HOH

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Components

#1: Protein Endo-1,4-beta-xylanase


Mass: 46589.574 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: GH11-CBM36-1
Source: (gene. exp.) uncultured bacterium (environmental samples)
Production host: Escherichia coli (E. coli) / References: UniProt: A0A140HJ20, endo-1,4-beta-xylanase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 136 / 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: 1.97 Å3/Da / Density % sol: 37.48 %
Crystal growTemperature: 293.16 K / Method: vapor diffusion, hanging drop / pH: 4.8 / Details: Na acetate, (NH4)2SO4

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.65 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Dec 14, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.65 Å / Relative weight: 1
ReflectionResolution: 1.47→93.69 Å / Num. obs: 65364 / % possible obs: 99.9 % / Redundancy: 1 % / Biso Wilson estimate: 14.6903258564 Å2 / CC1/2: 0.999 / Net I/σ(I): 15.81
Reflection shellResolution: 1.47→3.9 Å / Num. unique obs: 3225 / CC1/2: 0.814 / % possible all: 99

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Processing

SoftwareName: PHENIX / Version: 1.12_2829 / Classification: refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2DCJ

2dcj


Resolution: 1.70001286876→54.108 Å / SU ML: 0.143195300177 / Cross valid method: FREE R-VALUE / σ(F): 1.33571280734 / Phase error: 17.930989269
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.186893141955 1969 4.92373093273 %
Rwork0.170953978717 38021 -
obs0.171746959432 39990 99.9575074362 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 16.9406706224 Å2
Refinement stepCycle: LAST / Resolution: 1.70001286876→54.108 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1607 0 0 136 1743
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0060157026751650
X-RAY DIFFRACTIONf_angle_d0.9339782968782237
X-RAY DIFFRACTIONf_chiral_restr0.0623855398001221
X-RAY DIFFRACTIONf_plane_restr0.00506206016536295
X-RAY DIFFRACTIONf_dihedral_angle_d6.91375522318935
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.71-1.74250.2514624722391450.1984575749472699X-RAY DIFFRACTION99.894625922
1.7425-1.78960.1934650245341420.1805602351542677X-RAY DIFFRACTION99.9645390071
1.7896-1.84230.183479582591270.1715229977032718X-RAY DIFFRACTION100
1.8423-1.90180.1742287767411260.1674926689242694X-RAY DIFFRACTION99.9291282778
1.9018-1.96980.2182122779211350.1615713742942724X-RAY DIFFRACTION100
1.9698-2.04860.1649967274841250.1635501472242704X-RAY DIFFRACTION100
2.0486-2.14190.1688827363441640.165271035462687X-RAY DIFFRACTION99.9649368864
2.1419-2.25480.1944338632381560.1727109708982720X-RAY DIFFRACTION100
2.2548-2.39610.2054509473441520.1748086116442674X-RAY DIFFRACTION99.9646268129
2.3961-2.58110.2055862582611440.1903416436262728X-RAY DIFFRACTION100
2.5811-2.84080.1648609993771330.1883433646322719X-RAY DIFFRACTION100
2.8408-3.25180.2051564597431290.1864323501352735X-RAY DIFFRACTION100
3.2518-4.09670.1623865537061360.1533267561732741X-RAY DIFFRACTION100
4.0967-100.1858730545371550.159054227962801X-RAY DIFFRACTION99.831138129

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