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- PDB-7zsz: Crystal structure of the GH11 domain of a multidomain xylanase fr... -

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Basic information

Entry
Database: PDB / ID: 7zsz
TitleCrystal structure of the GH11 domain of a multidomain xylanase from the hindgut metagenome of Trinervitermes trinervoides
ComponentsEndo-1,4-beta-xylanaseXylanase
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
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 #0087-1D13 (environmental samples)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.5 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
DepositionMay 9, 2022Deposition site: PDBE / Processing site: PDBE
SupersessionJun 29, 2022ID: 7AYL
Revision 1.0Jun 29, 2022Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2022Group: Database references / Category: citation / citation_author
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
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
B: Endo-1,4-beta-xylanase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,5823
Polymers45,4862
Non-polymers961
Water9,548530
1
A: Endo-1,4-beta-xylanase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,8392
Polymers22,7431
Non-polymers961
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Endo-1,4-beta-xylanase


Theoretical massNumber of molelcules
Total (without water)22,7431
Polymers22,7431
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)38.490, 43.420, 69.900
Angle α, β, γ (deg.)100.870, 96.360, 116.000
Int Tables number1
Space group name H-MP1
Space group name HallP1
Symmetry operation#1: x,y,z

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Components

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


Mass: 22742.879 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) uncultured bacterium #0087-1D13 (environmental samples)
Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A140HJ20, endo-1,4-beta-xylanase
#2: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4 / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 530 / 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: 2.21 Å3/Da / Density % sol: 44.39 %
Crystal growTemperature: 293.15 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: 0.976 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: 0.976 Å / Relative weight: 1
ReflectionResolution: 1.39→37.31 Å / Num. obs: 68762 / % possible obs: 87.5 % / Redundancy: 1.6 % / Biso Wilson estimate: 16.2 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.049 / Net I/σ(I): 13.6
Reflection shellResolution: 1.39→1.413 Å / Redundancy: 1.6 % / Rmerge(I) obs: 0.278 / Num. unique obs: 2652 / CC1/2: 0.816 / % possible all: 67

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
PHENIX1.20.1_4487refinement
XDS1.12_2829data reduction
PDB_EXTRACT1.12_2829data extraction
autoPROCdata processing
Cootmodel building
xia2data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 7AYL

7ayl
PDB Unreleased entry


Resolution: 1.5→37.31 Å / SU ML: 0.15 / Cross valid method: FREE R-VALUE / σ(F): 1.99 / Phase error: 22.3496
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2166 2669 4.83 %
Rwork0.1805 52621 -
obs0.1822 55290 88.58 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 20.88 Å2
Refinement stepCycle: LAST / Resolution: 1.5→37.31 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3193 0 5 530 3728
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0063296
X-RAY DIFFRACTIONf_angle_d0.88624473
X-RAY DIFFRACTIONf_chiral_restr0.0595443
X-RAY DIFFRACTIONf_plane_restr0.0064588
X-RAY DIFFRACTIONf_dihedral_angle_d6.847452
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.5-1.530.24841500.21742799X-RAY DIFFRACTION90.21
1.53-1.560.2751470.21482820X-RAY DIFFRACTION89.29
1.56-1.590.21681300.20572752X-RAY DIFFRACTION88.87
1.59-1.620.2621190.21152824X-RAY DIFFRACTION88.81
1.62-1.660.2731370.20822870X-RAY DIFFRACTION91.29
1.66-1.70.23951530.19812825X-RAY DIFFRACTION91.69
1.7-1.750.26491540.20032899X-RAY DIFFRACTION91.43
1.75-1.80.21981350.19992825X-RAY DIFFRACTION91.44
1.8-1.860.25361240.19892831X-RAY DIFFRACTION90.37
1.86-1.920.25481450.21032605X-RAY DIFFRACTION82.68
1.92-20.24531310.20042743X-RAY DIFFRACTION87.97
2-2.090.2231480.1892846X-RAY DIFFRACTION91.22
2.09-2.20.24841550.19052797X-RAY DIFFRACTION90.05
2.2-2.340.23571310.19632654X-RAY DIFFRACTION84.81
2.34-2.520.20951510.19382737X-RAY DIFFRACTION87.78
2.52-2.770.24041510.18652779X-RAY DIFFRACTION88.92
2.78-3.180.21061350.18062737X-RAY DIFFRACTION87.11
3.18-40.17521570.1472621X-RAY DIFFRACTION85.03
4-37.310.17551160.14962657X-RAY DIFFRACTION84.34

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