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- PDB-7ay3: Crystal structure of the CBM36-1 domain of a multidomain xylanase... -

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Basic information

Entry
Database: PDB / ID: 7ay3
TitleCrystal structure of the CBM36-1 domain of a multidomain xylanase from the hindgut metagenome of Trinervitermes trinervoides
ComponentsEndo-1,4-beta-xylanase
KeywordsSUGAR BINDING PROTEIN / CBM36 / glycoside hydrolase / 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 / MOLECULAR REPLACEMENT / Resolution: 2.00001880273 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 11, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 18, 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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,2353
Polymers18,1551
Non-polymers802
Water2,090116
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: homology
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area170 Å2
ΔGint-24 kcal/mol
Surface area5920 Å2
MethodPISA
Unit cell
Length a, b, c (Å)28.432, 37.320, 108.020
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x,y+1/2,-z+1/2
#4: -x+1/2,-y,z+1/2

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Components

#1: Protein Endo-1,4-beta-xylanase / CBM36-1 domain of the multidomain xylanase protein Xyl


Mass: 18155.059 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: multidomain xylanase from the hindgut metagenome of the snouted harvester termite
Source: (gene. exp.) uncultured bacterium (environmental samples)
Gene: CBM36-1 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A140HJ20, endo-1,4-beta-xylanase
#2: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 116 / 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

CrystalDescription: hexagonal crystal
Crystal growTemperature: 293.15 K / Method: vapor diffusion, sitting drop / pH: 7.5 / Details: PEG 3000, Hepes

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.54 Å
DetectorType: RIGAKU SATURN 944 / Detector: CCD / Date: Jul 31, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 1.99→25.16 Å / Num. obs: 8260 / % possible obs: 98.3 % / Redundancy: 2 % / Biso Wilson estimate: 31.6049725646 Å2 / CC1/2: 0.999 / Net I/σ(I): 22
Reflection shellResolution: 1.99→2.06 Å / Num. unique obs: 715 / CC1/2: 0.988 / % possible all: 87

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Processing

Software
NameVersionClassification
PHENIX1.12_2829refinement
HKL-30001.12_2829data collection
MOSFLM1.12_2829data reduction
SCALA1.12_2829data scaling
PHASER1.12_2829phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2C71

2c71


Resolution: 2.00001880273→22.6164210804 Å / SU ML: 0.219286164382 / Cross valid method: FREE R-VALUE / σ(F): 0 / Phase error: 25.0213098228
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.249113269824 816 10.0492610837 %
Rwork0.175017543517 7304 -
obs0.182296205054 8120 98.0557903635 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 31.7846041482 Å2
Refinement stepCycle: LAST / Resolution: 2.00001880273→22.6164210804 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms930 0 2 116 1048
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00566449579868947
X-RAY DIFFRACTIONf_angle_d0.7845600820371282
X-RAY DIFFRACTIONf_chiral_restr0.0520791160927135
X-RAY DIFFRACTIONf_plane_restr0.0046408551556173
X-RAY DIFFRACTIONf_dihedral_angle_d3.1976109843538
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.05-2.12520.2936314802371260.218926957131113X-RAY DIFFRACTION92.1875
2.1252-2.28920.2784544327291330.1924057717291187X-RAY DIFFRACTION98.8023952096
2.2892-2.51930.2597000350581340.1951991685341213X-RAY DIFFRACTION98.8986784141
2.5193-2.88320.2527353447311380.1864529626051226X-RAY DIFFRACTION99.5620437956
2.8832-3.63010.2667563517471380.170854749561254X-RAY DIFFRACTION99.7849462366
3.6301-100.2194309629391470.1583441631491311X-RAY DIFFRACTION98.9145183175

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