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- PDB-7ax7: Crystal structure of the Xyl-CE4 domain of a multidomain xylanase... -

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Basic information

Entry
Database: PDB / ID: 7ax7
TitleCrystal structure of the Xyl-CE4 domain of a multidomain xylanase from the hindgut metagenome of Trinervitermes trinervoides
ComponentsEndo-1,4-beta-xylanase
KeywordsMETAL BINDING PROTEIN / Xyl-CE4 uses Co2+ to cleave acetyl groups from acetylated xylan molecules. As part of a multidomain assembly / CE4 functions independently of other domain components.
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
ACETATE ION / : / endo-1,4-beta-xylanase
Similarity search - Component
Biological speciesuncultured bacterium (environmental samples)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.05000181627 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 9, 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

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)23,9303
Polymers23,8121
Non-polymers1182
Water4,450247
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: homology
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area380 Å2
ΔGint-13 kcal/mol
Surface area8980 Å2
MethodPISA
Unit cell
Length a, b, c (Å)40.130, 59.700, 86.100
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


Mass: 23812.477 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) uncultured bacterium (environmental samples)
Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A140HJ20, endo-1,4-beta-xylanase
#2: Chemical ChemComp-CO / COBALT (II) ION


Mass: 58.933 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: Co
#3: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H3O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 247 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 2.17 Å3/Da / Density % sol: 43.2 %
Crystal growTemperature: 292.2 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 10 mg/mL in 20 mM Tris-HCl pH 7.5, 10 mM NaCl, 8 % (w/v) PEG 4000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.54 Å
DetectorType: RIGAKU SATURN 944 / Detector: CCD / Date: Apr 9, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 1.93→23.07 Å / Num. obs: 13512 / % possible obs: 99 % / Redundancy: 2 % / Biso Wilson estimate: 13.713555817 Å2 / CC1/2: 0.999 / Rpim(I) all: 0.019 / Net I/av σ(I): 18 / Net I/σ(I): 2.74
Reflection shellResolution: 2.05→2.12 Å / Num. unique obs: 722 / CC1/2: 0.991 / % possible all: 96.9

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Processing

Software
NameVersionClassification
HKL-30001.12_2829data collection
d*TREK1.12_2829data reduction
d*TREK1.12_2829data scaling
d*TREK1.12_2829data processing
d*TREK1.12_2829data scaling
PHASERphasing
PHASERrefinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2C71

2c71


Resolution: 2.05000181627→19.5413775456 Å / SU ML: 0.250769489372 / Cross valid method: FREE R-VALUE / σ(F): 1.4376150803 / Phase error: 25.4581162604
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.24277939068 683 5.05476613381 %
Rwork0.172865563929 12829 -
obs0.176291932968 13512 99.8817267889 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 14.1404325504 Å2
Refinement stepCycle: LAST / Resolution: 2.05000181627→19.5413775456 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1610 0 5 247 1862
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.006351436313051641
X-RAY DIFFRACTIONf_angle_d0.7076938156282224
X-RAY DIFFRACTIONf_chiral_restr0.0485426672537250
X-RAY DIFFRACTIONf_plane_restr0.00427123583596295
X-RAY DIFFRACTIONf_dihedral_angle_d13.4408772302984
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.06-2.20810.3717881824481270.2592179272582534X-RAY DIFFRACTION99.924896733
2.2081-2.42990.3192814490671450.2047314395782492X-RAY DIFFRACTION100
2.4299-2.78070.2540946879551480.1862539423632526X-RAY DIFFRACTION100
2.7807-3.50010.2019999196311310.1519053432762590X-RAY DIFFRACTION100
3.5-100.1883740364781320.1391685422172687X-RAY DIFFRACTION99.5058242146

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