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- PDB-5vqj: Discovery of a first GH11 exo-1,4-beta-xylanase from a diverse mi... -

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Basic information

Entry
Database: PDB / ID: 5vqj
TitleDiscovery of a first GH11 exo-1,4-beta-xylanase from a diverse microbial sugar cane bagasse composting community
Componentsexo-beta-1,4-xylanase
KeywordsHYDROLASE / beta-jelly roll
Function / homologyGlycoside hydrolase family 11/12, catalytic domain / Jelly Rolls / Sandwich / Mainly Beta
Function and homology information
Biological speciesunidentified (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.761 Å
AuthorsMello, B.L. / Polikarpov, I.
Funding support Brazil, 2items
OrganizationGrant numberCountry
Sao Paulo Research Foundation (FAPESP)2011/21608-1 Brazil
Sao Paulo Research Foundation (FAPESP)2010/52362-5 Brazil
CitationJournal: Biotechnol Biofuels / Year: 2017
Title: Targeted metatranscriptomics of compost-derived consortia reveals a GH11 exerting an unusual exo-1,4-beta-xylanase activity.
Authors: Mello, B.L. / Alessi, A.M. / Riano-Pachon, D.M. / deAzevedo, E.R. / Guimaraes, F.E.G. / Espirito Santo, M.C. / McQueen-Mason, S. / Bruce, N.C. / Polikarpov, I.
History
DepositionMay 9, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 21, 2018Provider: repository / Type: Initial release
Revision 1.1Apr 17, 2019Group: Author supporting evidence / Data collection / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.2Jan 1, 2020Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3Oct 4, 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: exo-beta-1,4-xylanase


Theoretical massNumber of molelcules
Total (without water)24,5371
Polymers24,5371
Non-polymers00
Water5,008278
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area9360 Å2
MethodPISA
Unit cell
Length a, b, c (Å)64.326, 64.326, 105.873
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number96
Space group name H-MP43212

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Components

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


Mass: 24537.000 Da / Num. of mol.: 1 / Fragment: glycoside hydrolase family 11
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) unidentified (others) / Plasmid: pETTRXA / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta(DE3) pLys
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 278 / 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: 2.24 Å3/Da / Density % sol: 45.18 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 7.5 / Details: BIS-TRIS propane, PEG 3350, NaI

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: LNLS / Beamline: W01B-MX2 / Wavelength: 1.459 Å
DetectorType: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Oct 21, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.459 Å / Relative weight: 1
ReflectionResolution: 1.76→45.49 Å / Num. obs: 22638 / % possible obs: 99.6 % / Redundancy: 24 % / CC1/2: 0.999 / Rmerge(I) obs: 0.125 / Rpim(I) all: 0.026 / Rrim(I) all: 0.128 / Net I/σ(I): 23.4 / Num. measured all: 543074 / Scaling rejects: 0
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allCC1/2Rpim(I) allRrim(I) all% possible all
1.76-1.818.31.5312260.7670.361.57396
8.98-45.4918.40.04410.010.04599.6

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Processing

Software
NameVersionClassification
Aimless0.3.11data scaling
PHENIX1.9_1692refinement
PDB_EXTRACT3.22data extraction
XDSdata reduction
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1XNK

1xnk


Resolution: 1.761→41.792 Å / SU ML: 0.21 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 21.2
RfactorNum. reflection% reflection
Rfree0.2183 1131 5.01 %
Rwork0.194 --
obs0.1953 22585 99.39 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 61.6 Å2 / Biso mean: 19.5011 Å2 / Biso min: 4.98 Å2
Refinement stepCycle: final / Resolution: 1.761→41.792 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1731 0 0 281 2012
Biso mean---30.44 -
Num. residues----216
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0051787
X-RAY DIFFRACTIONf_angle_d1.0422432
X-RAY DIFFRACTIONf_chiral_restr0.045243
X-RAY DIFFRACTIONf_plane_restr0.004312
X-RAY DIFFRACTIONf_dihedral_angle_d13.84615
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 8

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.7608-1.84090.29691370.25122574271197
1.8409-1.93790.2641350.21492632276799
1.9379-2.05940.22311420.18222614275699
2.0594-2.21840.23751400.188226562796100
2.2184-2.44160.22961470.195326502797100
2.4416-2.79480.22981340.202827142848100
2.7948-3.52090.21211430.187627272870100
3.5209-41.80350.18931530.186528873040100

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