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- PDB-6g00: Crystal Structure of a GH8 xylanase from Teredinibacter turnerae -

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Basic information

Entry
Database: PDB / ID: 6g00
TitleCrystal Structure of a GH8 xylanase from Teredinibacter turnerae
ComponentsGlycoside hydrolase family 8 domain protein
KeywordsHYDROLASE / Xylanse / native / carbohydrate
Function / homology
Function and homology information


cellulase / cellulase activity / cellulose catabolic process
Similarity search - Function
Glycoside hydrolase, family 8 / Glycosyl hydrolases family 8 / Glycosyltransferase - #10 / Six-hairpin glycosidase-like superfamily / Six-hairpin glycosidase superfamily / Glycosyltransferase / Alpha/alpha barrel / Prokaryotic membrane lipoprotein lipid attachment site profile. / Mainly Alpha
Similarity search - Domain/homology
Biological speciesTeredinibacter turnerae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.4 Å
AuthorsFowler, C.A. / Davies, G.J. / Walton, P.H.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
Biotechnology and Biological Sciences Research CouncilBB/L001926/1 United Kingdom
CitationJournal: Acta Crystallogr D Struct Biol / Year: 2018
Title: Structure and function of a glycoside hydrolase family 8 endoxylanase from Teredinibacter turnerae.
Authors: Fowler, C.A. / Hemsworth, G.R. / Cuskin, F. / Hart, S. / Turkenburg, J. / Gilbert, H.J. / Walton, P.H. / Davies, G.J.
History
DepositionMar 15, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 10, 2018Provider: repository / Type: Initial release
Revision 1.1Oct 17, 2018Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID
Revision 1.2Jan 17, 2024Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / entity / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _entity.formula_weight

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Glycoside hydrolase family 8 domain protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,5088
Polymers45,1131
Non-polymers3957
Water5,585310
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: mass spectrometry, gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1270 Å2
ΔGint7 kcal/mol
Surface area14290 Å2
MethodPISA
Unit cell
Length a, b, c (Å)61.540, 72.995, 90.866
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Glycoside hydrolase family 8 domain protein


Mass: 45112.891 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Teredinibacter turnerae (strain ATCC 39867 / T7901) (bacteria)
Gene: TERTU_4506 / Plasmid: pET-28 / Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: C5BJ89, Hydrolases; Glycosylases; Glycosidases, i.e. enzymes that hydrolyse O- and S-glycosyl compounds
#2: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 6 / Source method: isolated from a natural source / Formula: C2H6O2
#3: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 310 / 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: 2.26 Å3/Da / Density % sol: 45.7 %
Crystal growTemperature: 291.2 K / Method: vapor diffusion, hanging drop / pH: 5
Details: sodium acetate (0.1M, pH 5.0), NaCl (0.2 M), polyethylene glycol 6000 16%.
PH range: 4.6-5.2 / Temp details: temperature controlled room

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I02 / Wavelength: 0.98 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Feb 1, 2016
RadiationMonochromator: double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 1.4→51 Å / Num. obs: 80610 / % possible obs: 99.4 % / Redundancy: 4.3 % / Net I/σ(I): 9.6
Reflection shellResolution: 1.4→1.42 Å

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Processing

Software
NameVersionClassification
REFMAC5.8.0189refinement
xia2data reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1WU4

1wu4


Resolution: 1.4→56.97 Å / Cor.coef. Fo:Fc: 0.975 / Cor.coef. Fo:Fc free: 0.97 / SU B: 1.017 / SU ML: 0.038 / Cross valid method: THROUGHOUT / ESU R: 0.052 / ESU R Free: 0.052 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.17142 3924 4.9 %RANDOM
Rwork0.15279 ---
obs0.15369 76616 99.17 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 14.305 Å2
Baniso -1Baniso -2Baniso -3
1-0.94 Å20 Å20 Å2
2--0.54 Å2-0 Å2
3----1.48 Å2
Refinement stepCycle: 1 / Resolution: 1.4→56.97 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3139 0 25 310 3474
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.0193289
X-RAY DIFFRACTIONr_bond_other_d0.0020.022821
X-RAY DIFFRACTIONr_angle_refined_deg1.6831.9154473
X-RAY DIFFRACTIONr_angle_other_deg1.05136525
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.6325400
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.93823.547172
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.89415475
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.7411521
X-RAY DIFFRACTIONr_chiral_restr0.1140.2438
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.0213769
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02764
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.061.2611579
X-RAY DIFFRACTIONr_mcbond_other1.0531.261578
X-RAY DIFFRACTIONr_mcangle_it1.5671.8931974
X-RAY DIFFRACTIONr_mcangle_other1.5691.8941975
X-RAY DIFFRACTIONr_scbond_it1.9191.4711710
X-RAY DIFFRACTIONr_scbond_other1.9191.471710
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other2.9172.1212496
X-RAY DIFFRACTIONr_long_range_B_refined3.83715.7434027
X-RAY DIFFRACTIONr_long_range_B_other3.83715.7494028
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.4→1.436 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.288 280 -
Rwork0.293 5640 -
obs--99.78 %

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