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- PDB-6g09: Crystal Structure of a GH8 xylobiose complex from Teredinibacter ... -

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Basic information

Entry
Database: PDB / ID: 6g09
TitleCrystal Structure of a GH8 xylobiose complex from Teredinibacter turnerae
ComponentsGlycoside hydrolase family 8 domain protein
KeywordsHYDROLASE / Xylanse / native / carbohydrate
Function / homology
Function and homology information


cellulase / cellulase activity / carbohydrate metabolic 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
4beta-beta-xylobiose / cellulase
Similarity search - Component
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 16, 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 2.0Jul 29, 2020Group: Atomic model / Data collection ...Atomic model / Data collection / Derived calculations / Non-polymer description / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / entity / entity_name_com / pdbx_branch_scheme / pdbx_chem_comp_identifier / pdbx_entity_branch / pdbx_entity_branch_descriptor / pdbx_entity_branch_link / pdbx_entity_branch_list / pdbx_entity_nonpoly / pdbx_molecule_features / pdbx_nonpoly_scheme / struct_conn / struct_site / struct_site_gen
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_asym_id / _atom_site.auth_atom_id / _atom_site.auth_comp_id / _atom_site.auth_seq_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.type_symbol / _chem_comp.formula / _chem_comp.formula_weight / _chem_comp.id / _chem_comp.mon_nstd_flag / _chem_comp.name / _chem_comp.pdbx_synonyms / _chem_comp.type / _entity.formula_weight / _entity.pdbx_description / _entity.type
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Jan 17, 2024Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _chem_comp.pdbx_synonyms / _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: Glycoside hydrolase family 8 domain protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,4573
Polymers45,1131
Non-polymers3442
Water5,945330
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration, mass spectrometry
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area970 Å2
ΔGint-4 kcal/mol
Surface area13990 Å2
MethodPISA
Unit cell
Length a, b, c (Å)61.702, 79.035, 87.588
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 / Production host: Escherichia coli (E. coli)
References: UniProt: C5BJ89, Hydrolases; Glycosylases; Glycosidases, i.e. enzymes that hydrolyse O- and S-glycosyl compounds
#2: Polysaccharide beta-D-xylopyranose-(1-4)-beta-D-xylopyranose / 4beta-beta-xylobiose


Type: oligosaccharide, Oligosaccharide / Class: Metabolism / Mass: 282.245 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: oligosaccharide / References: 4beta-beta-xylobiose
DescriptorTypeProgram
DXylpb1-4DXylpb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/1,2,1/[a212h-1b_1-5]/1-1/a4-b1WURCSPDB2Glycan 1.1.0
[][b-D-Xylp]{[(4+1)][b-D-Xylp]{}}LINUCSPDB-CARE
#3: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Formula: C2H6O2
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 330 / 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: 2.37 Å3/Da / Density % sol: 48.1 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 5
Details: 0.1 M sodium acetate, pH 5, 0.2 M ammonium sulfate, 20 % PEG 6000

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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: Apr 18, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 1.4→50.49 Å / Num. obs: 84123 / % possible obs: 99.1 % / Redundancy: 6.3 % / Rpim(I) all: 0.051 / Net I/σ(I): 10.1
Reflection shellResolution: 1.4→1.42 Å / Rpim(I) all: 0.549

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Processing

Software
NameVersionClassification
REFMAC5.8.0232refinement
xia2data reduction
Aimlessdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6G00

6g00


Resolution: 1.4→50.49 Å / Cor.coef. Fo:Fc: 0.97 / Cor.coef. Fo:Fc free: 0.963 / SU B: 0.984 / SU ML: 0.037 / Cross valid method: THROUGHOUT / ESU R: 0.051 / ESU R Free: 0.053 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.17737 4274 5.1 %RANDOM
Rwork0.15498 ---
obs0.15611 79780 98.95 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 11.189 Å2
Baniso -1Baniso -2Baniso -3
1-0.36 Å20 Å20 Å2
2--0.47 Å2-0 Å2
3----0.83 Å2
Refinement stepCycle: 1 / Resolution: 1.4→50.49 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3125 0 23 330 3478
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0133276
X-RAY DIFFRACTIONr_bond_other_d0.0010.0172777
X-RAY DIFFRACTIONr_angle_refined_deg1.8011.6534470
X-RAY DIFFRACTIONr_angle_other_deg1.6791.5816428
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.1015399
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.48722.199191
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.4915464
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.6091520
X-RAY DIFFRACTIONr_chiral_restr0.0990.2407
X-RAY DIFFRACTIONr_gen_planes_refined0.0120.023777
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02779
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_it0.8661.0511575
X-RAY DIFFRACTIONr_mcbond_other0.8631.0511574
X-RAY DIFFRACTIONr_mcangle_it1.271.5781969
X-RAY DIFFRACTIONr_mcangle_other1.2711.5781970
X-RAY DIFFRACTIONr_scbond_it1.8021.2041701
X-RAY DIFFRACTIONr_scbond_other1.8011.2051702
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other2.6721.7462498
X-RAY DIFFRACTIONr_long_range_B_refined3.31913.0813984
X-RAY DIFFRACTIONr_long_range_B_other3.31913.0893985
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
Rfree0.268 276 -
Rwork0.274 5330 -
obs--89.78 %

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