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- PDB-6g0n: Crystal Structure of a GH8 catalytic mutant xylohexaose complex x... -

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Basic information

Entry
Database: PDB / ID: 6g0n
TitleCrystal Structure of a GH8 catalytic mutant xylohexaose complex xylanase from Teredinibacter turnerae
ComponentsGlycoside hydrolase family 8 domain protein
KeywordsHYDROLASE / Xylanse / mutant / 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
beta-D-xylopyranose / cellulase
Similarity search - Component
Biological speciesTeredinibacter turnerae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 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 19, 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: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Derived calculations / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / entity / 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_nonpoly_scheme / pdbx_struct_assembly_gen / pdbx_unobs_or_zero_occ_atoms / pdbx_validate_close_contact / struct_asym / 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_seq_id / _atom_site.label_asym_id / _atom_site.label_atom_id / _atom_site.label_entity_id / _atom_site.type_symbol / _chem_comp.name / _chem_comp.type / _pdbx_entity_nonpoly.entity_id / _pdbx_entity_nonpoly.name / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_unobs_or_zero_occ_atoms.auth_atom_id / _pdbx_unobs_or_zero_occ_atoms.label_asym_id / _pdbx_unobs_or_zero_occ_atoms.label_atom_id / _pdbx_validate_close_contact.auth_asym_id_1 / _pdbx_validate_close_contact.auth_atom_id_1 / _pdbx_validate_close_contact.auth_atom_id_2 / _pdbx_validate_close_contact.auth_seq_id_1 / _pdbx_validate_close_contact.auth_seq_id_2 / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation

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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)46,0334
Polymers45,1121
Non-polymers9213
Water3,495194
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: mass spectrometry, gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2360 Å2
ΔGint-27 kcal/mol
Surface area13580 Å2
MethodPISA
Unit cell
Length a, b, c (Å)60.973, 79.694, 88.010
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: 45111.906 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Teredinibacter turnerae (strain ATCC 39867 / T7901) (bacteria)
Strain: ATCC 39867 / T7901 / 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-(1-4)-beta-D-xylopyranose-(1-4)-beta-D-xylopyranose- ...beta-D-xylopyranose-(1-4)-beta-D-xylopyranose-(1-4)-beta-D-xylopyranose-(1-4)-beta-D-xylopyranose-(1-4)-beta-D-xylopyranose


Type: oligosaccharide / Mass: 678.589 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DXylpb1-4DXylpb1-4DXylpb1-4DXylpb1-4DXylpb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/1,5,4/[a212h-1b_1-5]/1-1-1-1-1/a4-b1_b4-c1_c4-d1_d4-e1WURCSPDB2Glycan 1.1.0
[][b-D-Xylp]{[(4+1)][b-D-Xylp]{[(4+1)][b-D-Xylp]{[(4+1)][b-D-Xylp]{[(4+1)][b-D-Xylp]{}}}}}LINUCSPDB-CARE
#3: Sugar ChemComp-XYP / beta-D-xylopyranose / Xylose


Type: D-saccharide, beta linking / Mass: 150.130 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Formula: C5H10O5
IdentifierTypeProgram
DXylpbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
b-D-xylopyranoseCOMMON NAMEGMML 1.0
b-D-XylpIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
XylSNFG CARBOHYDRATE SYMBOLGMML 1.0
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: C3H8O3
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 194 / 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: 6.8
Details: 0.1 M HEPES pH 6.8, 0.2 M ammonium sulfate, 20% PEG 6000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.98 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Jul 5, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 1.8→60.97 Å / Num. obs: 40046 / % possible obs: 99 % / Redundancy: 7.8 % / Net I/σ(I): 8.2
Reflection shellResolution: 1.8→1.84 Å

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Processing

Software
NameVersionClassification
REFMAC5.8.0189refinement
iMOSFLMdata reduction
Aimlessdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.8→59.14 Å / Cor.coef. Fo:Fc: 0.959 / Cor.coef. Fo:Fc free: 0.94 / SU B: 2.525 / SU ML: 0.077 / Cross valid method: THROUGHOUT / ESU R: 0.116 / ESU R Free: 0.109 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.19899 1942 4.9 %RANDOM
Rwork0.16907 ---
obs0.17049 38051 98.83 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 16.125 Å2
Baniso -1Baniso -2Baniso -3
1-1.06 Å20 Å20 Å2
2--0.45 Å2-0 Å2
3----1.51 Å2
Refinement stepCycle: 1 / Resolution: 1.8→59.14 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3128 0 61 194 3383
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0193305
X-RAY DIFFRACTIONr_bond_other_d0.0020.022787
X-RAY DIFFRACTIONr_angle_refined_deg1.5011.9324510
X-RAY DIFFRACTIONr_angle_other_deg1.04336461
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.7815393
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.24223.626171
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.68415460
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.31520
X-RAY DIFFRACTIONr_chiral_restr0.0960.2457
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.0213743
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02757
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_it0.8531.5361572
X-RAY DIFFRACTIONr_mcbond_other0.8531.5351571
X-RAY DIFFRACTIONr_mcangle_it1.2442.2991965
X-RAY DIFFRACTIONr_mcangle_other1.2442.2991966
X-RAY DIFFRACTIONr_scbond_it1.3441.7031733
X-RAY DIFFRACTIONr_scbond_other1.3391.7031733
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other2.0952.5032546
X-RAY DIFFRACTIONr_long_range_B_refined2.79218.1823888
X-RAY DIFFRACTIONr_long_range_B_other2.78918.1833888
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.8→1.847 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.254 134 -
Rwork0.226 2766 -
obs--97.64 %

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