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- PDB-6ex6: The GH127, Beta-arabinofuranosidase, BT3674 -

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ID or keywords:

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Basic information

Entry
Database: PDB / ID: 6ex6
TitleThe GH127, Beta-arabinofuranosidase, BT3674
ComponentsSix-hairpin glycosidase
KeywordsHYDROLASE / Arabiogalactan / GH127 / Beta arabinofuranosidase
Function / homology
Function and homology information


hydrolase activity, acting on glycosyl bonds / carbohydrate metabolic process / metal ion binding
Similarity search - Function
: / : / Glycoside hydrolase family 127 C-terminal domain / Beta-L-arabinofuranosidase, GH127 / : / Beta-L-arabinofuranosidase, GH127 catalytic domain / Beta-L-arabinofuranosidase, GH127 middle domain / Six-hairpin glycosidase superfamily
Similarity search - Domain/homology
Six-hairpin glycosidase
Similarity search - Component
Biological speciesBacteroides thetaiotaomicron (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.16 Å
AuthorsMunoz-Munoz, J. / Gilbert, H.J.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
European Research Council322820 United Kingdom
CitationJournal: To Be Published
Title: The cellular location of endo-acting galactanases confers keystone or recipient status to arabinogalactan degrading organisms of the human gut microbiota
Authors: Munoz-Munoz, J. / Cartmell, A. / Ndeh, D. / Lowe, E.C. / Briggs, J. / Basle, A. / Terrapon, N. / Stott, K. / Dupree, P. / Fernnandes, P.Z. / Shah, S. / Williams, S.J. / Labourel, A. / ...Authors: Munoz-Munoz, J. / Cartmell, A. / Ndeh, D. / Lowe, E.C. / Briggs, J. / Basle, A. / Terrapon, N. / Stott, K. / Dupree, P. / Fernnandes, P.Z. / Shah, S. / Williams, S.J. / Labourel, A. / Henrissat, B. / Gilbert, H.J.
History
DepositionNov 7, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 21, 2018Provider: repository / Type: Initial release
Revision 1.1Jan 17, 2024Group: 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

Downloads & links

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Assembly

Deposited unit
B: Six-hairpin glycosidase
A: Six-hairpin glycosidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)146,2544
Polymers146,1232
Non-polymers1312
Water13,097727
1
B: Six-hairpin glycosidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)73,1272
Polymers73,0611
Non-polymers651
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: Six-hairpin glycosidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)73,1272
Polymers73,0611
Non-polymers651
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)136.821, 136.821, 135.582
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number170
Space group name H-MP65

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Components

#1: Protein Six-hairpin glycosidase


Mass: 73061.375 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacteroides thetaiotaomicron (strain ATCC 29148 / DSM 2079 / NCTC 10582 / E50 / VPI-5482) (bacteria)
Strain: ATCC 29148 / DSM 2079 / NCTC 10582 / E50 / VPI-5482 / Gene: BT_3674 / Production host: Escherichia coli (E. coli) / References: UniProt: Q8A1I7
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 727 / 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: 2.51 Å3/Da / Density % sol: 50.94 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8.5 / Details: 0.1M Tris buffer, 0.2M LiSO4, 40% PEG400

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I02 / Wavelength: 0.9795 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Feb 2, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 2.16→68.4 Å / Num. obs: 77030 / % possible obs: 100 % / Redundancy: 11.5 % / Net I/σ(I): 12.9
Reflection shellResolution: 2.16→2.22 Å / Redundancy: 11.6 % / Mean I/σ(I) obs: 1.4 / Num. unique obs: 5696 / CC1/2: 0.578 / % possible all: 99.9

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Processing

Software
NameVersionClassification
REFMAC5.8.0158refinement
xia2data reduction
pointlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3WKX

3wkx


Resolution: 2.16→19.75 Å / Cor.coef. Fo:Fc: 0.961 / Cor.coef. Fo:Fc free: 0.941 / SU B: 5.593 / SU ML: 0.14 / Cross valid method: THROUGHOUT / ESU R: 0.222 / ESU R Free: 0.183 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.22072 3944 5.1 %RANDOM
Rwork0.17614 ---
obs0.17844 74000 99.8 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 34.617 Å2
Baniso -1Baniso -2Baniso -3
1-0.01 Å20 Å20 Å2
2--0.01 Å2-0 Å2
3----0.02 Å2
Refinement stepCycle: 1 / Resolution: 2.16→19.75 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9787 0 2 727 10516
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0190.01910100
X-RAY DIFFRACTIONr_bond_other_d0.0020.028816
X-RAY DIFFRACTIONr_angle_refined_deg1.9121.93713796
X-RAY DIFFRACTIONr_angle_other_deg1.1320392
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.37851269
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.21524.207473
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.332151472
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.7051544
X-RAY DIFFRACTIONr_chiral_restr0.1120.21489
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.02111552
X-RAY DIFFRACTIONr_gen_planes_other0.0020.022140
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_it2.7893.455076
X-RAY DIFFRACTIONr_mcbond_other2.7823.4495075
X-RAY DIFFRACTIONr_mcangle_it3.7255.1686345
X-RAY DIFFRACTIONr_mcangle_other3.7245.1696346
X-RAY DIFFRACTIONr_scbond_it3.3173.6535024
X-RAY DIFFRACTIONr_scbond_other3.3163.6545025
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other4.7625.3847452
X-RAY DIFFRACTIONr_long_range_B_refined9.58440.62611784
X-RAY DIFFRACTIONr_long_range_B_other9.58540.63211785
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.15→2.205 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.285 295 -
Rwork0.259 5382 -
obs--99.96 %

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