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- PDB-5mqo: Glycoside hydrolase BT_1003 -

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Basic information

Entry
Database: PDB / ID: 5mqo
TitleGlycoside hydrolase BT_1003
ComponentsNon-reducing end beta-L-arabinofuranosidase
KeywordsHYDROLASE / glycoside hydrolase / aceric acidase / plant pectin / CAZy family GH127
Function / homology
Function and homology information


beta-L-arabinofuranosidase activity / hydrolase activity, acting on glycosyl bonds / carbohydrate metabolic process
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
Glycoside hydrolase family 127 protein / Six-hairpin glycosidase
Similarity search - Component
Biological speciesBacteroides thetaiotaomicron (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å
AuthorsBasle, A. / Ndeh, D. / Rogowski, A. / Cartmell, A. / Luis, A.S. / Venditto, I. / Labourel, A. / Gilbert, H.J.
Funding support United Kingdom, 4items
OrganizationGrant numberCountry
iotechnology and Biological Research CouncilBB/K020358/1 United Kingdom
Biotechnology and Biological Sciences Research CouncilBB/K001949/1 United Kingdom
Wellcome TrustWT097907MA United Kingdom
European Research Council322820 United Kingdom
CitationJournal: Nature / Year: 2017
Title: Complex pectin metabolism by gut bacteria reveals novel catalytic functions.
Authors: Ndeh, D. / Rogowski, A. / Cartmell, A. / Luis, A.S. / Basle, A. / Gray, J. / Venditto, I. / Briggs, J. / Zhang, X. / Labourel, A. / Terrapon, N. / Buffetto, F. / Nepogodiev, S. / Xiao, Y. / ...Authors: Ndeh, D. / Rogowski, A. / Cartmell, A. / Luis, A.S. / Basle, A. / Gray, J. / Venditto, I. / Briggs, J. / Zhang, X. / Labourel, A. / Terrapon, N. / Buffetto, F. / Nepogodiev, S. / Xiao, Y. / Field, R.A. / Zhu, Y. / O'Neill, M.A. / Urbanowicz, B.R. / York, W.S. / Davies, G.J. / Abbott, D.W. / Ralet, M.C. / Martens, E.C. / Henrissat, B. / Gilbert, H.J.
History
DepositionDec 20, 2016Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 22, 2017Provider: repository / Type: Initial release
Revision 1.1Apr 5, 2017Group: Database references
Revision 1.2Apr 12, 2017Group: Database references
Revision 1.3Aug 23, 2017Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.4Aug 30, 2017Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.5Jan 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
Revision 1.6Nov 13, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Non-reducing end beta-L-arabinofuranosidase


Theoretical massNumber of molelcules
Total (without water)78,1651
Polymers78,1651
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area25010 Å2
MethodPISA
Unit cell
Length a, b, c (Å)219.440, 219.440, 91.809
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number155
Space group name H-MH32

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Components

#1: Protein Non-reducing end beta-L-arabinofuranosidase / BT_1003


Mass: 78164.734 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacteroides thetaiotaomicron (bacteria)
Gene: hypBA1_2, Btheta7330_02619 / Plasmid: pET28b / Production host: Escherichia coli (E. coli)
References: UniProt: A0A0P0FFP9, UniProt: Q8A914*PLUS, non-reducing end beta-L-arabinofuranosidase
Has protein modificationY

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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: 2.72 Å3/Da / Density % sol: 54.8 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, sitting drop / Details: 20% (w/v) PEG 3350 and 0.2 M potassium acetate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.775 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jul 15, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.775 Å / Relative weight: 1
ReflectionResolution: 2.5→109.72 Å / Num. all: 143341 / Num. obs: 29265 / % possible obs: 100 % / Observed criterion σ(I): 1.5 / Redundancy: 4.9 % / CC1/2: 0.992 / Rmerge(I) obs: 0.133 / Net I/σ(I): 5.2
Reflection shellResolution: 2.5→2.6 Å / Redundancy: 4.9 % / Rmerge(I) obs: 0.954 / Mean I/σ(I) obs: 1.5 / Num. unique all: 3300 / CC1/2: 0.339 / % possible all: 100

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Processing

Software
NameVersionClassification
DIALS5.8.0155data reduction
Aimlessdata scaling
PHASERphasing
Cootmodel building
REFMAC5.8.0155refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3WKX, 4QJY

3wkx

4qjy


Resolution: 2.5→109.72 Å / Cor.coef. Fo:Fc: 0.959 / Cor.coef. Fo:Fc free: 0.935 / SU B: 31.661 / SU ML: 0.282 / Cross valid method: THROUGHOUT / ESU R: 0.368 / ESU R Free: 0.252 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.23899 1464 5 %RANDOM
Rwork0.19411 ---
obs0.19647 27801 99.96 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 67.308 Å2
Baniso -1Baniso -2Baniso -3
1--1.55 Å2-0.77 Å2-0 Å2
2---1.55 Å2-0 Å2
3---5.02 Å2
Refinement stepCycle: 1 / Resolution: 2.5→109.72 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4792 0 0 0 4792
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0194904
X-RAY DIFFRACTIONr_bond_other_d0.0020.024586
X-RAY DIFFRACTIONr_angle_refined_deg1.5921.9466662
X-RAY DIFFRACTIONr_angle_other_deg0.975310537
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.8075606
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.42824.036223
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.73815812
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.5361530
X-RAY DIFFRACTIONr_chiral_restr0.0850.2730
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0215573
X-RAY DIFFRACTIONr_gen_planes_other0.0020.021139
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_it2.5225.4142433
X-RAY DIFFRACTIONr_mcbond_other2.5215.4142432
X-RAY DIFFRACTIONr_mcangle_it4.1588.1123036
X-RAY DIFFRACTIONr_mcangle_other4.1588.1123037
X-RAY DIFFRACTIONr_scbond_it2.5035.6682471
X-RAY DIFFRACTIONr_scbond_other2.5035.672472
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other4.2768.3893627
X-RAY DIFFRACTIONr_long_range_B_refined6.40961.7925409
X-RAY DIFFRACTIONr_long_range_B_other6.40961.7915410
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.5→2.565 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.378 106 -
Rwork0.377 2049 -
obs--99.95 %
Refinement TLS params.Method: refined / Origin x: 5.919 Å / Origin y: 36.844 Å / Origin z: 21.377 Å
111213212223313233
T0.1935 Å2-0.0094 Å20.067 Å2-0.0456 Å2-0.024 Å2--0.0813 Å2
L0.195 °20.1939 °2-0.2656 °2-0.3946 °20.0007 °2--0.7623 °2
S0.0696 Å °0.0324 Å °0.0724 Å °0.0938 Å °0.033 Å °0.034 Å °-0.0066 Å °-0.0679 Å °-0.1026 Å °

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