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- PDB-5mt2: Glycoside hydrolase BT_0996 -

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Basic information

Entry
Database: PDB / ID: 5mt2
TitleGlycoside hydrolase BT_0996
ComponentsBeta-galactosidase
KeywordsHYDROLASE / glycoside hydrolase / arabinofuranosidase / plant pectin / RGII
Function / homology
Function and homology information


hydrolase activity, hydrolyzing O-glycosyl compounds / carbohydrate metabolic process / metal ion binding
Similarity search - Function
Malectin domain / Malectin domain / : / Glycoside hydrolase, family 2 / Glycosyl hydrolases family 2, sugar binding domain / Glycoside hydrolase family 2, catalytic domain / Glycosyl hydrolases family 2, sugar binding domain / Glycosyl hydrolases family 2, TIM barrel domain / Glycoside hydrolase, family 2, immunoglobulin-like beta-sandwich / Glycosyl hydrolases family 2 ...Malectin domain / Malectin domain / : / Glycoside hydrolase, family 2 / Glycosyl hydrolases family 2, sugar binding domain / Glycoside hydrolase family 2, catalytic domain / Glycosyl hydrolases family 2, sugar binding domain / Glycosyl hydrolases family 2, TIM barrel domain / Glycoside hydrolase, family 2, immunoglobulin-like beta-sandwich / Glycosyl hydrolases family 2 / Beta-Galactosidase/glucuronidase domain superfamily / Glycosyl hydrolase, five-bladed beta-propellor domain superfamily / Galactose-binding-like domain superfamily / Glycoside hydrolase superfamily / Immunoglobulin-like fold
Similarity search - Domain/homology
Biological speciesBacteroides thetaiotaomicron (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 1.41 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
Biotechnology and Biological Sciences 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
DepositionJan 6, 2017Deposition 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 30, 2017Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.4Oct 9, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature
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
A: Beta-galactosidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,3323
Polymers44,1481
Non-polymers1842
Water6,215345
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area460 Å2
ΔGint1 kcal/mol
Surface area13820 Å2
MethodPISA
Unit cell
Length a, b, c (Å)42.020, 78.565, 48.793
Angle α, β, γ (deg.)90.00, 108.36, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Beta-galactosidase


Mass: 44148.199 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacteroides thetaiotaomicron (strain ATCC 29148 / DSM 2079 / NCTC 10582 / E50 / VPI-5482) (bacteria)
Gene: BT_0996 / Production host: Escherichia coli (E. coli) / References: UniProt: Q8A921
#2: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 345 / Source method: isolated from a natural source / Formula: H2O
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

Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: 20 % (w/v) PEG 8000, 0.1 M Tris pH 8.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.979 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Jan 17, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 1.41→46.31 Å / Num. obs: 57609 / % possible obs: 99.5 % / Redundancy: 98.3 % / Net I/σ(I): 25.1
Reflection shellResolution: 1.41→1.43 Å / Redundancy: 81.7 % / Rmerge(I) obs: 0.62 / Mean I/σ(I) obs: 1.6 / CC1/2: 0.792 / % possible all: 93.5

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Processing

Software
NameVersionClassification
REFMAC5.8.0158refinement
xia2data reduction
xia2data scaling
SHELXCDphasing
RefinementResolution: 1.41→46.31 Å / Cor.coef. Fo:Fc: 0.977 / Cor.coef. Fo:Fc free: 0.969 / SU B: 2.221 / SU ML: 0.039 / Cross valid method: THROUGHOUT / ESU R: 0.065 / ESU R Free: 0.058 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.16629 2879 5 %RANDOM
Rwork0.12784 ---
obs0.12977 54710 99.46 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 15.423 Å2
Baniso -1Baniso -2Baniso -3
1-0.22 Å2-0 Å2-0.02 Å2
2---0.37 Å20 Å2
3---0.13 Å2
Refinement stepCycle: 1 / Resolution: 1.41→46.31 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2824 0 12 345 3181
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0192980
X-RAY DIFFRACTIONr_bond_other_d0.0020.022609
X-RAY DIFFRACTIONr_angle_refined_deg1.51.9384063
X-RAY DIFFRACTIONr_angle_other_deg0.9536053
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.3145369
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.37323.472144
X-RAY DIFFRACTIONr_dihedral_angle_3_deg10.75415432
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.4621516
X-RAY DIFFRACTIONr_chiral_restr0.0910.2414
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.0213371
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02673
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_it1.1561.3431428
X-RAY DIFFRACTIONr_mcbond_other1.1411.3421427
X-RAY DIFFRACTIONr_mcangle_it1.42.0261789
X-RAY DIFFRACTIONr_mcangle_other1.4042.0261790
X-RAY DIFFRACTIONr_scbond_it1.6611.5671552
X-RAY DIFFRACTIONr_scbond_other1.6491.5671552
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other1.9072.2642267
X-RAY DIFFRACTIONr_long_range_B_refined2.8717.1573507
X-RAY DIFFRACTIONr_long_range_B_other2.86917.1543507
X-RAY DIFFRACTIONr_rigid_bond_restr1.36535589
X-RAY DIFFRACTIONr_sphericity_free21.8895194
X-RAY DIFFRACTIONr_sphericity_bonded6.49855647
LS refinement shellResolution: 1.41→1.447 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.25 186 -
Rwork0.219 3900 -
obs--95.13 %

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