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- PDB-7zvo: Structure of CBM BT0996-C from Bacteroides thetaiotaomicron -

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Basic information

Entry
Database: PDB / ID: 7zvo
TitleStructure of CBM BT0996-C from Bacteroides thetaiotaomicron
ComponentsBeta-galactosidase
KeywordsSUGAR BINDING PROTEIN / CBM / Carbohydrate-binding Module / Carbohydrate / Rhamnogalacturonan II / bacterial / microbiome / human gut
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 / Glycoside hydrolase family 2, catalytic domain / Glycosyl hydrolases family 2, TIM barrel domain / Glycoside hydrolase, family 2, immunoglobulin-like beta-sandwich / Glycosyl hydrolases family 2, sugar binding domain / Glycosyl hydrolases family 2 / Glycosyl hydrolases family 2, sugar binding domain / Beta-Galactosidase/glucuronidase domain superfamily ...Malectin domain / Malectin domain / Glycoside hydrolase, family 2 / Glycoside hydrolase family 2, catalytic domain / Glycosyl hydrolases family 2, TIM barrel domain / Glycoside hydrolase, family 2, immunoglobulin-like beta-sandwich / Glycosyl hydrolases family 2, sugar binding domain / Glycosyl hydrolases family 2 / Glycosyl hydrolases family 2, sugar binding domain / 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
ALANINE / BETA-MERCAPTOETHANOL / SERINE / Beta-galactosidase
Similarity search - Component
Biological speciesBacteroides thetaiotaomicron VPI-5482 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.65 Å
AuthorsTrovao, F. / Pinheiro, B.A. / Correia, V.G. / Palma, A.S. / Carvalho, A.L.
Funding support1items
OrganizationGrant numberCountry
Other governmentPTDC/BIA-MIB/31730/2017
CitationJournal: J Struct Biol X / Year: 2023
Title: The structure of a Bacteroides thetaiotaomicron carbohydrate-binding module provides new insight into the recognition of complex pectic polysaccharides by the human microbiome.
Authors: Trovao, F. / Correia, V.G. / Lourenco, F.M. / Ribeiro, D.O. / Carvalho, A.L. / Palma, A.S. / Pinheiro, B.A.
History
DepositionMay 16, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 8, 2023Provider: repository / Type: Initial release
Revision 1.1May 1, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Beta-galactosidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,4168
Polymers15,9141
Non-polymers5017
Water2,324129
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area680 Å2
ΔGint-38 kcal/mol
Surface area6970 Å2
MethodPISA
Unit cell
Length a, b, c (Å)34.978, 45.938, 85.823
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x,y+1/2,-z+1/2
#4: -x+1/2,-y,z+1/2

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Components

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Protein , 1 types, 1 molecules A

#1: Protein Beta-galactosidase


Mass: 15914.272 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacteroides thetaiotaomicron VPI-5482 (bacteria)
Strain: ATCC 29148 / DSM 2079 / JCM 5827 / CCUG 10774 / NCTC 10582 / VPI-5482 / E50
Gene: BT_0996 / Production host: Escherichia coli (E. coli) / References: UniProt: Q8A921

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Non-polymers , 7 types, 136 molecules

#2: Chemical ChemComp-MPD / (4S)-2-METHYL-2,4-PENTANEDIOL


Mass: 118.174 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H14O2 / Comment: precipitant*YM
#3: Chemical ChemComp-SER / SERINE


Type: L-peptide linking / Mass: 105.093 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H7NO3
#4: Chemical ChemComp-BME / BETA-MERCAPTOETHANOL


Mass: 78.133 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6OS
#5: Chemical ChemComp-ALA / ALANINE


Type: L-peptide linking / Mass: 89.093 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H7NO2
#6: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#7: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 129 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestN

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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: 2.18 Å3/Da / Density % sol: 43.5 % / Description: Long plates
Crystal growTemperature: 277.15 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 0.1 M Amino acids mix (DL- Glu, Ala, Gly, Lys, Ser), 0.1 M Buffer system 3 (Tris, Bicine pH 8.5) and 37.5% Precipitant Mix 4 (25% MPD, 25% PEG 1000, 25% PEG 3350)

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALBA / Beamline: XALOC / Wavelength: 0.976 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jun 19, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.976 Å / Relative weight: 1
ReflectionResolution: 1.65→42.91 Å / Num. obs: 31987 / % possible obs: 99.71 % / Redundancy: 2 % / Biso Wilson estimate: 20.2 Å2 / CC1/2: 0.99 / Net I/σ(I): 15.4
Reflection shellResolution: 1.65→1.709 Å / Num. unique obs: 17221 / CC1/2: 0.92

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
PHENIX1.20.1_4487refinement
autoPROCdata reduction
autoPROCdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: from a previous seleno SAD model

Resolution: 1.65→42.91 Å / SU ML: 0.2006 / Cross valid method: FREE R-VALUE / σ(F): 1.94 / Phase error: 24.3958
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2252 1557 4.87 %
Rwork0.1736 30430 -
obs0.1759 31987 99.57 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 27.55 Å2
Refinement stepCycle: LAST / Resolution: 1.65→42.91 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1034 0 27 129 1190
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00661103
X-RAY DIFFRACTIONf_angle_d0.87521483
X-RAY DIFFRACTIONf_chiral_restr0.0592161
X-RAY DIFFRACTIONf_plane_restr0.0067186
X-RAY DIFFRACTIONf_dihedral_angle_d9.7622151
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.65-1.70.33131350.27962751X-RAY DIFFRACTION99.65
1.7-1.760.28891620.23952753X-RAY DIFFRACTION99.52
1.76-1.830.30391180.22332797X-RAY DIFFRACTION99.69
1.83-1.920.26111560.22882749X-RAY DIFFRACTION99.45
1.92-2.020.23881490.19952747X-RAY DIFFRACTION99.52
2.02-2.150.24251530.18252760X-RAY DIFFRACTION99.45
2.15-2.310.21171350.18332793X-RAY DIFFRACTION99.32
2.31-2.540.25551250.18192770X-RAY DIFFRACTION99.9
2.54-2.910.23541560.17552763X-RAY DIFFRACTION99.45
2.91-3.670.23271340.1562754X-RAY DIFFRACTION99.69
3.67-42.910.15461340.13642793X-RAY DIFFRACTION99.8
Refinement TLS params.Method: refined / Origin x: -6.4048665374 Å / Origin y: -1.0009252974 Å / Origin z: 13.565410281 Å
111213212223313233
T0.138152495574 Å20.0072488414897 Å2-0.0116120273739 Å2-0.150979237478 Å2-0.0151263775715 Å2--0.148868140707 Å2
L1.05685625759 °20.269991070173 °20.598462657034 °2-1.70358284228 °2-0.258821082874 °2--1.74134095744 °2
S-0.0505514890922 Å °-0.00227603778137 Å °0.0504075394889 Å °0.114420640496 Å °-0.000555251957985 Å °0.0547575013692 Å °-0.067000557316 Å °-0.0672489514476 Å °-0.00714645349834 Å °
Refinement TLS groupSelection details: all

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