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- PDB-7lh6: The structure of Bacteroides plebeius L-galactose dehydrogenase -

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Basic information

Entry
Database: PDB / ID: 7lh6
TitleThe structure of Bacteroides plebeius L-galactose dehydrogenase
ComponentsL-galactose dehydrogenase
KeywordsOXIDOREDUCTASE / dehydrogenase / L-galactose / carbohydrate
Function / homologyL-galactose dehydrogenase activity / L-galactose dehydrogenase-like / D-threo-aldose 1-dehydrogenase activity / Aldo-keto reductase / NADP-dependent oxidoreductase domain / Aldo/keto reductase family / NADP-dependent oxidoreductase domain superfamily / Oxidoreductase, aldo/keto reductase family protein
Function and homology information
Biological speciesBacteroides plebeius (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.85 Å
AuthorsRobb, C.S. / Pluvinage, B. / Vickers, C. / Boraston, A.B.
CitationJournal: Nat.Chem.Biol. / Year: 2022
Title: Metabolism of a hybrid algal galactan by members of the human gut microbiome.
Authors: Robb, C.S. / Hobbs, J.K. / Pluvinage, B. / Reintjes, G. / Klassen, L. / Monteith, S. / Giljan, G. / Amundsen, C. / Vickers, C. / Hettle, A.G. / Hills, R. / Xing, X. / Montina, T. / Zandberg, ...Authors: Robb, C.S. / Hobbs, J.K. / Pluvinage, B. / Reintjes, G. / Klassen, L. / Monteith, S. / Giljan, G. / Amundsen, C. / Vickers, C. / Hettle, A.G. / Hills, R. / Xing, X. / Montina, T. / Zandberg, W.F. / Abbott, D.W. / Boraston, A.B.
History
DepositionJan 21, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 9, 2022Provider: repository / Type: Initial release
Revision 1.1Mar 30, 2022Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2May 11, 2022Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID
Revision 1.3Oct 18, 2023Group: 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
B: L-galactose dehydrogenase
A: L-galactose dehydrogenase


Theoretical massNumber of molelcules
Total (without water)74,1942
Polymers74,1942
Non-polymers00
Water30617
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2170 Å2
ΔGint-15 kcal/mol
Surface area24360 Å2
MethodPISA
Unit cell
Length a, b, c (Å)55.754, 84.461, 129.499
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

#1: Protein L-galactose dehydrogenase


Mass: 37096.914 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacteroides plebeius (bacteria) / Strain: DSM 17135 / JCM 12973 / M2 / Gene: BACPLE_01679 / Production host: Escherichia coli (E. coli) / References: UniProt: B5CY82
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 17 / 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: 2.04 Å3/Da / Density % sol: 39.61 %
Crystal growTemperature: 291.15 K / Method: vapor diffusion, hanging drop
Details: 0.2 M ammonium citrate dibasic (pH 5.5), 20% (w/v) PEG 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.5418 Å
DetectorType: DECTRIS PILATUS 200K / Detector: PIXEL / Date: Jan 21, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.85→30 Å / Num. obs: 14732 / % possible obs: 98.6 % / Redundancy: 5.8 % / Biso Wilson estimate: 54.55 Å2 / CC1/2: 0.994 / Rmerge(I) obs: 0.106 / Rpim(I) all: 0.046 / Net I/σ(I): 14.7
Reflection shellResolution: 2.85→2.9 Å / Redundancy: 3.5 % / Rmerge(I) obs: 0.819 / Mean I/σ(I) obs: 1.7 / Num. unique obs: 704 / CC1/2: 0.82 / Rpim(I) all: 0.478 / % possible all: 95.5

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Processing

Software
NameVersionClassification
PHENIX1.13_2998refinement
PHASERphasing
HKL-3000data reduction
HKL-3000data scaling
HKL-3000data collection
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1ynp

1ynp


Resolution: 2.85→29.87 Å / SU ML: 0.3823 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 28.6946 / Stereochemistry target values: GeoStd + Monomer Library
RfactorNum. reflection% reflection
Rfree0.2826 1416 10 %
Rwork0.2321 12737 -
obs0.2371 14153 94.94 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 51.17 Å2
Refinement stepCycle: LAST / Resolution: 2.85→29.87 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4419 0 0 17 4436
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00324514
X-RAY DIFFRACTIONf_angle_d0.71446131
X-RAY DIFFRACTIONf_chiral_restr0.0517703
X-RAY DIFFRACTIONf_plane_restr0.005783
X-RAY DIFFRACTIONf_dihedral_angle_d5.80342691
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.85-2.950.41631080.3506973X-RAY DIFFRACTION73.79
2.95-3.070.37431260.32551132X-RAY DIFFRACTION85.99
3.07-3.210.36261370.3191236X-RAY DIFFRACTION95.08
3.21-3.380.33571460.27051314X-RAY DIFFRACTION98.72
3.38-3.590.30881460.22671308X-RAY DIFFRACTION98.98
3.59-3.860.28541460.23051318X-RAY DIFFRACTION98.99
3.86-4.250.30151490.22871331X-RAY DIFFRACTION99.4
4.25-4.860.22961480.19691337X-RAY DIFFRACTION99.66
4.86-6.120.23121520.21861367X-RAY DIFFRACTION99.61
6.12-29.870.24791580.19911421X-RAY DIFFRACTION98.56
Refinement TLS params.Method: refined / Origin x: 46.71393857 Å / Origin y: 40.0006137785 Å / Origin z: 85.9097596471 Å
111213212223313233
T0.261534176019 Å2-0.0128899164328 Å20.00823188736708 Å2-0.240381823372 Å20.0245480895303 Å2--0.349156861428 Å2
L0.124913022699 °20.0496965496453 °20.360160371106 °2-0.693423215002 °2-0.47885650287 °2--1.5888951046 °2
S0.0310813474068 Å °0.0589065387859 Å °0.0576809066747 Å °-0.020797202186 Å °-0.0647832196003 Å °-0.0188038205074 Å °0.0944497753968 Å °0.195407390816 Å °0.0289524666816 Å °
Refinement TLS groupSelection details: all

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