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- PDB-7lnp: Structure of the exo-alpha-L-galactosidase BpGH29 (D264N mutant) ... -

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Basic information

Entry
Database: PDB / ID: 7lnp
TitleStructure of the exo-alpha-L-galactosidase BpGH29 (D264N mutant) from Bacteroides plebeius in complex with paranitrophenyl-alpha-L-galactopyranoside
ComponentsExo-alpha-L-galactosidase
KeywordsHYDROLASE / glycoside hydrolase / porphyran / carbohydrate
Function / homology
Function and homology information


alpha-L-fucosidase activity / fucose metabolic process / glycoside catabolic process / lysosome / metal ion binding
Similarity search - Function
Alpha-L-fucosidase, C-terminal / Alpha-L-fucosidase C-terminal domain / Alpha-L-fucosidase, metazoa-type / Alpha-L-fucosidase / Glycoside hydrolase, family 29 / Alpha-L-fucosidase / Glycosyl hydrolase, all-beta / Glycosidases / Prokaryotic membrane lipoprotein lipid attachment site profile. / Glycoside hydrolase superfamily ...Alpha-L-fucosidase, C-terminal / Alpha-L-fucosidase C-terminal domain / Alpha-L-fucosidase, metazoa-type / Alpha-L-fucosidase / Glycoside hydrolase, family 29 / Alpha-L-fucosidase / Glycosyl hydrolase, all-beta / Glycosidases / Prokaryotic membrane lipoprotein lipid attachment site profile. / Glycoside hydrolase superfamily / TIM Barrel / Alpha-Beta Barrel / Alpha Beta
Similarity search - Domain/homology
NICKEL (II) ION / paranitrophenyl-alpha-L-galactopyranoside / Alpha-L-fucosidase
Similarity search - Component
Biological speciesBacteroides plebeius (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.7 Å
AuthorsBoraston, A.B. / Robb, C.S.
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
DepositionFeb 8, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 9, 2022Provider: repository / Type: Initial release
Revision 1.1Apr 20, 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

Downloads & links

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Assembly

Deposited unit
A: Exo-alpha-L-galactosidase
C: Exo-alpha-L-galactosidase
D: Exo-alpha-L-galactosidase
E: Exo-alpha-L-galactosidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)275,59233
Polymers273,3974
Non-polymers2,19429
Water12,214678
1
A: Exo-alpha-L-galactosidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)68,9129
Polymers68,3491
Non-polymers5638
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
C: Exo-alpha-L-galactosidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)68,9138
Polymers68,3491
Non-polymers5637
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
D: Exo-alpha-L-galactosidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)68,8547
Polymers68,3491
Non-polymers5056
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
E: Exo-alpha-L-galactosidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)68,9129
Polymers68,3491
Non-polymers5638
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)157.325, 106.637, 155.896
Angle α, β, γ (deg.)90.000, 114.970, 90.000
Int Tables number5
Space group name H-MC121
Space group name HallC2y
Symmetry operation#1: x,y,z
#2: -x,y,-z
#3: x+1/2,y+1/2,z
#4: -x+1/2,y+1/2,-z

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Components

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Protein , 1 types, 4 molecules ACDE

#1: Protein
Exo-alpha-L-galactosidase


Mass: 68349.344 Da / Num. of mol.: 4 / Mutation: D264N
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacteroides plebeius (bacteria) / Strain: DSM 17135 / JCM 12973 / M2 / Gene: BACPLE_01702 / Production host: Escherichia coli (E. coli) / References: UniProt: B5CYA5

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Non-polymers , 6 types, 707 molecules

#2: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Ca
#3: Chemical
ChemComp-Y9Y / paranitrophenyl-alpha-L-galactopyranoside / (2~{S},3~{S},4~{R},5~{S},6~{S})-2-(hydroxymethyl)-6-(4-nitrophenoxy)oxane-3,4,5-triol


Mass: 301.249 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C12H15NO8
#4: Chemical
ChemComp-NI / NICKEL (II) ION


Mass: 58.693 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: Ni
#5: Chemical
ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: Na
#6: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Formula: Cl
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 678 / 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: 2.21 Å3/Da / Density % sol: 44.38 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop
Details: 0.1 M BIS-TRIS (pH 5.5), 0.2 M (NH4)2SO4, 25% (w/v) PEG 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SEALED TUBE / Type: RIGAKU MICROMAX-003 / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Feb 11, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.7→32 Å / Num. obs: 64080 / % possible obs: 97.4 % / Redundancy: 3.7 % / Biso Wilson estimate: 20.59 Å2 / CC1/2: 0.986 / Rmerge(I) obs: 0.172 / Rpim(I) all: 0.119 / Net I/σ(I): 4.5
Reflection shellResolution: 2.7→2.77 Å / Rmerge(I) obs: 0.556 / Mean I/σ(I) obs: 1.7 / Num. unique obs: 4449 / CC1/2: 0.844 / Rpim(I) all: 0.396

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Processing

Software
NameVersionClassification
PHENIX1.13_2998refinement
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 7ljj

7ljj


Resolution: 2.7→31.57 Å / SU ML: 0.3317 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 35.0048 / Stereochemistry target values: GeoStd + Monomer Library
RfactorNum. reflection% reflection
Rfree0.2844 3197 5.01 %
Rwork0.2297 60655 -
obs0.2325 63852 99.4 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 20.57 Å2
Refinement stepCycle: LAST / Resolution: 2.7→31.57 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms17709 0 109 678 18496
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.001518289
X-RAY DIFFRACTIONf_angle_d0.419424851
X-RAY DIFFRACTIONf_chiral_restr0.0412612
X-RAY DIFFRACTIONf_plane_restr0.00293184
X-RAY DIFFRACTIONf_dihedral_angle_d2.484210634
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.7-2.740.41281470.3022606X-RAY DIFFRACTION99.06
2.74-2.780.35441320.29972612X-RAY DIFFRACTION99.28
2.78-2.830.35221210.29292596X-RAY DIFFRACTION98.91
2.83-2.880.36761410.27482664X-RAY DIFFRACTION99.19
2.88-2.930.32361400.27392595X-RAY DIFFRACTION99.27
2.93-2.990.27611230.28012641X-RAY DIFFRACTION99.25
2.99-3.050.3411410.26932625X-RAY DIFFRACTION99.32
3.05-3.110.31131490.27092614X-RAY DIFFRACTION99.42
3.11-3.190.30521370.25442644X-RAY DIFFRACTION99.61
3.19-3.260.28851420.24542622X-RAY DIFFRACTION99.71
3.26-3.350.32141610.242613X-RAY DIFFRACTION99.86
3.35-3.450.34271390.23342639X-RAY DIFFRACTION99.75
3.45-3.560.28981310.2282674X-RAY DIFFRACTION99.79
3.56-3.690.27471350.22232632X-RAY DIFFRACTION99.75
3.69-3.840.33341290.20782649X-RAY DIFFRACTION99.86
3.84-4.010.22341400.2022640X-RAY DIFFRACTION99.75
4.01-4.220.22091450.20042628X-RAY DIFFRACTION99.75
4.22-4.490.2511330.18982664X-RAY DIFFRACTION99.68
4.49-4.830.21621280.18052661X-RAY DIFFRACTION99.47
4.83-5.320.24521480.19282649X-RAY DIFFRACTION99.54
5.32-6.080.271510.21032648X-RAY DIFFRACTION99.64
6.08-7.640.25671260.21812687X-RAY DIFFRACTION99.47
7.64-31.570.21571580.20332652X-RAY DIFFRACTION97.06

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