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- PDB-7lha: Structure of the Exo-L-galactose-6-sulfatase BuS1_11 from Bactero... -

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Basic information

Entry
Database: PDB / ID: 7lha
TitleStructure of the Exo-L-galactose-6-sulfatase BuS1_11 from Bacteroides uniformis
ComponentsExo-L-galactose-6-sulfatase
KeywordsHYDROLASE / sulfatase / porphyran / carbohydrate
Function / homology
Function and homology information


hydrolase activity / metal ion binding
Similarity search - Function
N-sulphoglucosamine sulphohydrolase, C-terminal / N-sulphoglucosamine sulphohydrolase, C-terminal / Sulfatases signature 2. / Sulfatases signature 1. / Sulfatase, conserved site / Sulfatase, N-terminal / Sulfatase / Alkaline-phosphatase-like, core domain superfamily
Similarity search - Domain/homology
NICKEL (II) ION / Acetylglucosamine-6-sulfatase
Similarity search - Component
Biological speciesBacteroides uniformis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.95 Å
AuthorsRobb, C.S. / 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

Downloads & links

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Assembly

Deposited unit
A: Exo-L-galactose-6-sulfatase
B: Exo-L-galactose-6-sulfatase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)124,8248
Polymers124,5092
Non-polymers3156
Water16,970942
1
A: Exo-L-galactose-6-sulfatase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)62,4124
Polymers62,2541
Non-polymers1573
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Exo-L-galactose-6-sulfatase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)62,4124
Polymers62,2541
Non-polymers1573
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)89.410, 89.410, 264.790
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number92
Space group name H-MP41212
Space group name HallP4abw2nw
Symmetry operation#1: x,y,z
#2: -y+1/2,x+1/2,z+1/4
#3: y+1/2,-x+1/2,z+3/4
#4: x+1/2,-y+1/2,-z+3/4
#5: -x+1/2,y+1/2,-z+1/4
#6: -x,-y,z+1/2
#7: y,x,-z
#8: -y,-x,-z+1/2

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Components

#1: Protein Exo-L-galactose-6-sulfatase


Mass: 62254.398 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacteroides uniformis (bacteria) / Gene: Bun01g_38470 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A4Y1VMZ7
#2: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca
#3: Chemical
ChemComp-NI / NICKEL (II) ION


Mass: 58.693 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Formula: Ni
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 942 / Source method: isolated from a natural source / Formula: H2O
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: 2.23 Å3/Da / Density % sol: 44.93 %
Crystal growTemperature: 291.15 K / Method: vapor diffusion, hanging drop
Details: 0.1 M HEPES (pH 7.5), 0.2 M MgCl2, 25% (w/v) PEG 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: CLSI / Beamline: 08ID-1 / Wavelength: 0.9792 Å
DetectorType: RAYONIX MX-300 / Detector: CCD / Date: May 14, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 1.95→45 Å / Num. obs: 79225 / % possible obs: 100 % / Redundancy: 10.5 % / Biso Wilson estimate: 16 Å2 / CC1/2: 0.993 / Rmerge(I) obs: 0.166 / Rpim(I) all: 0.053 / Net I/σ(I): 13.8
Reflection shellResolution: 1.95→1.99 Å / Redundancy: 10.4 % / Rmerge(I) obs: 0.92 / Mean I/σ(I) obs: 2.3 / Num. unique obs: 79363 / CC1/2: 0.92 / Rpim(I) all: 0.178 / % possible all: 100

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Processing

Software
NameVersionClassification
PHASERphasing
PHENIX1.13_2998refinement
MOSFLMdata reduction
SCALAdata scaling
BUCCANEERmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2qzu

2qzu


Resolution: 1.95→40.6 Å / SU ML: 0.1724 / Cross valid method: FREE R-VALUE / σ(F): 1.91 / Phase error: 16.9413 / Stereochemistry target values: GeoStd + Monomer Library
RfactorNum. reflection% reflection
Rfree0.1935 3978 5.02 %
Rwork0.1483 75247 -
obs0.1505 79225 99.96 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 18.11 Å2
Refinement stepCycle: LAST / Resolution: 1.95→40.6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8166 0 6 942 9114
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00898409
X-RAY DIFFRACTIONf_angle_d0.948911383
X-RAY DIFFRACTIONf_chiral_restr0.05861178
X-RAY DIFFRACTIONf_plane_restr0.00641469
X-RAY DIFFRACTIONf_dihedral_angle_d5.02597026
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.95-1.970.26411450.18952643X-RAY DIFFRACTION100
1.97-20.20821410.1682645X-RAY DIFFRACTION99.96
2-2.030.21321240.16252633X-RAY DIFFRACTION99.96
2.03-2.050.21541350.15852639X-RAY DIFFRACTION99.96
2.05-2.080.24121580.16442659X-RAY DIFFRACTION100
2.08-2.110.20081370.16082617X-RAY DIFFRACTION100
2.11-2.150.20971460.16112643X-RAY DIFFRACTION100
2.15-2.180.21881410.16342690X-RAY DIFFRACTION100
2.18-2.220.25191360.16092627X-RAY DIFFRACTION99.96
2.22-2.260.23981380.15292660X-RAY DIFFRACTION100
2.26-2.30.22731520.15192651X-RAY DIFFRACTION99.96
2.3-2.350.17461470.14462667X-RAY DIFFRACTION100
2.35-2.40.19071380.1472612X-RAY DIFFRACTION99.93
2.4-2.460.20961460.14652664X-RAY DIFFRACTION99.89
2.46-2.520.18441350.15092671X-RAY DIFFRACTION100
2.52-2.590.19131300.15222677X-RAY DIFFRACTION100
2.59-2.660.24021320.15222684X-RAY DIFFRACTION99.96
2.66-2.750.19971240.15492706X-RAY DIFFRACTION99.96
2.75-2.850.22051420.15082655X-RAY DIFFRACTION99.96
2.85-2.960.19721450.15482704X-RAY DIFFRACTION99.96
2.96-3.10.21891630.15492678X-RAY DIFFRACTION100
3.1-3.260.20531540.15142685X-RAY DIFFRACTION99.96
3.26-3.460.19491420.14582707X-RAY DIFFRACTION99.96
3.46-3.730.1531310.13582757X-RAY DIFFRACTION100
3.73-4.10.1481320.12572742X-RAY DIFFRACTION100
4.1-4.70.14691470.11252761X-RAY DIFFRACTION100
4.7-5.920.15491600.13972798X-RAY DIFFRACTION100
5.92-40.60.17891570.17012972X-RAY DIFFRACTION99.65

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