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- PDB-6d8g: D341A D367A calcium binding mutant of Bacteroides uniformis beta-... -

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Basic information

Entry
Database: PDB / ID: 6d8g
TitleD341A D367A calcium binding mutant of Bacteroides uniformis beta-glucuronidase 2
ComponentsGlycosyl hydrolases family 2, sugar binding domain protein
KeywordsHYDROLASE / beta-glucuronidase
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 / Domain of unknown function DUF4982 / Domain of unknown function (DUF4982) / : / 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 ...Malectin domain / Malectin domain / Domain of unknown function DUF4982 / Domain of unknown function (DUF4982) / : / 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 / Galactose-binding domain-like / Galactose-binding-like domain superfamily / Glycosidases / Glycoside hydrolase superfamily / Jelly Rolls / TIM Barrel / Alpha-Beta Barrel / Immunoglobulin-like fold / Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
Glycosyl hydrolases family 2, sugar binding domain protein
Similarity search - Component
Biological speciesBacteroides uniformis str. 3978 T3 ii (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3 Å
AuthorsWalton, W.G. / Pellock, S.J. / Redinbo, M.R.
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Cancer Institute (NIH/NCI)CA098468 United States
National Institutes of Health/National Cancer Institute (NIH/NCI)CA207416 United States
CitationJournal: J. Biol. Chem. / Year: 2018
Title: Three structurally and functionally distinct beta-glucuronidases from the human gut microbeBacteroides uniformis.
Authors: Pellock, S.J. / Walton, W.G. / Biernat, K.A. / Torres-Rivera, D. / Creekmore, B.C. / Xu, Y. / Liu, J. / Tripathy, A. / Stewart, L.J. / Redinbo, M.R.
History
DepositionApr 26, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 17, 2018Provider: repository / Type: Initial release
Revision 1.1Oct 24, 2018Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.journal_abbrev / _citation.pdbx_database_id_DOI ..._citation.journal_abbrev / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.name
Revision 1.2Dec 19, 2018Group: Data collection / Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title
Revision 1.3Dec 4, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.4Oct 4, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
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: Glycosyl hydrolases family 2, sugar binding domain protein
B: Glycosyl hydrolases family 2, sugar binding domain protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)202,7444
Polymers202,6982
Non-polymers462
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: light scattering
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6380 Å2
ΔGint1 kcal/mol
Surface area60480 Å2
MethodPISA
Unit cell
Length a, b, c (Å)74.990, 142.018, 181.239
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Glycosyl hydrolases family 2, sugar binding domain protein


Mass: 101348.812 Da / Num. of mol.: 2 / Mutation: D341A, D367A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacteroides uniformis str. 3978 T3 ii (bacteria)
Gene: M094_3283 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A078SUX9
#2: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Na

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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: 2.38 Å3/Da / Density % sol: 48.33 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, hanging drop / Details: 0.2 M Potassium Chloride, 20% PEG 3350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-B / Wavelength: 0.98618 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Oct 15, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98618 Å / Relative weight: 1
ReflectionResolution: 3→29.55 Å / Num. obs: 39566 / % possible obs: 99.9 % / Redundancy: 13.3 % / Net I/σ(I): 18.1
Reflection shellResolution: 3→3.12 Å

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Processing

Software
NameVersionClassification
PHENIX(1.11.1_2575)refinement
XDSdata reduction
Aimlessdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5UJ6

5uj6


Resolution: 3→29.546 Å / SU ML: 0.42 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 25.21 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2414 2000 5.06 %
Rwork0.1664 --
obs0.1702 39496 99.97 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 3→29.546 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms13435 0 2 0 13437
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00913789
X-RAY DIFFRACTIONf_angle_d1.01618722
X-RAY DIFFRACTIONf_dihedral_angle_d14.0098120
X-RAY DIFFRACTIONf_chiral_restr0.0561987
X-RAY DIFFRACTIONf_plane_restr0.0062440
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3-3.0750.33321390.22562612X-RAY DIFFRACTION100
3.075-3.1580.35231420.2292660X-RAY DIFFRACTION100
3.158-3.25080.35131400.23612625X-RAY DIFFRACTION100
3.2508-3.35560.31941410.21512637X-RAY DIFFRACTION100
3.3556-3.47540.30761410.20952642X-RAY DIFFRACTION100
3.4754-3.61430.32471420.21172665X-RAY DIFFRACTION100
3.6143-3.77850.28091420.19612665X-RAY DIFFRACTION100
3.7785-3.97720.26321410.17092653X-RAY DIFFRACTION100
3.9772-4.22570.231430.16072664X-RAY DIFFRACTION100
4.2257-4.55090.21091420.13922670X-RAY DIFFRACTION100
4.5509-5.00690.16831450.13142713X-RAY DIFFRACTION100
5.0069-5.72680.20081440.13392705X-RAY DIFFRACTION100
5.7268-7.1980.2441450.15862721X-RAY DIFFRACTION100
7.198-29.5470.18081530.13912864X-RAY DIFFRACTION100

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