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- PDB-6d1p: Apo structure of Bacteroides uniformis beta-glucuronidase 3 -

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Basic information

Entry
Database: PDB / ID: 6d1p
TitleApo structure of Bacteroides uniformis beta-glucuronidase 3
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
Similarity search - Function
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 ...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-like domain superfamily / Glycosidases / Glycoside hydrolase superfamily / TIM Barrel / Alpha-Beta Barrel / Immunoglobulin-like fold / Alpha Beta
Similarity search - Domain/homology
: / THIOCYANATE ION / 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: 2.35 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 12, 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 1.4Mar 13, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id

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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)187,21818
Polymers186,3702
Non-polymers84816
Water14,682815
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: light scattering
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7390 Å2
ΔGint-79 kcal/mol
Surface area57020 Å2
MethodPISA
Unit cell
Length a, b, c (Å)209.721, 68.209, 167.300
Angle α, β, γ (deg.)90.00, 122.49, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-1014-

HOH

21A-1372-

HOH

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Components

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Protein , 1 types, 2 molecules AB

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


Mass: 93185.133 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacteroides uniformis str. 3978 T3 ii (bacteria)
Gene: M094_3281 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A078SSU5

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Non-polymers , 5 types, 831 molecules

#2: Chemical
ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Na
#3: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical ChemComp-SCN / THIOCYANATE ION


Mass: 58.082 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: CNS
#5: Chemical
ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: K
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 815 / 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: 2.71 Å3/Da / Density % sol: 54.57 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, hanging drop
Details: 8% PEG 3350, 0.2 M Potassium Thiocyanate and 0.1M Hepes pH 8.0

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-D / Wavelength: 1.03316 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Nov 5, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.03316 Å / Relative weight: 1
ReflectionResolution: 2.35→29.48 Å / Num. obs: 83426 / % possible obs: 99.9 % / Redundancy: 6.8 % / Net I/σ(I): 21
Reflection shellResolution: 2.35→2.39 Å

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Processing

Software
NameVersionClassification
PHENIX(1.14_3260)refinement
XDSdata reduction
Aimlessdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.35→29.095 Å / SU ML: 0.26 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 23.81 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2224 2000 2.4 %
Rwork0.1755 --
obs0.1766 83424 99.96 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.35→29.095 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms12598 0 45 815 13458
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00812958
X-RAY DIFFRACTIONf_angle_d0.94617530
X-RAY DIFFRACTIONf_dihedral_angle_d15.3447686
X-RAY DIFFRACTIONf_chiral_restr0.0541815
X-RAY DIFFRACTIONf_plane_restr0.0062303
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.35-2.40870.26251400.22675704X-RAY DIFFRACTION100
2.4087-2.47380.28751430.21935801X-RAY DIFFRACTION100
2.4738-2.54660.28221410.21355746X-RAY DIFFRACTION100
2.5466-2.62870.30831430.20985822X-RAY DIFFRACTION100
2.6287-2.72260.28191420.21015776X-RAY DIFFRACTION100
2.7226-2.83150.25611420.20585797X-RAY DIFFRACTION100
2.8315-2.96030.26061420.21145784X-RAY DIFFRACTION100
2.9603-3.11620.26731430.19965816X-RAY DIFFRACTION100
3.1162-3.31120.2391420.19125782X-RAY DIFFRACTION100
3.3112-3.56640.22421440.17375857X-RAY DIFFRACTION100
3.5664-3.92460.19851420.15955798X-RAY DIFFRACTION100
3.9246-4.49070.18111440.14125838X-RAY DIFFRACTION100
4.4907-5.6510.17781440.14275905X-RAY DIFFRACTION100
5.651-29.0970.17691480.15715998X-RAY DIFFRACTION100

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