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- PDB-6xxw: Structure of beta-D-Glucuronidase for Dictyoglomus thermophilum. -

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Basic information

Entry
Database: PDB / ID: 6xxw
TitleStructure of beta-D-Glucuronidase for Dictyoglomus thermophilum.
ComponentsBeta-glucuronidase
KeywordsHYDROLASE / Glycoside hydrolase / Glucuronide
Function / homology
Function and homology information


beta-glucuronidase / beta-glucuronidase activity / carbohydrate metabolic process
Similarity search - Function
Glycoside hydrolase, family 2, active site / Glycosyl hydrolases family 2 acid/base catalyst. / Glycoside hydrolase, family 2 / Glycoside hydrolase family 2, catalytic domain / Glycosyl hydrolases family 2, TIM barrel domain / Glycoside hydrolase, family 2, immunoglobulin-like beta-sandwich / Glycosyl hydrolases family 2, sugar binding domain / Glycosyl hydrolases family 2 / Glycosyl hydrolases family 2, sugar binding domain / Beta-Galactosidase/glucuronidase domain superfamily ...Glycoside hydrolase, family 2, active site / Glycosyl hydrolases family 2 acid/base catalyst. / Glycoside hydrolase, family 2 / Glycoside hydrolase family 2, catalytic domain / Glycosyl hydrolases family 2, TIM barrel domain / Glycoside hydrolase, family 2, immunoglobulin-like beta-sandwich / Glycosyl hydrolases family 2, sugar binding domain / Glycosyl hydrolases family 2 / Glycosyl hydrolases family 2, sugar binding domain / Beta-Galactosidase/glucuronidase domain superfamily / Galactose-binding-like domain superfamily / Glycoside hydrolase superfamily / Immunoglobulin-like fold
Similarity search - Domain/homology
Biological speciesDictyoglomus thermophilum (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.851 Å
AuthorsLafite, P. / Daniellou, R.
CitationJournal: Org.Biomol.Chem. / Year: 2020
Title: Thioglycoligation of aromatic thiols using a natural glucuronide donor.
Authors: Kurdziel, M. / Kopec, M. / Paris, A. / Lewinski, K. / Lafite, P. / Daniellou, R.
History
DepositionJan 28, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 15, 2020Provider: repository / Type: Initial release
Revision 1.1Jul 29, 2020Group: Database references / Category: citation / citation_author
Item: _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed ..._citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID / _citation_author.name
Revision 1.2Aug 5, 2020Group: 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 1.3Jan 24, 2024Group: 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

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Assembly

Deposited unit
A: Beta-glucuronidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)71,19711
Polymers70,0661
Non-polymers1,13110
Water6,557364
1
A: Beta-glucuronidase
hetero molecules

A: Beta-glucuronidase
hetero molecules

A: Beta-glucuronidase
hetero molecules

A: Beta-glucuronidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)284,78944
Polymers280,2664
Non-polymers4,52340
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_565-x,-y+1,z1
crystal symmetry operation3_556-x,y,-z+11
crystal symmetry operation4_566x,-y+1,-z+11
Buried area28500 Å2
ΔGint-83 kcal/mol
Surface area72050 Å2
MethodPISA
Unit cell
Length a, b, c (Å)79.130, 115.820, 130.540
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number23
Space group name H-MI222
Components on special symmetry positions
IDModelComponents
11A-759-

HOH

21A-998-

HOH

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Components

#1: Protein Beta-glucuronidase /


Mass: 70066.414 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Dictyoglomus thermophilum (strain ATCC 35947 / DSM 3960 / H-6-12) (bacteria)
Gene: DICTH_1429 / Production host: Escherichia coli (E. coli) / References: UniProt: B5YFE0, beta-glucuronidase
#2: Chemical
ChemComp-TRS / 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL / TRIS BUFFER / Tris


Mass: 122.143 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C4H12NO3 / Comment: pH buffer*YM
#3: Chemical ChemComp-MPD / (4S)-2-METHYL-2,4-PENTANEDIOL / 2-Methyl-2,4-pentanediol


Mass: 118.174 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H14O2 / Comment: precipitant*YM
#4: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 364 / 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: 2.13 Å3/Da / Density % sol: 42.37 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 8
Details: 20% w/v 2-Methylpentane-2,2-diol 100mM NaHEPES pH 7.5 100mM Citrate sodium

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 1 / Wavelength: 0.98 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jun 27, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 1.85→33.834 Å / Num. obs: 50245 / % possible obs: 97.7 % / Redundancy: 4.679 % / Biso Wilson estimate: 28.998 Å2 / CC1/2: 0.997 / Rmerge(I) obs: 0.111 / Rrim(I) all: 0.125 / Χ2: 0.936 / Net I/σ(I): 12.15 / Num. measured all: 235094
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. possibleNum. unique obsCC1/2Rrim(I) all% possible all
1.85-1.964.5310.7432.4636224823779940.7090.83797
1.96-2.14.7390.456436044770676060.8890.51198.7
2.1-2.274.7090.3575.9933339722070800.9230.40198.1
2.27-2.484.7420.2498.2530859663065070.9450.2898.1
2.48-2.774.840.17111.3228868605259640.9770.19298.5
2.77-3.24.7250.11317.2824871535952640.9880.12798.2
3.2-3.924.6990.05326.920763454344190.9970.0697.3
3.92-5.524.4450.03834.0815241357634290.9980.04395.9
5.52-33.8344.4830.0335.438885209919820.9990.03494.4

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Phasing

PhasingMethod: molecular replacement
Phasing MR
Highest resolutionLowest resolution
Rotation6.03 Å46.18 Å
Translation6.03 Å46.18 Å

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Processing

Software
NameVersionClassification
XDS20180808data reduction
XDS20180808data scaling
PHASER2.8.2phasing
PHENIX1.14_3260refinement
PDB_EXTRACT3.25data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1BHG

1bhg


Resolution: 1.851→33.834 Å / SU ML: 0.21 / Cross valid method: THROUGHOUT / σ(F): 1.32 / Phase error: 20.02
RfactorNum. reflection% reflection
Rfree0.2069 1998 3.98 %
Rwork0.1603 --
obs0.1622 50180 97.61 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 74.65 Å2 / Biso mean: 25.4197 Å2 / Biso min: 9.29 Å2
Refinement stepCycle: final / Resolution: 1.851→33.834 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4741 0 73 364 5178
Biso mean--39.55 34.83 -
Num. residues----578
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.851-1.89710.30231360.2596328894
1.8971-1.94840.28531430.2138345099
1.9484-2.00570.23421420.1871342099
2.0057-2.07040.21641430.1726345399
2.0704-2.14440.23191420.1749343198
2.1444-2.23020.2361440.1673344898
2.2302-2.33170.20811420.1615343398
2.3317-2.45460.22371420.16344498
2.4546-2.60830.22851430.1578345399
2.6083-2.80970.22761440.1617348199
2.8097-3.09220.21941440.1504345998
3.0922-3.53930.16191440.1376348098
3.5393-4.45750.1551440.1285344096
4.4575-33.8340.21471450.1768350294

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