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- PDB-6jz7: b-glucuronidase from Ruminococcus gnavus in complex with N1-subst... -

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Basic information

Entry
Database: PDB / ID: 6jz7
Titleb-glucuronidase from Ruminococcus gnavus in complex with N1-substituted uronic isofagomine
ComponentsBeta-glucuronidase
KeywordsHYDROLASE / b-glucuronidase
Function / homology
Function and homology information


glucuronoside catabolic process / beta-glucuronidase / beta-glucuronidase activity / beta-galactosidase activity / carbohydrate binding / carbohydrate metabolic process
Similarity search - Function
Glycoside hydrolase, family 2, conserved site / Glycosyl hydrolases family 2 signature 1. / 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 ...Glycoside hydrolase, family 2, conserved site / Glycosyl hydrolases family 2 signature 1. / 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 / Immunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
Chem-CKU / Beta-glucuronidase
Similarity search - Component
Biological speciesRuminococcus gnavus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.45 Å
AuthorsDashnyam, P. / Lin, H.Y.
Funding support Taiwan, 1items
OrganizationGrant numberCountry
Ministry of Science and Technology (MoST, Taiwan) Taiwan
CitationJournal: J.Med.Chem. / Year: 2020
Title: Substituent Position of Iminocyclitols Determines the Potency and Selectivity for Gut Microbial Xenobiotic-Reactivating Enzymes.
Authors: Dashnyam, P. / Lin, H.Y. / Chen, C.Y. / Gao, S. / Yeh, L.F. / Hsieh, W.C. / Tu, Z. / Lin, C.H.
History
DepositionApr 30, 2019Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jun 10, 2020Provider: repository / Type: Initial release
Revision 1.1Dec 23, 2020Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Nov 22, 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: Beta-glucuronidase
B: Beta-glucuronidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)140,4844
Polymers140,0782
Non-polymers4062
Water20,0331112
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3040 Å2
ΔGint-21 kcal/mol
Surface area41070 Å2
MethodPISA
Unit cell
Length a, b, c (Å)160.539, 102.397, 110.776
Angle α, β, γ (deg.)90.00, 130.78, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-1015-

HOH

21B-1054-

HOH

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Components

#1: Protein Beta-glucuronidase


Mass: 70038.883 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Ruminococcus gnavus (bacteria) / Gene: uidA / Production host: Escherichia coli (E. coli) / References: UniProt: Q6W7J7
#2: Chemical ChemComp-CKU / (3~{S},4~{R},5~{R})-4,5-bis(oxidanyl)-1-propyl-piperidine-3-carboxylic acid


Mass: 203.236 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Formula: C9H17NO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1112 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.46 Å3/Da / Density % sol: 50.02 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / Details: 70% MPD, 0.1 M HEPES, pH 7.5, 0.2 M CaCl2

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Data collection

DiffractionMean temperature: 277 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: NSRRC / Beamline: BL13C1 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Feb 23, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.446→30 Å / Num. obs: 358160 / % possible obs: 99.8 % / Redundancy: 4.5 % / Rmerge(I) obs: 0.076 / Net I/σ(I): 10.3
Reflection shellResolution: 1.45→1.5 Å / Redundancy: 3.8 % / Rmerge(I) obs: 0.595 / Num. unique obs: 53100 / % possible all: 99.8

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
HKL-2000data scaling
PDB_EXTRACT3.25data extraction
HKL-2000data reduction
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5Z19

5z19


Resolution: 1.45→29.56 Å / SU ML: 0.1 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 17 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.159 3047 0.85 %
Rwork0.146 --
obs0.146 358160 75.1 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 19.1 Å2
Refinement stepCycle: LAST / Resolution: 1.45→29.56 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9346 0 28 1112 10486
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0069638
X-RAY DIFFRACTIONf_angle_d1.15513066
X-RAY DIFFRACTIONf_dihedral_angle_d12.8173510
X-RAY DIFFRACTIONf_chiral_restr0.0761350
X-RAY DIFFRACTIONf_plane_restr0.0051689
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.45-1.46910.3198520.23277581X-RAY DIFFRACTION35
1.4691-1.49320.2412740.220810412X-RAY DIFFRACTION48
1.4932-1.51890.2107930.209210722X-RAY DIFFRACTION50
1.5189-1.54650.2175940.200210841X-RAY DIFFRACTION50
1.5465-1.57630.19571090.191610963X-RAY DIFFRACTION51
1.5763-1.60850.1748830.17811141X-RAY DIFFRACTION52
1.6085-1.64340.2038950.175411407X-RAY DIFFRACTION53
1.6434-1.68170.16421250.165511819X-RAY DIFFRACTION55
1.6817-1.72370.197930.156412618X-RAY DIFFRACTION59
1.7237-1.77030.13451090.150714117X-RAY DIFFRACTION65
1.7703-1.82240.14271400.147115755X-RAY DIFFRACTION73
1.8224-1.88120.14711670.143717350X-RAY DIFFRACTION81
1.8812-1.94840.15361550.141219131X-RAY DIFFRACTION89
1.9484-2.02640.14921940.138420391X-RAY DIFFRACTION95
2.0264-2.11860.12721590.1421232X-RAY DIFFRACTION98
2.1186-2.23030.15791860.142321313X-RAY DIFFRACTION99
2.2303-2.370.16581970.148121366X-RAY DIFFRACTION99
2.37-2.55290.18541740.148121430X-RAY DIFFRACTION100
2.5529-2.80960.16861900.15121418X-RAY DIFFRACTION100
2.8096-3.21570.16161850.138821324X-RAY DIFFRACTION99
3.2157-4.04980.14831940.122921325X-RAY DIFFRACTION99
4.0498-29.5570.151790.146921457X-RAY DIFFRACTION100
Refinement TLS params.Method: refined / Origin x: 130.0696 Å / Origin y: -872.4237 Å / Origin z: 274.5641 Å
111213212223313233
T0.0871 Å20.0119 Å20.007 Å2-0.0943 Å2-0.0031 Å2--0.0975 Å2
L0.3451 °20.0664 °20.0906 °2-0.1784 °2-0.023 °2--0.266 °2
S0.0028 Å °0.03 Å °0.0134 Å °-0.0229 Å °0.0006 Å °0.0197 Å °-0.009 Å °-0.0126 Å °-0.0024 Å °
Refinement TLS groupSelection details: ALL

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