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- PDB-6jz6: b-glucuronidase from Ruminococcus gnavus in complex with C6-subst... -

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Basic information

Entry
Database: PDB / ID: 6jz6
Titleb-glucuronidase from Ruminococcus gnavus in complex with C6-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 / signaling receptor binding / extracellular space
Similarity search - Function
Glycoside hydrolase, family 2, conserved site / Glycosyl hydrolases family 2 signature 1. / 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, conserved site / Glycosyl hydrolases family 2 signature 1. / 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 domain-like / Galactose-binding-like domain superfamily / Glycosidases / Glycoside hydrolase superfamily / Jelly Rolls / Immunoglobulins / TIM Barrel / Alpha-Beta Barrel / Immunoglobulin-like fold / Immunoglobulin-like / Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
Chem-CKX / Beta-glucuronidase
Similarity search - Component
Biological speciesRuminococcus gnavus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.605 Å
AuthorsDashnyam, P. / Lin, H.Y.
Funding support Taiwan, 1items
OrganizationGrant numberCountry
Ministry of Science and Technology (MoST, Taiwan)107-2627-M-001-006 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
Water20,3571130
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3030 Å2
ΔGint-21 kcal/mol
Surface area41480 Å2
MethodPISA
Unit cell
Length a, b, c (Å)161.945, 102.533, 111.961
Angle α, β, γ (deg.)90.000, 130.910, 90.000
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-1058-

HOH

21B-1113-

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-CKX / (2~{S},3~{S},4~{R},5~{R})-4,5-bis(oxidanyl)-2-propyl-piperidine-3-carboxylic acid


Mass: 203.236 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C9H17NO4 / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1130 / 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: 2.51 Å3/Da / Density % sol: 50.95 %
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: Oct 17, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.6→30 Å / Num. obs: 174580 / % possible obs: 97.2 % / Redundancy: 5.2 % / Rmerge(I) obs: 0.068 / Rpim(I) all: 0.033 / Rrim(I) all: 0.076 / Χ2: 0.874 / Net I/σ(I): 10.3 / Num. measured all: 908745
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
1.6-1.664.90.796171100.7240.4010.8940.76295.5
1.66-1.725.10.603172080.8410.2960.6730.896.1
1.72-1.85.20.429173210.9160.2090.4780.85196.4
1.8-1.95.30.297173140.9560.1440.330.90696.7
1.9-2.025.30.185173680.9810.090.2060.95197.1
2.02-2.175.30.123174750.990.060.1370.98997.4
2.17-2.395.30.092175240.9930.0450.1031.02597.8
2.39-2.745.20.066176470.9950.0320.0730.97498
2.74-3.455.10.037175580.9980.0180.0410.84997.6
3.45-305.30.024180550.9990.0120.0270.62199.2

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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: 5Z18

5z18


Resolution: 1.605→29.001 Å / SU ML: 0.12 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 17.51 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1775 2014 1.24 %
Rwork0.152 160976 -
obs0.1523 162990 90.52 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 102.19 Å2 / Biso mean: 18.4676 Å2 / Biso min: 3.02 Å2
Refinement stepCycle: final / Resolution: 1.605→29.001 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9512 0 28 1130 10670
Biso mean--16.32 28.98 -
Num. residues----1160
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0069812
X-RAY DIFFRACTIONf_angle_d1.11913304
X-RAY DIFFRACTIONf_chiral_restr0.0451374
X-RAY DIFFRACTIONf_plane_restr0.0061722
X-RAY DIFFRACTIONf_dihedral_angle_d13.113580
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.605-1.64490.22221050.1723805764
1.6449-1.68940.19971090.1682901571
1.6894-1.73910.21931260.1734987678
1.7391-1.79520.18191320.16361065084
1.7952-1.85940.18211400.16191148891
1.8594-1.93380.18341530.16151215296
1.9338-2.02180.18211480.15541233497
2.0218-2.12840.19851610.15091234497
2.1284-2.26170.18711500.15221239198
2.2617-2.43620.17471590.15741243598
2.4362-2.68130.20261560.16311245798
2.6813-3.06890.18681570.15451248798
3.0689-3.8650.15061580.13131245398
3.865-29.0010.15681600.14611283799
Refinement TLS params.Method: refined / Origin x: 218.9248 Å / Origin y: -859.9004 Å / Origin z: 361.7432 Å
111213212223313233
T0.0732 Å20.0154 Å20.0071 Å2-0.0574 Å2-0.0026 Å2--0.0678 Å2
L0.4281 °20.0602 °20.1247 °2-0.1715 °2-0.025 °2--0.3091 °2
S0.0091 Å °0.0479 Å °0.0218 Å °-0.03 Å °-0.001 Å °0.0159 Å °-0.0138 Å °-0.0089 Å °-0.0105 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1allA2 - 597
2X-RAY DIFFRACTION1allB2 - 597
3X-RAY DIFFRACTION1allC1 - 2
4X-RAY DIFFRACTION1allS2 - 1255

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