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- PDB-6jz2: b-glucuronidase from Ruminococcus gnavus in complex with uronic i... -

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Basic information

Entry
Database: PDB / ID: 6jz2
Titleb-glucuronidase from Ruminococcus gnavus in complex with uronic isofagomine at 1.3 Angstroms resolution
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-SJ5 / Beta-glucuronidase
Similarity search - Component
Biological speciesRuminococcus gnavus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.29 Å
AuthorsDashnyam, P. / Lin, H.Y.
Funding support Taiwan, 1items
OrganizationGrant numberCountry
Ministry of Science and Technology (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)146,4519
Polymers145,5382
Non-polymers9137
Water20,0151111
1
A: Beta-glucuronidase
B: Beta-glucuronidase
hetero molecules

A: Beta-glucuronidase
B: Beta-glucuronidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)292,90218
Polymers291,0754
Non-polymers1,82614
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_556-x,y,-z+11
Buried area19050 Å2
ΔGint-115 kcal/mol
Surface area74270 Å2
MethodPISA
Unit cell
Length a, b, c (Å)163.236, 102.734, 112.714
Angle α, β, γ (deg.)90.000, 130.940, 90.000
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-1118-

HOH

21B-1107-

HOH

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Components

#1: Protein Beta-glucuronidase


Mass: 72768.805 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-SJ5 / (3S,4R,5R)-4,5-dihydroxypiperidine-3-carboxylic acid


Mass: 161.156 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H11NO4 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-MRD / (4R)-2-METHYLPENTANE-2,4-DIOL


Mass: 118.174 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C6H14O2 / Comment: precipitant*YM
#4: Chemical ChemComp-MPD / (4S)-2-METHYL-2,4-PENTANEDIOL


Mass: 118.174 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H14O2 / Comment: precipitant*YM
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1111 / 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: 2.55 Å3/Da / Density % sol: 51.73 %
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 16, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.286→30 Å / Num. obs: 66391 / % possible obs: 95.6 % / Redundancy: 5.1 % / Rmerge(I) obs: 0.045 / Rpim(I) all: 0.022 / Rrim(I) all: 0.05 / Χ2: 0.937 / Net I/σ(I): 13
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
1.29-1.344.90.621321630.7890.3090.6960.77691.1
1.34-1.394.90.451328280.8810.2220.5030.82492.7
1.39-1.454.90.329330260.9270.1610.3670.86893.6
1.45-1.5350.222334270.9660.1090.2480.91394.6
1.53-1.6350.15337720.9840.0730.1670.94695.6
1.63-1.755.10.101341670.9910.0490.1130.97396.4
1.75-1.935.20.066344280.9960.0320.0731.02897.3
1.93-2.215.20.046346430.9980.0220.0511.16697.8
2.21-2.785.20.034349280.9980.0160.0371.09998.3
2.78-305.20.024352160.9990.0120.0270.73898.4

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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: 1.29→27.094 Å / SU ML: 0.11 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 17.41
RfactorNum. reflection% reflection
Rfree0.1698 1998 6 %
Rwork0.156 --
obs0.1561 63072 93.47 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 137.54 Å2 / Biso mean: 20.4107 Å2 / Biso min: 8.12 Å2
Refinement stepCycle: final / Resolution: 1.29→27.094 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9714 0 62 1111 10887
Biso mean--26.39 32.06 -
Num. residues----1185
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00610060
X-RAY DIFFRACTIONf_angle_d1.1513645
X-RAY DIFFRACTIONf_chiral_restr0.0751406
X-RAY DIFFRACTIONf_plane_restr0.0061764
X-RAY DIFFRACTIONf_dihedral_angle_d13.2353669
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.29-1.3180.2772990.2491661666
1.318-1.35360.22021310.21832217488
1.3536-1.39350.19881490.20082316692
1.3935-1.43840.21241500.19022351493
1.4384-1.48980.19681390.18342372294
1.4898-1.54950.16991410.1682382795
1.5495-1.620.19451460.16292406096
1.62-1.70540.17341530.15992423596
1.7054-1.81220.17271410.15642446397
1.8122-1.95210.14811450.15482453097
1.9521-2.14850.15451530.14772467498
2.1485-2.45920.17991420.15262475898
2.4592-3.09760.18241550.15662468998
3.0976-27.0940.14971540.14032532299
Refinement TLS params.Method: refined / Origin x: -54.9105 Å / Origin y: -1.75 Å / Origin z: 24.0413 Å
111213212223313233
T0.1254 Å20.0121 Å20.0058 Å2-0.1091 Å2-0.0136 Å2--0.093 Å2
L0.3234 °20.0281 °20.0454 °2-0.2417 °2-0.0676 °2--0.2917 °2
S0.0052 Å °0.0628 Å °0.0059 Å °-0.054 Å °-0.0125 Å °0.0371 Å °0.0037 Å °-0.0371 Å °0.0043 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 DIFFRACTION1allD1 - 7
5X-RAY DIFFRACTION1allS1 - 1283

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