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- PDB-6d7j: The Crystal Structure of Parabacteroides merdae Beta-Glucuronidas... -

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Basic information

Entry
Database: PDB / ID: 6d7j
TitleThe Crystal Structure of Parabacteroides merdae Beta-Glucuronidase (GUS) with Glycerol in Active-Site
ComponentsBeta-Glucuronidase
KeywordsHYDROLASE / bacterial enzyme / glycoside hydrolase family 2 / GUS / Beta-Glucuronidase / carbohydrate binding protein
Function / homology
Function and homology information


hydrolase activity, hydrolyzing O-glycosyl compounds / carbohydrate metabolic process
Similarity search - Function
Glycoside hydrolase family 2, domain 5 / Glycoside hydrolase family 2 C-terminal domain 5 / Domain of unknown function DUF4982 / Domain of unknown function (DUF4982) / 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 ...Glycoside hydrolase family 2, domain 5 / Glycoside hydrolase family 2 C-terminal domain 5 / Domain of unknown function DUF4982 / Domain of unknown function (DUF4982) / 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
: / PROLINE / Uncharacterized protein
Similarity search - Component
Biological speciesParabacteroides merdae CL03T12C32 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.24 Å
AuthorsLittle, M.S. / Redinbo, M.R.
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Human Genome Research Institute (NIH/NHGRI)CA098468 United States
National Institutes of Health/National Human Genome Research Institute (NIH/NHGRI)CA207416 United States
Citation
Journal: Protein Sci. / Year: 2018
Title: Active site flexibility revealed in crystal structures of Parabacteroides merdae beta-glucuronidase from the human gut microbiome.
Authors: Little, M.S. / Ervin, S.M. / Walton, W.G. / Tripathy, A. / Xu, Y. / Liu, J. / Redinbo, M.R.
#1: Journal: J.Biol.Chem. / Year: 2019
Title: Gut microbial beta-glucuronidases reactivate estrogens as components of the estrobolome that reactivate estrogens.
Authors: Ervin, S.M. / Li, H. / Lim, L. / Roberts, L.R. / Liang, X. / Mani, S. / Redinbo, M.R.
History
DepositionApr 24, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 1, 2019Provider: repository / Type: Initial release
Revision 1.1Dec 18, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.2May 13, 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 1.3May 20, 2020Group: Database references / Category: citation / citation_author
Revision 1.4Mar 13, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / struct_conn / struct_ncs_dom_lim
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_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_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_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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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
C: Beta-Glucuronidase
D: Beta-Glucuronidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)384,85767
Polymers379,4974
Non-polymers5,36063
Water33,5801864
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: light scattering
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area25260 Å2
ΔGint-81 kcal/mol
Surface area107680 Å2
2
A: Beta-Glucuronidase
B: Beta-Glucuronidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)192,56635
Polymers189,7482
Non-polymers2,81833
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10910 Å2
ΔGint-45 kcal/mol
Surface area56250 Å2
MethodPISA
3
C: Beta-Glucuronidase
D: Beta-Glucuronidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)192,29032
Polymers189,7482
Non-polymers2,54230
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10880 Å2
ΔGint-38 kcal/mol
Surface area54920 Å2
MethodPISA
Unit cell
Length a, b, c (Å)92.920, 171.968, 125.322
Angle α, β, γ (deg.)90.000, 107.840, 90.000
Int Tables number4
Space group name H-MP1211
Space group name HallP2yb
Symmetry operation#1: x,y,z
#2: -x,y+1/2,-z
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-ID
11
21
31
41

NCS domain segments:

Ens-ID: 1

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11ASNASNHISHIS(chain 'A' and ((resid 22 through 24 and (name N...AA22 - 41622 - 416
12ASNASNLEULEU(chain 'A' and ((resid 22 through 24 and (name N...AA418 - 532418 - 532
13PROPROSERSER(chain 'A' and ((resid 22 through 24 and (name N...AA555 - 828555 - 828
24ASNASNHISHIS(chain 'B' and ((resid 22 through 24 and (name N...BB22 - 41622 - 416
25ASNASNLEULEU(chain 'B' and ((resid 22 through 24 and (name N...BB418 - 532418 - 532
26PROPROSERSER(chain 'B' and ((resid 22 through 24 and (name N...BB555 - 828555 - 828
37ASNASNHISHIS(chain 'C' and ((resid 22 through 24 and (name N...CC22 - 41622 - 416
38ASNASNLEULEU(chain 'C' and ((resid 22 through 24 and (name N...CC418 - 532418 - 532
39PROPROSERSER(chain 'C' and ((resid 22 through 24 and (name N...CC555 - 828555 - 828
410ASNASNHISHIS(chain 'D' and ((resid 22 through 24 and (name N...DD22 - 41622 - 416
411ASNASNLEULEU(chain 'D' and ((resid 22 through 24 and (name N...DD418 - 532418 - 532
412PROPROSERSER(chain 'D' and ((resid 22 through 24 and (name N...DD555 - 828555 - 828

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Components

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Protein , 1 types, 4 molecules ABCD

#1: Protein
Beta-Glucuronidase / GUS


Mass: 94874.227 Da / Num. of mol.: 4 / Fragment: residues 19-826
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Parabacteroides merdae CL03T12C32 (bacteria)
Gene: HMPREF1060_00403
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
References: UniProt: K5ZWV5

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Non-polymers , 5 types, 1927 molecules

#2: Chemical
ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: K
#3: Chemical...
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 53 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical ChemComp-PRO / PROLINE


Type: L-peptide linking / Mass: 115.130 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C5H9NO2
#5: Chemical
ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Na
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1864 / 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: 2.63 Å3/Da / Density % sol: 53.2 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, hanging drop / Details: 10% PEG 3350 0.2 M Proline 0.1 M HEPES pH 7.4

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-B / Wavelength: 0.97942 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Oct 15, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97942 Å / Relative weight: 1
ReflectionResolution: 2.24→48.34 Å / Num. obs: 335371 / % possible obs: 96.18 % / Redundancy: 6.6 % / Biso Wilson estimate: 25.71 Å2 / Net I/σ(I): 9.64
Reflection shellResolution: 2.244→2.325 Å

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Processing

Software
NameVersionClassification
PHENIX1.13_2998phasing
PHENIX1.13_2998refinement
HKL-2000data scaling
PHENIXmodel building
HKL-2000data reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.24→48.34 Å / SU ML: 0.2158 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 19.6781
RfactorNum. reflection% reflection
Rfree0.2002 3875 1.16 %
Rwork0.1649 --
obs0.1653 335371 94.96 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 30.54 Å2
Refinement stepCycle: LAST / Resolution: 2.24→48.34 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms25187 0 342 1864 27393
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.007226123
X-RAY DIFFRACTIONf_angle_d0.888835384
X-RAY DIFFRACTIONf_chiral_restr0.05493735
X-RAY DIFFRACTIONf_plane_restr0.00654572
X-RAY DIFFRACTIONf_dihedral_angle_d10.900815378
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.24-2.270.27331310.23539525X-RAY DIFFRACTION76.17
2.27-2.30.26091270.219211265X-RAY DIFFRACTION90.52
2.3-2.330.21641300.208411416X-RAY DIFFRACTION91.37
2.33-2.360.25261290.204311332X-RAY DIFFRACTION91.28
2.36-2.40.24911420.212311472X-RAY DIFFRACTION91.69
2.4-2.430.29651350.21211421X-RAY DIFFRACTION91.93
2.43-2.470.27351140.200611449X-RAY DIFFRACTION91.7
2.47-2.510.23451450.192311504X-RAY DIFFRACTION91.85
2.51-2.550.20221580.189811486X-RAY DIFFRACTION93.02
2.55-2.60.19741190.186311740X-RAY DIFFRACTION93.73
2.6-2.650.21561350.184511736X-RAY DIFFRACTION94.14
2.65-2.70.22741280.185611777X-RAY DIFFRACTION94.69
2.7-2.760.25231430.180411898X-RAY DIFFRACTION95.23
2.76-2.830.21671340.174511946X-RAY DIFFRACTION96.16
2.83-2.90.23011380.171712052X-RAY DIFFRACTION96.16
2.9-2.980.19131500.171612077X-RAY DIFFRACTION96.8
2.98-3.060.22241310.166312109X-RAY DIFFRACTION97.07
3.06-3.160.18091440.156912118X-RAY DIFFRACTION97.63
3.16-3.280.17581330.15212205X-RAY DIFFRACTION97.57
3.28-3.410.16821450.141812139X-RAY DIFFRACTION97.94
3.41-3.560.17661340.143512274X-RAY DIFFRACTION97.71
3.56-3.750.17181530.142912226X-RAY DIFFRACTION98.5
3.75-3.980.16011440.136212238X-RAY DIFFRACTION98.01
3.98-4.290.15981510.138712322X-RAY DIFFRACTION99.17
4.29-4.720.16351370.138712412X-RAY DIFFRACTION99.6
4.72-5.410.20271410.154312503X-RAY DIFFRACTION99.89
5.41-6.810.25221500.177812461X-RAY DIFFRACTION99.99
6.81-48.350.19441540.171412393X-RAY DIFFRACTION99.49

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