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- PDB-6dxu: Crystal Structure of Parabacteroides merdae Beta-Glucuronidase (GUS) -

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Basic information

Entry
Database: PDB / ID: 6dxu
TitleCrystal Structure of Parabacteroides merdae Beta-Glucuronidase (GUS)
ComponentsGlycosyl hydrolase family 2, TIM barrel domain protein
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 / 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 ...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 / 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-like domain superfamily / Glycoside hydrolase superfamily / Immunoglobulin-like fold
Similarity search - Domain/homology
Glycosyl hydrolase family 2, TIM barrel domain protein
Similarity search - Component
Biological speciesParabacteroides merdae ATCC 43184 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 1.9 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
CitationJournal: 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.
History
DepositionJun 30, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 27, 2019Provider: repository / Type: Initial release
Revision 1.1Dec 18, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.2Mar 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
D: Glycosyl hydrolase family 2, TIM barrel domain protein
A: Glycosyl hydrolase family 2, TIM barrel domain protein
B: Glycosyl hydrolase family 2, TIM barrel domain protein
C: Glycosyl hydrolase family 2, TIM barrel domain protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)380,17015
Polymers379,4974
Non-polymers67311
Water48,9472717
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: light scattering
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area12710 Å2
ΔGint-115 kcal/mol
Surface area111270 Å2
MethodPISA
Unit cell
Length a, b, c (Å)91.371, 163.393, 120.607
Angle α, β, γ (deg.)90.000, 103.351, 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
11ASNASNLYSLYS(chain 'A' and (resid 29 through 99 or (resid 100...AB29 - 31329 - 313
12LYSLYSLEULEU(chain 'A' and (resid 29 through 99 or (resid 100...AB315 - 532315 - 532
13ASPASPSERSER(chain 'A' and (resid 29 through 99 or (resid 100...AB560 - 828560 - 828
21ASNASNLYSLYS(chain 'B' and (resid 29 through 103 or (resid 104...BC29 - 31329 - 313
22LYSLYSLEULEU(chain 'B' and (resid 29 through 103 or (resid 104...BC315 - 532315 - 532
23ASPASPSERSER(chain 'B' and (resid 29 through 103 or (resid 104...BC560 - 828560 - 828
31ASNASNLYSLYS(chain 'C' and ((resid 29 and (name N or name...CD29 - 31329 - 313
32LYSLYSLEULEU(chain 'C' and ((resid 29 and (name N or name...CD315 - 532315 - 532
33ASPASPSERSER(chain 'C' and ((resid 29 and (name N or name...CD560 - 828560 - 828
41ASNASNLYSLYS(chain 'D' and ((resid 29 and (name N or name...DA29 - 31329 - 313
42LYSLYSLEULEU(chain 'D' and ((resid 29 and (name N or name...DA315 - 532315 - 532
43ASPASPSERSER(chain 'D' and ((resid 29 and (name N or name...DA560 - 828560 - 828

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Components

#1: Protein
Glycosyl hydrolase family 2, TIM barrel domain protein


Mass: 94874.227 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Parabacteroides merdae ATCC 43184 (bacteria)
Gene: PARMER_02407
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
References: UniProt: A7AG62
#2: Chemical ChemComp-BCN / BICINE


Mass: 163.172 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C6H13NO4 / Comment: pH buffer*YM
#3: Chemical
ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Na
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 2717 / 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: 2.4 Å3/Da / Density % sol: 48.84 %
Crystal growTemperature: 298.15 K / Method: vapor diffusion, hanging drop
Details: 8% PEG Monomethyl-ether 5000 0.1M Bicine pH 8.5 5mM Mannuronic Acid Pentamer

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-D / Wavelength: 0.97942 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Apr 12, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97942 Å / Relative weight: 1
ReflectionResolution: 1.9→29.63 Å / Num. obs: 269582 / % possible obs: 99.91 % / Redundancy: 6.7 % / Biso Wilson estimate: 24.32 Å2 / Net I/σ(I): 15.57
Reflection shellResolution: 1.9→29.63 Å

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Processing

Software
NameVersionClassification
PHENIX1.13_2998refinement
PHENIX1.13_2998refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementResolution: 1.9→29.63 Å / SU ML: 0.1669 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 18.6341
RfactorNum. reflection% reflection
Rfree0.1842 2000 -
Rwork0.1535 --
obs0.1537 269537 99.94 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 28.72 Å2
Refinement stepCycle: LAST / Resolution: 1.9→29.63 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms25295 0 41 2717 28053
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.007125977
X-RAY DIFFRACTIONf_angle_d0.908435248
X-RAY DIFFRACTIONf_chiral_restr0.05893737
X-RAY DIFFRACTIONf_plane_restr0.00614580
X-RAY DIFFRACTIONf_dihedral_angle_d13.775615336
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.9-1.950.23911420.20319049X-RAY DIFFRACTION99.97
1.95-20.24991420.190719009X-RAY DIFFRACTION99.96
2-2.060.20041440.176119099X-RAY DIFFRACTION99.97
2.06-2.130.19141420.1719119X-RAY DIFFRACTION99.99
2.13-2.20.21151430.167419025X-RAY DIFFRACTION99.95
2.2-2.290.20851420.170519115X-RAY DIFFRACTION99.98
2.29-2.390.23371430.167519063X-RAY DIFFRACTION99.97
2.39-2.520.18611430.165819105X-RAY DIFFRACTION99.98
2.52-2.680.21461430.166619152X-RAY DIFFRACTION100
2.68-2.880.18521430.165119083X-RAY DIFFRACTION99.92
2.88-3.170.19721430.156719138X-RAY DIFFRACTION99.92
3.17-3.630.16141420.13719128X-RAY DIFFRACTION99.91
3.63-4.570.16881430.122719127X-RAY DIFFRACTION99.77
4.57-29.640.14751450.147719325X-RAY DIFFRACTION99.89

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