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- PDB-9o4u: Apo-structure of a beta-D-glucuronate dehydratase -

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Basic information

Entry
Database: PDB / ID: 9o4u
TitleApo-structure of a beta-D-glucuronate dehydratase
ComponentsBeta-D-glucuronic acid dehydratase
KeywordsLYASE / Beta-D-glucuronate dehydratase
Function / homologyUncharacterised conserved protein UCP014753 / : / Uncharacterized protein conserved in bacteria (DUF2264) / hydrolase activity / DUF2264 domain-containing protein
Function and homology information
Biological speciesBacteroides caccae (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.19 Å
AuthorsAlvarez, B. / Hettle, A. / Boraston, A.B.
Funding support Canada, 1items
OrganizationGrant numberCountry
Natural Sciences and Engineering Research Council (NSERC, Canada)04355 Canada
CitationJournal: J.Biol.Chem. / Year: 2025
Title: Analysis of chondroitin degradation by components of a Bacteroides caccae polysaccharide utilization locus.
Authors: Alvarez, B. / Canil, O.F. / Low, K.E. / Hettle, A.G. / Abbott, D.W. / Boraston, A.B.
History
DepositionApr 8, 2025Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 11, 2025Provider: repository / Type: Initial release
Revision 1.1Jun 25, 2025Group: 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.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Jul 9, 2025Group: Database references / Category: citation / Item: _citation.journal_volume

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Beta-D-glucuronic acid dehydratase
B: Beta-D-glucuronic acid dehydratase
C: Beta-D-glucuronic acid dehydratase
D: Beta-D-glucuronic acid dehydratase


Theoretical massNumber of molelcules
Total (without water)182,3634
Polymers182,3634
Non-polymers00
Water18,1231006
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area11880 Å2
ΔGint-60 kcal/mol
Surface area47850 Å2
MethodPISA
Unit cell
Length a, b, c (Å)53.525, 161.369, 88.610
Angle α, β, γ (deg.)90.000, 95.699, 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

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Components

#1: Protein
Beta-D-glucuronic acid dehydratase


Mass: 45590.852 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacteroides caccae (bacteria) / Strain: ATCC 43185
Gene: DW190_12820, DW794_00720, DXA49_19590, ERS852494_00337, F2Y31_01635, F2Y35_19060, F2Y36_02775, F2Y39_01210, NXW23_04330
Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A174GN40
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1006 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationN

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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: 2.09 Å3/Da / Density % sol: 41.09 %
Crystal growTemperature: 291.15 K / Method: vapor diffusion, hanging drop / pH: 8 / Details: 220 mM KCl, 24% PEG 3350

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Data collection

DiffractionMean temperature: 291.15 K / Serial crystal experiment: N
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.5418 Å
DetectorType: DECTRIS PILATUS 200K / Detector: PIXEL / Date: Mar 5, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.19→20 Å / Num. obs: 76109 / % possible obs: 94.1 % / Redundancy: 2.7 % / Biso Wilson estimate: 31.11 Å2 / CC1/2: 0.968 / Rpim(I) all: 0.046 / Rrim(I) all: 0.083 / Net I/σ(I): 13.2
Reflection shellResolution: 2.2→2.24 Å / Redundancy: 2 % / Mean I/σ(I) obs: 3 / Num. unique obs: 76109 / CC1/2: 0.997 / Rpim(I) all: 0.199 / Rrim(I) all: 0.325 / % possible all: 80.7

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Processing

Software
NameVersionClassification
REFMAC9.0.005refinement
PHENIX1.21.2_5419refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.19→19.84 Å / SU ML: 0.2576 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 24.2601
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2163 3597 5.11 %
Rwork0.1632 66772 -
obs0.166 70369 91.9 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 32.07 Å2
Refinement stepCycle: LAST / Resolution: 2.19→19.84 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms12270 0 0 1006 13276
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.006212614
X-RAY DIFFRACTIONf_angle_d0.806617135
X-RAY DIFFRACTIONf_chiral_restr0.04731807
X-RAY DIFFRACTIONf_plane_restr0.0072202
X-RAY DIFFRACTIONf_dihedral_angle_d14.5184556
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.19-2.220.2761930.18711807X-RAY DIFFRACTION64.02
2.22-2.250.2951220.18952349X-RAY DIFFRACTION84.19
2.25-2.280.29071270.17542375X-RAY DIFFRACTION85.63
2.28-2.320.29531220.17872435X-RAY DIFFRACTION87.15
2.32-2.350.25851350.16552474X-RAY DIFFRACTION88.8
2.35-2.390.23241390.16862491X-RAY DIFFRACTION89.49
2.39-2.430.26491160.17932535X-RAY DIFFRACTION89.89
2.43-2.480.25311470.1782499X-RAY DIFFRACTION91.43
2.48-2.520.25011380.17512573X-RAY DIFFRACTION91.43
2.52-2.570.25441510.18912577X-RAY DIFFRACTION92.73
2.57-2.630.30311310.19862582X-RAY DIFFRACTION93.39
2.63-2.690.27591570.19632642X-RAY DIFFRACTION93.71
2.69-2.760.28011420.19272584X-RAY DIFFRACTION93.74
2.76-2.830.28271380.18992664X-RAY DIFFRACTION94.31
2.83-2.920.24481540.19092576X-RAY DIFFRACTION93.88
2.92-3.010.26851470.19522637X-RAY DIFFRACTION94.57
3.01-3.120.26111290.19732672X-RAY DIFFRACTION94.76
3.12-3.240.26061370.19492689X-RAY DIFFRACTION96.35
3.24-3.390.24831610.18542712X-RAY DIFFRACTION97.32
3.39-3.570.21981380.1642732X-RAY DIFFRACTION96.67
3.57-3.790.20181230.15082727X-RAY DIFFRACTION97.07
3.79-4.080.181370.14392661X-RAY DIFFRACTION95.3
4.08-4.480.15231610.12652682X-RAY DIFFRACTION95.56
4.48-5.120.15941520.12292676X-RAY DIFFRACTION96.35
5.12-6.420.17891390.14582703X-RAY DIFFRACTION96.01
6.42-19.840.13871610.13372718X-RAY DIFFRACTION95.74

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