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- PDB-9nwf: Structure of an inactive beta-D-glucuronate dehydratase mutant in... -

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Basic information

Entry
Database: PDB / ID: 9nwf
TitleStructure of an inactive beta-D-glucuronate dehydratase mutant in complex with chondrosine
ComponentsGlucuronate dehydratase
KeywordsLYASE / dehydratase / complex / chondrosine / chondroitin
Function / homologyUncharacterised conserved protein UCP014753 / : / Uncharacterized protein conserved in bacteria (DUF2264) / hydrolase activity / IODIDE ION / DUF2264 domain-containing protein
Function and homology information
Biological speciesBacteroides caccae (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.6 Å
AuthorsBoraston, A.B. / Alvarez, B. / Canil, O.
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
DepositionMar 22, 2025Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 4, 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Glucuronate dehydratase
B: Glucuronate dehydratase
C: Glucuronate dehydratase
D: Glucuronate dehydratase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)188,80535
Polymers183,9574
Non-polymers4,84831
Water7,422412
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area18230 Å2
ΔGint-31 kcal/mol
Surface area49190 Å2
MethodPISA
Unit cell
Length a, b, c (Å)99.543, 105.840, 179.944
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab

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Components

#1: Protein
Glucuronate dehydratase


Mass: 45989.293 Da / Num. of mol.: 4 / Mutation: R285A
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 (E. coli) / References: UniProt: A0A174GN40
#2: Polysaccharide
beta-D-glucopyranuronic acid-(1-3)-2-amino-2-deoxy-beta-D-galactopyranose


Type: oligosaccharide / Mass: 355.295 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGlcpAb1-3DGalpNb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/2,2,1/[a2112h-1b_1-5_2*N][a2122A-1b_1-5]/1-2/a3-b1WURCSPDB2Glycan 1.1.0
[][b-D-GalpN]{[(3+1)][b-D-GlcpA]{}}LINUCSPDB-CARE
#3: Chemical...
ChemComp-IOD / IODIDE ION


Mass: 126.904 Da / Num. of mol.: 27 / Source method: obtained synthetically / Formula: I
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 412 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
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: 2.56 Å3/Da / Density % sol: 51.96 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop
Details: 0.25M sodium iodide, 5-13% glycerol, and 8-13% PEG 3350

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Data collection

DiffractionMean temperature: 100 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: Jan 29, 2025 / Details: VariMaxTM-HF ArcSec
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.6→20 Å / Num. obs: 58307 / % possible obs: 98.7 % / Redundancy: 4 % / CC1/2: 0.995 / Rpim(I) all: 0.092 / Rrim(I) all: 0.191 / Net I/σ(I): 7.5
Reflection shellResolution: 2.6→2.65 Å / Redundancy: 3.9 % / Mean I/σ(I) obs: 1.3 / Num. unique obs: 2858 / CC1/2: 0.844 / Rpim(I) all: 0.5 / Rrim(I) all: 0.994 / % possible all: 98.9

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Processing

Software
NameVersionClassification
PHENIX1.21.2_5419refinement
HKL-2000data scaling
HKL-2000data reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.6→19.96 Å / SU ML: 0.3754 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 28.8321
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2615 2731 5.06 %
Rwork0.1912 51220 -
obs0.1948 53951 91.38 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 46.78 Å2
Refinement stepCycle: LAST / Resolution: 2.6→19.96 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms12322 0 123 412 12857
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.008112819
X-RAY DIFFRACTIONf_angle_d0.962217409
X-RAY DIFFRACTIONf_chiral_restr0.05061857
X-RAY DIFFRACTIONf_plane_restr0.00832222
X-RAY DIFFRACTIONf_dihedral_angle_d16.00294791
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.6-2.640.3491210.26162200X-RAY DIFFRACTION79.9
2.64-2.690.37031100.25312372X-RAY DIFFRACTION85.35
2.69-2.740.41961400.2542404X-RAY DIFFRACTION87.66
2.74-2.80.34391210.242484X-RAY DIFFRACTION89.86
2.8-2.860.35841250.25092607X-RAY DIFFRACTION92.55
2.86-2.930.33391510.23812590X-RAY DIFFRACTION94.06
2.93-30.35631380.23442605X-RAY DIFFRACTION94.16
3-3.080.30651270.23812626X-RAY DIFFRACTION94.18
3.08-3.170.30481220.21932638X-RAY DIFFRACTION93.97
3.17-3.270.29341430.22872578X-RAY DIFFRACTION93.6
3.27-3.390.3191490.21272636X-RAY DIFFRACTION94.15
3.39-3.520.24921510.18762593X-RAY DIFFRACTION93.65
3.52-3.680.2511210.17972658X-RAY DIFFRACTION94.17
3.68-3.880.22871530.17682599X-RAY DIFFRACTION93.7
3.88-4.120.23411520.16922608X-RAY DIFFRACTION92.84
4.12-4.430.25041300.15532613X-RAY DIFFRACTION92.67
4.43-4.870.18941390.14662617X-RAY DIFFRACTION92.27
4.87-5.560.21241570.16862592X-RAY DIFFRACTION91.48
5.56-6.960.25881510.19332584X-RAY DIFFRACTION90.56
6.96-19.960.22521300.17442616X-RAY DIFFRACTION87.12

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