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- PDB-9o3q: Apo-structure of a chondroitinase -

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Basic information

Entry
Database: PDB / ID: 9o3q
TitleApo-structure of a chondroitinase
ComponentsPL35 chondroitinase
KeywordsLYASE / Chondroitinase / Polysaccharide Lyase 35
Function / homologyHeparinase II/III-like / Heparinase II/III-like, C-terminal / Chondroitin AC/alginate lyase / cell envelope / lyase activity / Heparinase II/III-like C-terminal domain-containing protein
Function and homology information
Biological speciesBacteroides caccae (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.75 Å
AuthorsAlvarez, B. / Boraston, A.B.
Funding support Canada, 1items
OrganizationGrant numberCountry
Natural Sciences and Engineering Research Council (NSERC, Canada)FRN 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 7, 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: PL35 chondroitinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)67,5693
Polymers67,5201
Non-polymers492
Water12,196677
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)69.284, 84.043, 112.870
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x,y+1/2,-z+1/2
#4: -x+1/2,-y,z+1/2

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Components

#1: Protein PL35 chondroitinase


Mass: 67520.492 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacteroides caccae (bacteria) / Strain: ATCC 43185 / Gene: DXA49_19620, F2Y36_02745 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A413IVG5
#2: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 677 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
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: 2.43 Å3/Da / Density % sol: 49.45 %
Crystal growTemperature: 291.15 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 100 mM MES:NaOH pH 6.5, 300 mM MgCl2, and 12.5% PEG 4000

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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: Jun 27, 2024
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.75→30 Å / Num. obs: 2203325 / % possible obs: 99.8 % / Redundancy: 4.9 % / Biso Wilson estimate: 20.2 Å2 / CC1/2: 0.998 / Rpim(I) all: 0.031 / Rrim(I) all: 0.083 / Net I/σ(I): 20.6
Reflection shellResolution: 1.75→1.78 Å / Redundancy: 3 % / Mean I/σ(I) obs: 1.8 / Num. unique obs: 67228 / CC1/2: 0.924 / Rpim(I) all: 0.357 / Rrim(I) all: 0.649 / % possible all: 99.5

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Processing

Software
NameVersionClassification
REFMAC5.0.32refinement
PHENIX1.19.2_4158refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.75→29.52 Å / SU ML: 0.2072 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 21.9729
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2177 3330 5 %
Rwork0.1854 63240 -
obs0.187 66570 99.14 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 21.86 Å2
Refinement stepCycle: LAST / Resolution: 1.75→29.52 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4632 0 2 677 5311
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00754751
X-RAY DIFFRACTIONf_angle_d0.98196451
X-RAY DIFFRACTIONf_chiral_restr0.0571689
X-RAY DIFFRACTIONf_plane_restr0.0082833
X-RAY DIFFRACTIONf_dihedral_angle_d6.1512638
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.75-1.770.30891140.2772441X-RAY DIFFRACTION92.44
1.77-1.80.29021400.26782523X-RAY DIFFRACTION96.45
1.8-1.830.31931450.26842606X-RAY DIFFRACTION98.36
1.83-1.860.2621170.2622601X-RAY DIFFRACTION99.12
1.86-1.890.27141580.24042577X-RAY DIFFRACTION99.42
1.89-1.930.25411350.2172609X-RAY DIFFRACTION99.46
1.93-1.960.26091440.20862610X-RAY DIFFRACTION99.57
1.96-20.25221420.20612631X-RAY DIFFRACTION99.68
2-2.050.24571430.19612618X-RAY DIFFRACTION99.64
2.05-2.090.25711360.2012637X-RAY DIFFRACTION99.64
2.09-2.150.26011190.19782626X-RAY DIFFRACTION99.49
2.15-2.20.22831360.1932617X-RAY DIFFRACTION99.57
2.2-2.270.24681480.18982640X-RAY DIFFRACTION99.71
2.27-2.340.23891200.19282653X-RAY DIFFRACTION99.96
2.34-2.430.2641260.19972632X-RAY DIFFRACTION99.78
2.43-2.520.22311460.18632658X-RAY DIFFRACTION99.61
2.52-2.640.22561290.19192670X-RAY DIFFRACTION99.71
2.64-2.780.2421330.19832639X-RAY DIFFRACTION99.39
2.78-2.950.22891440.19442655X-RAY DIFFRACTION99.57
2.95-3.180.22471560.18682641X-RAY DIFFRACTION99.54
3.18-3.50.18921590.17012687X-RAY DIFFRACTION99.86
3.5-40.1781400.14732690X-RAY DIFFRACTION99.82
4-5.040.15041450.14222716X-RAY DIFFRACTION99.58
5.04-29.520.19641550.17562863X-RAY DIFFRACTION99.93

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