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- PDB-7wr2: Cryatal structure of OspC3 C-terminal ankyrin-repeat domain -

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Basic information

Entry
Database: PDB / ID: 7wr2
TitleCryatal structure of OspC3 C-terminal ankyrin-repeat domain
ComponentsOspC3
KeywordsTRANSFERASE / ADP-riboxanase / effector / ankyrin-repeat domain
Function / homology
Function and homology information


symbiont-mediated suppression of host signal transduction pathway / symbiont-mediated suppression of host calcium-mediated signal transduction / Lyases; Carbon-nitrogen lyases; Other carbon-nitrogen lyases / ADP-riboxanase activity / symbiont-mediated suppression of host programmed cell death / symbiont-mediated perturbation of host programmed cell death / toxin activity / host cell cytoplasm / calmodulin binding / extracellular region
Similarity search - Function
Arginine ADP-riboxanase OspC1-3 / Shigella flexneri OspC protein
Similarity search - Domain/homology
Arginine ADP-riboxanase OspC3
Similarity search - Component
Biological speciesShigella flexneri (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.54 Å
AuthorsHou, Y.J. / Zeng, H. / Shao, F. / Ding, J.
Funding support China, 1items
OrganizationGrant numberCountry
Chinese Academy of Sciences China
CitationJournal: Nat.Struct.Mol.Biol. / Year: 2023
Title: Structural mechanisms of calmodulin activation of Shigella effector OspC3 to ADP-riboxanate caspase-4/11 and block pyroptosis.
Authors: Hou, Y. / Zeng, H. / Li, Z. / Feng, N. / Meng, F. / Xu, Y. / Li, L. / Shao, F. / Ding, J.
History
DepositionJan 26, 2022Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jan 25, 2023Provider: repository / Type: Initial release
Revision 1.1Feb 1, 2023Group: Database references / Category: citation / Item: _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2Mar 29, 2023Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID
Revision 1.3Nov 29, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: OspC3


Theoretical massNumber of molelcules
Total (without water)18,3661
Polymers18,3661
Non-polymers00
Water3,171176
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area7120 Å2
Unit cell
Length a, b, c (Å)39.215, 53.943, 59.932
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 OspC3


Mass: 18366.213 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Shigella flexneri (bacteria) / Gene: ospC3 / Plasmid: pGEX-6p-2 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: R4X5L7
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 176 / 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: 1.73 Å3/Da / Density % sol: 28.72 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 20% PEG monomethyl ether 550, 0.1 M Bis-Tris propane pH 9.0

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Data collection

DiffractionMean temperature: 93 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.97892 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: May 31, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97892 Å / Relative weight: 1
ReflectionResolution: 1.54→40.1 Å / Num. obs: 19087 / % possible obs: 98.6 % / Redundancy: 6.02 % / Biso Wilson estimate: 17.32 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.045 / Rrim(I) all: 0.049 / Net I/σ(I): 22.58
Reflection shellResolution: 1.54→1.58 Å / Rmerge(I) obs: 0.158 / Mean I/σ(I) obs: 7.87 / Num. unique obs: 1304 / CC1/2: 0.977 / Rrim(I) all: 0.176 / % possible all: 92.6

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Processing

Software
NameVersionClassification
PHENIX1.18.2_3874refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 7WR1

7wr1


Resolution: 1.54→40.09 Å / SU ML: 0.1318 / Cross valid method: FREE R-VALUE / σ(F): 1.4 / Phase error: 18.0133
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1903 1905 10 %
Rwork0.1683 17142 -
obs0.1705 19047 98.67 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 21.83 Å2
Refinement stepCycle: LAST / Resolution: 1.54→40.09 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1088 0 0 176 1264
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00611107
X-RAY DIFFRACTIONf_angle_d0.83711481
X-RAY DIFFRACTIONf_chiral_restr0.0469163
X-RAY DIFFRACTIONf_plane_restr0.0039189
X-RAY DIFFRACTIONf_dihedral_angle_d16.1985428
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.54-1.580.22821250.17891124X-RAY DIFFRACTION92.45
1.58-1.620.22481340.17131208X-RAY DIFFRACTION98.97
1.62-1.670.18511320.181193X-RAY DIFFRACTION98.88
1.67-1.730.2281350.1751208X-RAY DIFFRACTION99.04
1.73-1.790.22871360.18511223X-RAY DIFFRACTION99.2
1.79-1.860.19971340.17541209X-RAY DIFFRACTION98.9
1.86-1.940.23761350.17961222X-RAY DIFFRACTION99.49
1.94-2.050.21141360.16731217X-RAY DIFFRACTION99.49
2.05-2.170.20281360.16341228X-RAY DIFFRACTION99.13
2.18-2.340.19181370.16281222X-RAY DIFFRACTION98.91
2.34-2.580.18111370.17341244X-RAY DIFFRACTION99.57
2.58-2.950.21681380.17181239X-RAY DIFFRACTION98.85
2.95-3.720.16081410.16571263X-RAY DIFFRACTION99.29
3.72-40.090.16671490.16091342X-RAY DIFFRACTION99.14

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