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- PDB-7wr0: P32 of caspase-4 C258A mutant -

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Basic information

Entry
Database: PDB / ID: 7wr0
TitleP32 of caspase-4 C258A mutant
ComponentsCaspase-4
KeywordsHYDROLASE / protease / mutant
Function / homology
Function and homology information


caspase-4 / non-canonical inflammasome complex / positive regulation of interleukin-18-mediated signaling pathway / non-canonical inflammasome complex assembly / NLRP1 inflammasome complex / CARD domain binding / positive regulation of tumor necrosis factor-mediated signaling pathway / pyroptotic inflammatory response / protein autoprocessing / intrinsic apoptotic signaling pathway in response to endoplasmic reticulum stress ...caspase-4 / non-canonical inflammasome complex / positive regulation of interleukin-18-mediated signaling pathway / non-canonical inflammasome complex assembly / NLRP1 inflammasome complex / CARD domain binding / positive regulation of tumor necrosis factor-mediated signaling pathway / pyroptotic inflammatory response / protein autoprocessing / intrinsic apoptotic signaling pathway in response to endoplasmic reticulum stress / Pyroptosis / intrinsic apoptotic signaling pathway / protein maturation / lipopolysaccharide binding / NOD1/2 Signaling Pathway / cellular response to amyloid-beta / positive regulation of inflammatory response / positive regulation of neuron apoptotic process / regulation of inflammatory response / defense response to Gram-positive bacterium / defense response to bacterium / innate immune response / cysteine-type endopeptidase activity / apoptotic process / lipid binding / endoplasmic reticulum membrane / endoplasmic reticulum / protein-containing complex / mitochondrion / proteolysis / extracellular region / plasma membrane / cytoplasm / cytosol
Similarity search - Function
Caspase recruitment domain / CARD domain / CARD caspase recruitment domain profile. / Caspase recruitment domain / Peptidase C14 family / Peptidase family C14A, His active site / Caspase family histidine active site. / Peptidase C14, caspase non-catalytic subunit p10 / Peptidase family C14A, cysteine active site / Caspase family cysteine active site. ...Caspase recruitment domain / CARD domain / CARD caspase recruitment domain profile. / Caspase recruitment domain / Peptidase C14 family / Peptidase family C14A, His active site / Caspase family histidine active site. / Peptidase C14, caspase non-catalytic subunit p10 / Peptidase family C14A, cysteine active site / Caspase family cysteine active site. / Caspase family p10 domain profile. / Peptidase C14A, caspase catalytic domain / Caspase, interleukin-1 beta converting enzyme (ICE) homologues / Peptidase C14, p20 domain / Caspase family p20 domain profile. / : / Caspase domain / Caspase-like domain superfamily / Death-like domain superfamily
Similarity search - Domain/homology
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.8 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: Caspase-4


Theoretical massNumber of molelcules
Total (without water)32,0951
Polymers32,0951
Non-polymers00
Water00
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 area11400 Å2
Unit cell
Length a, b, c (Å)77.571, 77.571, 85.820
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number154
Space group name H-MP3221
Space group name HallP322"
Symmetry operation#1: x,y,z
#2: -y,x-y,z+2/3
#3: -x+y,-x,z+1/3
#4: x-y,-y,-z+1/3
#5: -x,-x+y,-z+2/3
#6: y,x,-z

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Components

#1: Protein Caspase-4 / CASP-4


Mass: 32095.428 Da / Num. of mol.: 1 / Mutation: C258A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CASP4 / Plasmid: pET28a-SUMO / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P49662, caspase-4

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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: 2.3 Å3/Da / Density % sol: 46.5 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: 20% PEG3350, 0.2 M potassium chloride

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Data collection

DiffractionMean temperature: 93 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.97853 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Feb 26, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97853 Å / Relative weight: 1
ReflectionResolution: 2.8→42.91 Å / Num. obs: 7706 / % possible obs: 99.5 % / Redundancy: 18.72 % / Biso Wilson estimate: 73.15 Å2 / CC1/2: 1 / Rmerge(I) obs: 0.071 / Rrim(I) all: 0.073 / Net I/σ(I): 35.98
Reflection shellResolution: 2.8→2.87 Å / Rmerge(I) obs: 0.898 / Mean I/σ(I) obs: 3.66 / Num. unique obs: 551 / CC1/2: 0.882 / Rrim(I) all: 0.923

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Processing

Software
NameVersionClassification
PHENIX1.17.1_3660refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6KMT

6kmt


Resolution: 2.8→36.16 Å / SU ML: 0.4717 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 28.7611
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2659 765 9.94 %
Rwork0.2383 6932 -
obs0.2411 7697 99.74 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 70.66 Å2
Refinement stepCycle: LAST / Resolution: 2.8→36.16 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1921 0 0 0 1921
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00241962
X-RAY DIFFRACTIONf_angle_d0.46362649
X-RAY DIFFRACTIONf_chiral_restr0.0407294
X-RAY DIFFRACTIONf_plane_restr0.0032342
X-RAY DIFFRACTIONf_dihedral_angle_d22.1443740
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.8-3.010.41461480.33531353X-RAY DIFFRACTION99.21
3.01-3.310.33081520.31441363X-RAY DIFFRACTION99.93
3.32-3.790.28721500.2691361X-RAY DIFFRACTION99.87
3.8-4.770.25851530.22741402X-RAY DIFFRACTION100
4.78-36.160.22221620.19721453X-RAY DIFFRACTION99.69

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