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- PDB-9frr: Caspase recruitment domain (CARD) -

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Basic information

Entry
Database: PDB / ID: 9frr
TitleCaspase recruitment domain (CARD)
ComponentsProbable serine protease FE772_23065
KeywordsIMMUNE SYSTEM / Caspase recruitment domain (CARD)
Function / homology
Function and homology information


Hydrolases; Acting on peptide bonds (peptidases); Serine endopeptidases / serine-type peptidase activity / defense response to virus / proteolysis / plasma membrane
Similarity search - Function
Trypsin-like peptidase domain / Peptidase S1, PA clan, chymotrypsin-like fold / Peptidase S1, PA clan / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
Probable serine protease FE772_23065
Similarity search - Component
Biological speciesLysobacter enzymogenes (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.6 Å
AuthorsDym, O. / Amitai, G. / Wein, T. / Sorek, R.
Funding supportEuropean Union, 1items
OrganizationGrant numberCountry
European Research Council (ERC)ERC-AdG GA 101018520European Union
CitationJournal: Nature / Year: 2025
Title: CARD domains mediate anti-phage defence in bacterial gasdermin systems.
Authors: Wein, T. / Millman, A. / Lange, K. / Yirmiya, E. / Hadary, R. / Garb, J. / Melamed, S. / Amitai, G. / Dym, O. / Steinruecke, F. / Hill, A.B. / Kranzusch, P.J. / Sorek, R.
History
DepositionJun 19, 2024Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 29, 2025Provider: repository / Type: Initial release
Revision 1.1Feb 12, 2025Group: Database references / Category: citation / citation_author
Item: _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID
Revision 1.2Mar 26, 2025Group: 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Probable serine protease FE772_23065
B: Probable serine protease FE772_23065


Theoretical massNumber of molelcules
Total (without water)21,2142
Polymers21,2142
Non-polymers00
Water3,027168
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1300 Å2
ΔGint2 kcal/mol
Surface area9320 Å2
Unit cell
Length a, b, c (Å)58.414, 58.414, 122.111
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number170
Space group name H-MP65

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Components

#1: Protein Probable serine protease FE772_23065 / Trypsin-like protease 2


Mass: 10606.770 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Lysobacter enzymogenes (bacteria) / Gene: FE772_23065, Ga0399710_4915, GLE_4745 / Production host: Escherichia coli (E. coli)
References: UniProt: A0A0S2DN74, Hydrolases; Acting on peptide bonds (peptidases); Serine endopeptidases
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 168 / 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: 2.93 Å3/Da / Density % sol: 58 %
Crystal growTemperature: 292 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 0.9M Sodium citrate trihydrate 0.05M BIS-TRIS propane pH=7

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.34 Å
DetectorType: RIGAKU HyPix-Arc 150 / Detector: PIXEL / Date: May 15, 2024
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.34 Å / Relative weight: 1
ReflectionResolution: 1.6→17.569 Å / Num. obs: 31052 / % possible obs: 99.88 % / Redundancy: 17.1 % / Biso Wilson estimate: 14.87 Å2 / CC1/2: 1 / CC star: 1 / Rmerge(I) obs: 0.0606 / Rpim(I) all: 0.01496 / Net I/σ(I): 35.31
Reflection shellResolution: 1.6→1.657 Å / Rmerge(I) obs: 0.512 / Mean I/σ(I) obs: 5.66 / Num. unique obs: 3119 / CC1/2: 0.966 / CC star: 0.991 / Rpim(I) all: 0.1349 / % possible all: 99.97

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Processing

Software
NameVersionClassification
PHENIX(1.15.2_3472: ???)refinement
CrysalisProdata reduction
CrysalisProdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.6→17.569 Å / SU ML: 0.16 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 21.41 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2083 1564 5.04 %
Rwork0.1841 --
obs0.1854 31042 99.96 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.6→17.569 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1441 0 0 169 1610
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0051498
X-RAY DIFFRACTIONf_angle_d0.6582037
X-RAY DIFFRACTIONf_dihedral_angle_d10.6081189
X-RAY DIFFRACTIONf_chiral_restr0.044214
X-RAY DIFFRACTIONf_plane_restr0.004269
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.6-1.65160.27531340.21152708X-RAY DIFFRACTION100
1.6516-1.71060.26361590.20862656X-RAY DIFFRACTION100
1.7106-1.77910.20651320.20332683X-RAY DIFFRACTION100
1.7791-1.85990.24751520.20322658X-RAY DIFFRACTION100
1.8599-1.95790.22371640.20732647X-RAY DIFFRACTION100
1.9579-2.08040.23781310.1922685X-RAY DIFFRACTION100
2.0804-2.24070.19351270.17492699X-RAY DIFFRACTION100
2.2407-2.46560.21781470.18392661X-RAY DIFFRACTION100
2.4656-2.82110.20781420.19772681X-RAY DIFFRACTION100
2.8211-3.54950.22391340.18972681X-RAY DIFFRACTION100
3.5495-17.5690.16141420.15352719X-RAY DIFFRACTION100

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