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- PDB-8wra: The Crystal Structure of CASP1 from Biortus -

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Basic information

Entry
Database: PDB / ID: 8wra
TitleThe Crystal Structure of CASP1 from Biortus
ComponentsCaspase-1
KeywordsHYDROLASE / Protease / Thiol protease / Apoptosis
Function / homology
Function and homology information


caspase-1 / protease inhibitor complex / AIM2 inflammasome complex assembly / The AIM2 inflammasome / AIM2 inflammasome complex / IPAF inflammasome complex / The IPAF inflammasome / icosanoid biosynthetic process / NLRP1 inflammasome complex / cytokine precursor processing ...caspase-1 / protease inhibitor complex / AIM2 inflammasome complex assembly / The AIM2 inflammasome / AIM2 inflammasome complex / IPAF inflammasome complex / The IPAF inflammasome / icosanoid biosynthetic process / NLRP1 inflammasome complex / cytokine precursor processing / canonical inflammasome complex / positive regulation of interleukin-18 production / NLRP3 inflammasome complex / caspase binding / CARD domain binding / osmosensory signaling pathway / positive regulation of tumor necrosis factor-mediated signaling pathway / Interleukin-1 processing / Interleukin-37 signaling / pattern recognition receptor signaling pathway / signaling receptor ligand precursor processing / TP53 Regulates Transcription of Caspase Activators and Caspases / pyroptotic inflammatory response / : / cytokine binding / cysteine-type endopeptidase activator activity involved in apoptotic process / The NLRP3 inflammasome / protein autoprocessing / protein maturation / Pyroptosis / Purinergic signaling in leishmaniasis infection / positive regulation of interleukin-1 beta production / NOD1/2 Signaling Pathway / kinase binding / cellular response to type II interferon / positive regulation of inflammatory response / cellular response to mechanical stimulus / SARS-CoV-1 activates/modulates innate immune responses / regulation of inflammatory response / cellular response to lipopolysaccharide / defense response to virus / regulation of apoptotic process / positive regulation of canonical NF-kappaB signal transduction / endopeptidase activity / microtubule / defense response to bacterium / cysteine-type endopeptidase activity / nucleolus / apoptotic process / signal transduction / protein-containing complex / proteolysis / identical protein binding / plasma membrane / cytosol / cytoplasm
Similarity search - Function
Caspase recruitment domain / CARD domain / CARD caspase recruitment domain profile. / Caspase recruitment domain / 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. ...Caspase recruitment domain / CARD domain / CARD caspase recruitment domain profile. / Caspase recruitment domain / 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: 1.45 Å
AuthorsWang, F. / Cheng, W. / Yuan, Z. / Lin, D. / Guo, S.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: To Be Published
Title: The Crystal Structure of CASP1 from Biortus.
Authors: Wang, F. / Cheng, W. / Yuan, Z. / Lin, D. / Guo, S.
History
DepositionOct 13, 2023Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Nov 15, 2023Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Caspase-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,2454
Polymers32,0591
Non-polymers1863
Water5,405300
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: Caspase-1
hetero molecules

A: Caspase-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)64,4908
Polymers64,1172
Non-polymers3726
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_555y,x,-z1
Buried area5480 Å2
ΔGint-8 kcal/mol
Surface area21400 Å2
MethodPISA
Unit cell
Length a, b, c (Å)62.807, 62.807, 144.132
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number96
Space group name H-MP43212
Components on special symmetry positions
IDModelComponents
11A-818-

HOH

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Components

#1: Protein Caspase-1 / CASP-1 / Interleukin-1 beta convertase / IL-1BC / Interleukin-1 beta-converting enzyme / ICE / IL-1 ...CASP-1 / Interleukin-1 beta convertase / IL-1BC / Interleukin-1 beta-converting enzyme / ICE / IL-1 beta-converting enzyme / p45


Mass: 32058.590 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CASP1, IL1BC, IL1BCE / Production host: Escherichia coli (E. coli) / References: UniProt: P29466, caspase-1
#2: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H6O2
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 300 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 2.36 Å3/Da / Density % sol: 47.94 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / Details: 0.15M Na formate, 14% PEG3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL45XU / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jun 16, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.45→48.04 Å / Num. obs: 52141 / % possible obs: 100 % / Redundancy: 12.7 % / Rmerge(I) obs: 0.101 / Net I/σ(I): 17.6
Reflection shellResolution: 1.45→1.47 Å / Rmerge(I) obs: 1.042 / Mean I/σ(I) obs: 2.6 / Num. unique obs: 2526

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Processing

Software
NameVersionClassification
REFMAC5.8.0419refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.45→47.394 Å / Cor.coef. Fo:Fc: 0.955 / Cor.coef. Fo:Fc free: 0.942 / SU B: 1.116 / SU ML: 0.043 / Cross valid method: FREE R-VALUE / ESU R: 0.069 / ESU R Free: 0.069
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2129 2618 5.03 %
Rwork0.1916 49427 -
all0.193 --
obs-52045 99.99 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 14.006 Å2
Baniso -1Baniso -2Baniso -3
1-0.074 Å2-0 Å2-0 Å2
2--0.074 Å2-0 Å2
3----0.148 Å2
Refinement stepCycle: LAST / Resolution: 1.45→47.394 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1960 0 12 300 2272
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0040.0122153
X-RAY DIFFRACTIONr_bond_other_d0.0010.0162086
X-RAY DIFFRACTIONr_angle_refined_deg1.0871.662919
X-RAY DIFFRACTIONr_angle_other_deg0.3891.5784854
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.1545285
X-RAY DIFFRACTIONr_dihedral_angle_2_deg5.671517
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.33910417
X-RAY DIFFRACTIONr_dihedral_angle_6_deg14.51310102
X-RAY DIFFRACTIONr_chiral_restr0.0540.2323
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.022541
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02487
X-RAY DIFFRACTIONr_nbd_refined0.2080.2385
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1890.21790
X-RAY DIFFRACTIONr_nbtor_refined0.1760.2985
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0770.21055
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1320.2252
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.1660.236
X-RAY DIFFRACTIONr_nbd_other0.2110.2135
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.10.243
X-RAY DIFFRACTIONr_mcbond_it1.2551.3721036
X-RAY DIFFRACTIONr_mcbond_other1.2551.3721036
X-RAY DIFFRACTIONr_mcangle_it2.2242.4521301
X-RAY DIFFRACTIONr_mcangle_other2.2232.4521302
X-RAY DIFFRACTIONr_scbond_it1.3261.5671117
X-RAY DIFFRACTIONr_scbond_other1.3261.5681118
X-RAY DIFFRACTIONr_scangle_it2.2562.7751599
X-RAY DIFFRACTIONr_scangle_other2.2562.7761600
X-RAY DIFFRACTIONr_lrange_it5.49418.4372521
X-RAY DIFFRACTIONr_lrange_other5.12415.7462399
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.45-1.4880.3352070.3043563X-RAY DIFFRACTION99.9735
1.488-1.5280.2632040.2633500X-RAY DIFFRACTION100
1.528-1.5730.2351860.233396X-RAY DIFFRACTION100
1.573-1.6210.2111480.2113334X-RAY DIFFRACTION99.9713
1.621-1.6740.2091660.23211X-RAY DIFFRACTION100
1.674-1.7330.2431700.1993105X-RAY DIFFRACTION99.9695
1.733-1.7980.2361550.1943018X-RAY DIFFRACTION100
1.798-1.8710.1981650.1912882X-RAY DIFFRACTION100
1.871-1.9540.2261540.1952784X-RAY DIFFRACTION100
1.954-2.050.1971480.1892650X-RAY DIFFRACTION100
2.05-2.160.21400.1862565X-RAY DIFFRACTION100
2.16-2.2910.1861250.1782417X-RAY DIFFRACTION100
2.291-2.4490.1991060.1722290X-RAY DIFFRACTION100
2.449-2.6440.203950.1772156X-RAY DIFFRACTION100
2.644-2.8960.194970.1651980X-RAY DIFFRACTION100
2.896-3.2360.192870.1781810X-RAY DIFFRACTION100
3.236-3.7340.197820.1711620X-RAY DIFFRACTION100
3.734-4.5660.178730.171380X-RAY DIFFRACTION99.9312
4.566-6.4280.251710.2131092X-RAY DIFFRACTION100
6.428-47.3940.249390.221674X-RAY DIFFRACTION100

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