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- PDB-7lvj: CASP8 isoform G DED domain -

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Basic information

Entry
Database: PDB / ID: 7lvj
TitleCASP8 isoform G DED domain
ComponentsIsoform 9 of Caspase-8
KeywordsHYDROLASE / CASP8g / CASP8 / GENE ID: 841 / CASP8G DED
Function / homologycaspase-8 / Isoform 9 of Caspase-8
Function and homology information
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.5 Å
AuthorsWeichert, K. / Lu, F. / Kodandapani, L. / Sauder, J.M.
CitationJournal: ACR Open Rheumatol / Year: 2022
Title: Caspase-8 Variant G Regulates Rheumatoid Arthritis Fibroblast-Like Synoviocyte Aggressive Behavior.
Authors: Ansalone, C. / Ainsworth, R.I. / Nygaard, G. / Ai, R. / Prideaux, E.B. / Hammaker, D. / Perumal, N.B. / Weichert, K. / Tung, F. / Kodandapani, L. / Sauder, J.M. / Mertsching, E.C. / ...Authors: Ansalone, C. / Ainsworth, R.I. / Nygaard, G. / Ai, R. / Prideaux, E.B. / Hammaker, D. / Perumal, N.B. / Weichert, K. / Tung, F. / Kodandapani, L. / Sauder, J.M. / Mertsching, E.C. / Benschop, R.J. / Boyle, D.L. / Wang, W. / Firestein, G.S.
History
DepositionFeb 25, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 2, 2022Provider: repository / Type: Initial release
Revision 1.1Apr 20, 2022Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.year / _citation_author.identifier_ORCID
Revision 1.2Apr 3, 2024Group: 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: Isoform 9 of Caspase-8


Theoretical massNumber of molelcules
Total (without water)30,0151
Polymers30,0151
Non-polymers00
Water3,369187
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 area10850 Å2
Unit cell
Length a, b, c (Å)100.912, 49.766, 52.271
Angle α, β, γ (deg.)90.000, 116.360, 90.000
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-457-

HOH

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Components

#1: Protein Isoform 9 of Caspase-8 / CASP-8 / Apoptotic cysteine protease / Apoptotic protease Mch-5 / CAP4 / FADD-homologous ICE/ced-3- ...CASP-8 / Apoptotic cysteine protease / Apoptotic protease Mch-5 / CAP4 / FADD-homologous ICE/ced-3-like protease / FADD-like ICE / FLICE / ICE-like apoptotic protease 5 / MORT1-associated ced-3 homolog / MACH


Mass: 30014.520 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CASP8, MCH5 / Variant: Ge. / Production host: Escherichia coli BL21 (bacteria) / References: UniProt: Q14790-9, caspase-8
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 187 / 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: 1.96 Å3/Da / Density % sol: 37.22 %
Crystal growTemperature: 281 K / Method: vapor diffusion, sitting drop / pH: 8
Details: 20% PEG 3350, 200mM Potassium Sodium Tartrate tetrahydrate
Temp details: 8C

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID30B / Wavelength: 0.984 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Sep 7, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.984 Å / Relative weight: 1
ReflectionResolution: 1.5→35.98 Å / Num. obs: 36268 / % possible obs: 97.3 % / Redundancy: 2.8 % / CC1/2: 0.996 / Rmerge(I) obs: 0.054 / Rpim(I) all: 0.037 / Rrim(I) all: 0.066 / Net I/σ(I): 10.6 / Num. measured all: 101116 / Scaling rejects: 1
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique obsCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs% possible all
1.5-1.582.70.271449253090.9290.1880.3312.798
4.74-35.9830.045337111310.9950.030.05422.592.3

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Processing

Software
NameVersionClassification
REFMAC5.8.0049refinement
PDB_EXTRACT3.27data extraction
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: Internal structure

Resolution: 1.5→30 Å / Cor.coef. Fo:Fc: 0.961 / Cor.coef. Fo:Fc free: 0.949 / SU B: 1.485 / SU ML: 0.056 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.078 / ESU R Free: 0.081 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.23 1809 5 %RANDOM
Rwork0.1977 ---
obs0.1993 34457 97.13 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 90.33 Å2 / Biso mean: 23.198 Å2 / Biso min: 10.38 Å2
Baniso -1Baniso -2Baniso -3
1-0.31 Å20 Å2-0.53 Å2
2--1.9 Å20 Å2
3----1.13 Å2
Refinement stepCycle: final / Resolution: 1.5→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1537 0 0 196 1733
Biso mean---29.48 -
Num. residues----185
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0191637
X-RAY DIFFRACTIONr_angle_refined_deg1.1752.0012203
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.4155202
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.75224.88688
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.13215348
X-RAY DIFFRACTIONr_dihedral_angle_4_deg12.1271515
X-RAY DIFFRACTIONr_chiral_restr0.0780.2242
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.021234
LS refinement shellResolution: 1.5→1.539 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.25 139 -
Rwork0.24 2570 -
all-2709 -
obs--97.69 %

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