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- PDB-6kxg: Crystal structure of caspase-11-CARD -

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Basic information

Entry
Database: PDB / ID: 6kxg
TitleCrystal structure of caspase-11-CARD
Componentscaspase-11-CARD
KeywordsIMMUNE SYSTEM / CARD / inflammasome / caspase-11
Function / homology
Function and homology information


detection of maltose stimulus / maltose binding / maltose transport complex / maltose transport / maltodextrin transmembrane transport / carbohydrate transmembrane transporter activity / ATP-binding cassette (ABC) transporter complex, substrate-binding subunit-containing / carbohydrate transport / ATP-binding cassette (ABC) transporter complex / cell chemotaxis ...detection of maltose stimulus / maltose binding / maltose transport complex / maltose transport / maltodextrin transmembrane transport / carbohydrate transmembrane transporter activity / ATP-binding cassette (ABC) transporter complex, substrate-binding subunit-containing / carbohydrate transport / ATP-binding cassette (ABC) transporter complex / cell chemotaxis / outer membrane-bounded periplasmic space / periplasmic space / DNA damage response / membrane
Similarity search - Function
Maltose/Cyclodextrin ABC transporter, substrate-binding protein / Solute-binding family 1, conserved site / Bacterial extracellular solute-binding proteins, family 1 signature. / Bacterial extracellular solute-binding protein / Bacterial extracellular solute-binding protein
Similarity search - Domain/homology
Maltose/maltodextrin-binding periplasmic protein
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.805 Å
AuthorsLiu, M.Z.Y. / Jin, T.C.
Funding support China, 2items
OrganizationGrant numberCountry
National Natural Science Foundation of China81872110 China
National Natural Science Foundation of China81272881 China
CitationJournal: Cell Discov / Year: 2020
Title: Crystal structure of caspase-11 CARD provides insights into caspase-11 activation.
Authors: Liu, M. / Zhou, K. / Xu, Z. / Ma, H. / Cao, X. / Yin, X. / Zeng, W. / Zahid, A. / Fu, S. / Ni, K. / Ye, X. / Zhou, Y. / Bai, L. / Zhou, R. / Jin, T.
History
DepositionSep 11, 2019Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Sep 16, 2020Provider: repository / Type: Initial release
Revision 1.1Mar 31, 2021Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Nov 22, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: caspase-11-CARD
B: caspase-11-CARD
C: caspase-11-CARD
D: caspase-11-CARD


Theoretical massNumber of molelcules
Total (without water)203,7434
Polymers203,7434
Non-polymers00
Water543
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10290 Å2
ΔGint-61 kcal/mol
Surface area70620 Å2
MethodPISA
Unit cell
Length a, b, c (Å)77.310, 145.160, 187.720
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein
caspase-11-CARD


Mass: 50935.668 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P0AEX9*PLUS
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 3 / 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: 2.58 Å3/Da / Density % sol: 56.92 %
Crystal growTemperature: 289.15 K / Method: vapor diffusion, hanging drop / Details: 2.4M ammonium sulfate 5% isopropanol

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U1 / Wavelength: 0.979 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Sep 20, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2.8→50 Å / Num. obs: 51251 / % possible obs: 97.3 % / Redundancy: 5.89 % / CC1/2: 0.999 / Rrim(I) all: 0.069 / Net I/σ(I): 20.64
Reflection shellResolution: 2.8→2.97 Å / Redundancy: 5.77 % / Mean I/σ(I) obs: 2.03 / Num. unique obs: 7804 / CC1/2: 0.808 / Rrim(I) all: 0.826 / % possible all: 92.9

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Processing

Software
NameVersionClassification
PHENIX1.10.1_2155refinement
PDB_EXTRACT3.25data extraction
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1OMP

1omp


Resolution: 2.805→38.668 Å / SU ML: 0.55 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 38.75
RfactorNum. reflection% reflection
Rfree0.3401 2573 5.03 %
Rwork0.3055 --
obs0.3075 51187 97.37 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 354.06 Å2 / Biso mean: 123.7804 Å2 / Biso min: 41.52 Å2
Refinement stepCycle: final / Resolution: 2.805→38.668 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms12879 0 0 3 12882
Biso mean---47.32 -
Num. residues----1660
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01113163
X-RAY DIFFRACTIONf_angle_d1.17317852
X-RAY DIFFRACTIONf_chiral_restr0.0531972
X-RAY DIFFRACTIONf_plane_restr0.0072306
X-RAY DIFFRACTIONf_dihedral_angle_d17.3957885
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.805-2.85890.53881260.4524231384
2.8589-2.91730.43141210.4111260996
2.9173-2.98070.43181470.40812770100
2.9807-3.050.39681260.38592724100
3.05-3.12620.38711620.38172716100
3.1262-3.21070.39341430.37852726100
3.2107-3.30520.421500.3772270599
3.3052-3.41180.43441470.3714272999
3.4118-3.53360.39731330.3645271598
3.5336-3.6750.37351410.3519272198
3.675-3.84210.38561400.3353269898
3.8421-4.04450.36091510.3272271098
4.0445-4.29760.38391670.2971268798
4.2976-4.62890.31391240.2766274598
4.6289-5.09380.31341450.2665278699
5.0938-5.82870.30721610.29992781100
5.8287-7.33540.32781390.2792284299
7.3354-38.6680.24171500.231263789
Refinement TLS params.Method: refined / Origin x: -14.6655 Å / Origin y: -2.5571 Å / Origin z: 10.2543 Å
111213212223313233
T0.4491 Å20.0307 Å20.0184 Å2-0.4847 Å2-0.0117 Å2--0.5195 Å2
L0.1265 °2-0.0904 °20.0367 °2-0.3831 °20.0053 °2--0.3127 °2
S0.029 Å °-0.0207 Å °0.0225 Å °-0.0628 Å °-0.0032 Å °-0.0802 Å °0.0138 Å °0.0139 Å °-0.0226 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1allA5 - 440
2X-RAY DIFFRACTION1allB3 - 443
3X-RAY DIFFRACTION1allC2 - 439
4X-RAY DIFFRACTION1allD12 - 439
5X-RAY DIFFRACTION1allF1 - 4

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