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- PDB-6ns7: Crystal structure of murine caspase-11 -

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Basic information

Entry
Database: PDB / ID: 6ns7
TitleCrystal structure of murine caspase-11
ComponentsCaspase-11
KeywordsIMMUNE SYSTEM / inflammation / enzyme / caspase / pyroptosis
Function / homology
Function and homology information


caspase-11 / non-canonical inflammasome complex / Pyroptosis / positive regulation of interleukin-18-mediated signaling pathway / pyroptotic cell death / non-canonical inflammasome complex assembly / detection of lipopolysaccharide / canonical inflammasome complex / NOD1/2 Signaling Pathway / positive regulation of macrophage cytokine production ...caspase-11 / non-canonical inflammasome complex / Pyroptosis / positive regulation of interleukin-18-mediated signaling pathway / pyroptotic cell death / non-canonical inflammasome complex assembly / detection of lipopolysaccharide / canonical inflammasome complex / NOD1/2 Signaling Pathway / positive regulation of macrophage cytokine production / pyroptotic inflammatory response / positive regulation of NLRP3 inflammasome complex assembly / protein autoprocessing / ectopic germ cell programmed cell death / actin filament organization / protein maturation / positive regulation of interleukin-1 beta production / lipopolysaccharide binding / positive regulation of inflammatory response / regulation of inflammatory response / regulation of apoptotic process / defense response to Gram-positive bacterium / defense response to bacterium / innate immune response / cysteine-type endopeptidase activity / lipid binding / endoplasmic reticulum membrane / mitochondrion / extracellular region / cytoplasm / cytosol
Similarity search - Function
Caspase recruitment domain / CARD domain / CARD caspase recruitment domain profile. / Caspase recruitment domain / Rossmann fold - #1460 / 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 recruitment domain / CARD domain / CARD caspase recruitment domain profile. / Caspase recruitment domain / Rossmann fold - #1460 / 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 / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 Å
AuthorsYang, J. / Liu, Z. / Xiao, T.S.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Human Genome Research Institute (NIH/NHGRI)GM127609 United States
CitationJournal: To Be Published
Title: Crystal structure of murine caspase-11
Authors: Yang, J. / Liu, Z. / Xiao, T.S.
History
DepositionJan 24, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 29, 2020Provider: repository / Type: Initial release
Revision 1.1Oct 11, 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

Downloads & links

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Assembly

Deposited unit
A: Caspase-11
B: Caspase-11
C: Caspase-11
D: Caspase-11
hetero molecules


Theoretical massNumber of molelcules
Total (without water)129,8008
Polymers129,4164
Non-polymers3844
Water1,856103
1
A: Caspase-11
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,4502
Polymers32,3541
Non-polymers961
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Caspase-11
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,4502
Polymers32,3541
Non-polymers961
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Caspase-11
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,4502
Polymers32,3541
Non-polymers961
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Caspase-11
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,4502
Polymers32,3541
Non-polymers961
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)120.712, 121.092, 78.431
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212

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Components

#1: Protein
Caspase-11 / CASP-4 / Caspase-11 / CASP-11 / Protease ICH-3


Mass: 32353.969 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Casp4, Casp11, Caspl, Ich3 / Production host: Escherichia coli (E. coli) / References: UniProt: P70343, caspase-11
#2: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Formula: SO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 103 / 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: 2.21 Å3/Da / Density % sol: 44.46 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 5.5
Details: 25mM Bis-Tris, 0.2M ammonium sulfate, and 25% PEG3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-D / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Jul 22, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.4→47.93 Å / Num. obs: 86796 / % possible obs: 100 % / Redundancy: 7 % / CC1/2: 0.998 / Rrim(I) all: 0.124 / Net I/σ(I): 10.62
Reflection shellResolution: 2.4→2.486 Å / Redundancy: 6.9 % / Mean I/σ(I) obs: 1.57 / Num. unique obs: 14012 / CC1/2: 0.765 / % possible all: 99.8

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Processing

Software
NameVersionClassification
PHENIX(1.12_2829: ???)refinement
XDSdata reduction
XDSdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3e4c

3e4c


Resolution: 2.4→47.927 Å / SU ML: 0.31 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 27.54
RfactorNum. reflection% reflection
Rfree0.2416 1991 4.36 %
Rwork0.1943 --
obs0.1963 45613 99.87 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.4→47.927 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7764 0 20 103 7887
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.017952
X-RAY DIFFRACTIONf_angle_d1.3210717
X-RAY DIFFRACTIONf_dihedral_angle_d12.4194755
X-RAY DIFFRACTIONf_chiral_restr0.0721177
X-RAY DIFFRACTIONf_plane_restr0.0081368
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.4003-2.46040.3331390.27763044X-RAY DIFFRACTION100
2.4604-2.52690.34091400.27063082X-RAY DIFFRACTION100
2.5269-2.60120.311390.25023062X-RAY DIFFRACTION100
2.6012-2.68520.3371410.24773085X-RAY DIFFRACTION100
2.6852-2.78110.29571430.23033072X-RAY DIFFRACTION100
2.7811-2.89250.3041410.23933099X-RAY DIFFRACTION100
2.8925-3.02410.28581410.23433089X-RAY DIFFRACTION100
3.0241-3.18350.32491370.21873096X-RAY DIFFRACTION100
3.1835-3.38290.21771430.2153093X-RAY DIFFRACTION100
3.3829-3.6440.24921380.18773119X-RAY DIFFRACTION100
3.644-4.01060.20721450.17213139X-RAY DIFFRACTION100
4.0106-4.59050.20471460.15463148X-RAY DIFFRACTION100
4.5905-5.7820.21631460.1743181X-RAY DIFFRACTION100
5.782-47.93630.21251520.18363313X-RAY DIFFRACTION100
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
17.91132.75234.03628.3257-1.99363.68890.4050.5247-0.15-0.247-0.327-0.8843-0.03351.0335-0.16370.515-0.11340.2950.68390.01210.9697-4.893312.8829-41.1441
22.12150.77660.80863.41010.45322.96880.19970.0220.9495-0.35990.0572-0.3775-0.06130.0451-0.24290.49930.00180.15120.21550.07120.554-26.503116.8451-38.7281
35.18941.1572-0.08024.39421.0533.89280.29960.10650.7553-0.4316-0.23030.3301-0.4148-0.412-0.09150.48240.09830.10240.28320.0320.5073-33.461714.8749-40.506
45.1250.43390.23243.55761.79263.08120.4552-0.59020.25060.2114-0.1398-0.41270.0730.1216-0.28640.4697-0.07010.10360.2592-0.02530.4713-22.60696.4038-31.4111
59.08783.27111.05018.56836.24292.1608-0.452-0.4737-0.01580.45760.2941-0.5604-0.11921.01630.2270.61110.1238-0.2970.6185-0.03260.8523-5.6037-16.1638-38.2624
69.8218-2.75794.20844.8247-0.48469.10010.4178-0.4339-0.71811.07790.1822-0.89120.24030.7691-0.59770.6478-0.0593-0.1240.29690.02580.478-18.3878-18.0519-32.3872
74.72250.36240.60782.55890.81664.05360.3270.0776-0.85410.2433-0.18180.33790.6073-0.3989-0.10690.4085-0.0749-0.03660.2984-0.04730.5538-33.0263-21.9935-41.8327
86.5392-0.00170.75795.5020.66955.50630.3286-0.3759-0.09750.7073-0.34410.66530.1741-0.9290.09410.4111-0.08680.09560.308-0.01470.4152-37.6806-11.795-37.1821
94.8786-1.2555-1.06375.78911.5125.10980.2850.54450.0224-0.262-0.2322-0.3366-0.55430.0639-0.09340.3446-0.0024-0.00720.2549-0.01480.3652-23.2734-8.7353-47.49
103.3034-0.47280.66331.96481.62325.0609-0.0275-0.28811.32421.05080.34570.9289-2.06290.2846-0.39252.1447-0.25680.35660.7998-0.2961.259512.2699-10.63216.1556
115.1824-0.3775-1.88054.49050.35183.98780.0389-0.94250.16740.51290.1643-0.713-0.53610.9369-0.23870.4457-0.168-0.06760.8621-0.06080.479718.482-33.7225.0652
127.3683-8.0287-0.96642.1715-3.28728.735-0.1893-0.1586-1.0718-0.68330.01160.20281.04330.45710.21360.5474-0.06940.15620.4422-0.04860.743213.0825-51.3984-4.133
136.0053-0.0017-0.54819.57626.1822.2819-0.0741-1.2537-0.07721.4711-0.31920.69460.4953-0.02430.52170.6479-0.03490.04850.8440.06460.40518.356-39.323512.1399
144.248-0.6278-3.5366.0445-0.48342.8433-0.24170.0417-0.3457-0.03090.0835-0.14640.1673-0.0320.02220.2726-0.08490.00580.5955-0.13210.39498.5916-36.6603-4.033
152.2749-1.1918-0.05016.67895.05827.69690.25910.71421.3811-0.71080.23870.0062-1.64840.1384-0.45830.6592-0.05840.18750.6630.06880.60768.8485-23.2369-6.9788
168.05592.3026-2.11417.5442-1.90137.43640.44560.31270.70390.2033-0.1367-0.1455-1.0613-0.2909-0.42460.32890.09960.09870.5078-0.00230.4945.744-26.8139-0.602
171.743-0.07822.08015.3516-1.04324.4705-0.4956-0.09560.9116-0.8046-0.1393-0.2781-1.30680.12680.27951.77760.54190.60491.12960.67311.7372-15.2534-10.8754-5.2102
183.63551.0767-1.14464.0326-0.73823.7815-0.07491.28440.4785-0.23820.53960.8195-0.4467-1.4258-0.50310.44820.18610.0251.35010.28070.6364-20.4152-34.6409-4.6888
199.07672.3451-2.07349.21512.63126.3284-0.45580.5738-0.95450.63170.35490.35380.995-0.50960.13750.5202-0.05520.15410.5771-0.02650.5367-14.1174-52.2034.1582
205.18670.7959-1.27497.1971-3.50597.4803-0.14421.8549-0.043-0.92020.3153-0.34730.1703-0.541-0.12390.38850.02120.0711.03510.04070.4833-9.408-38.3743-8.7203
216.76270.6084-2.37163.8965-1.00914.84650.56860.01731.15850.56440.09060.5562-1.2919-0.351-0.67560.71810.18680.25910.63190.09760.5696-11.3571-28.89948.4528
226.7557-1.85050.4776.19210.46423.84140.45060.7231.088-0.13830.34130.1128-1.025-0.9349-0.87040.51080.08840.1610.72550.23240.6042-7.9974-27.19571.033
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 100 through 116 )
2X-RAY DIFFRACTION2chain 'A' and (resid 117 through 150 )
3X-RAY DIFFRACTION3chain 'A' and (resid 151 through 295 )
4X-RAY DIFFRACTION4chain 'A' and (resid 296 through 373 )
5X-RAY DIFFRACTION5chain 'B' and (resid 100 through 116 )
6X-RAY DIFFRACTION6chain 'B' and (resid 117 through 138 )
7X-RAY DIFFRACTION7chain 'B' and (resid 139 through 204 )
8X-RAY DIFFRACTION8chain 'B' and (resid 205 through 295 )
9X-RAY DIFFRACTION9chain 'B' and (resid 296 through 373 )
10X-RAY DIFFRACTION10chain 'C' and (resid 100 through 116 )
11X-RAY DIFFRACTION11chain 'C' and (resid 117 through 204 )
12X-RAY DIFFRACTION12chain 'C' and (resid 205 through 223 )
13X-RAY DIFFRACTION13chain 'C' and (resid 224 through 245 )
14X-RAY DIFFRACTION14chain 'C' and (resid 246 through 316 )
15X-RAY DIFFRACTION15chain 'C' and (resid 317 through 348 )
16X-RAY DIFFRACTION16chain 'C' and (resid 349 through 373 )
17X-RAY DIFFRACTION17chain 'D' and (resid 100 through 116 )
18X-RAY DIFFRACTION18chain 'D' and (resid 117 through 204 )
19X-RAY DIFFRACTION19chain 'D' and (resid 205 through 223 )
20X-RAY DIFFRACTION20chain 'D' and (resid 224 through 295 )
21X-RAY DIFFRACTION21chain 'D' and (resid 296 through 348 )
22X-RAY DIFFRACTION22chain 'D' and (resid 349 through 373 )

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