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- PDB-6w8s: Crystal structure of metacaspase 4 from Arabidopsis -

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Basic information

Entry
Database: PDB / ID: 6w8s
TitleCrystal structure of metacaspase 4 from Arabidopsis
ComponentsMetacaspase-4
KeywordsPLANT PROTEIN / HYDROLASE / metacaspase / protease / Ca2+-dependent activation / wild-type / plant immunity
Function / homology
Function and homology information


plasmodesma / positive regulation of programmed cell death / protein autoprocessing / cysteine-type peptidase activity / defense response / Hydrolases; Acting on peptide bonds (peptidases); Cysteine endopeptidases / cysteine-type endopeptidase activity / mitochondrion / identical protein binding / plasma membrane ...plasmodesma / positive regulation of programmed cell death / protein autoprocessing / cysteine-type peptidase activity / defense response / Hydrolases; Acting on peptide bonds (peptidases); Cysteine endopeptidases / cysteine-type endopeptidase activity / mitochondrion / identical protein binding / plasma membrane / cytoplasm / cytosol
Similarity search - Function
: / : / Caspase domain / Caspase-like domain superfamily
Similarity search - Domain/homology
Biological speciesArabidopsis thaliana (thale cress)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.484 Å
AuthorsZhu, P. / Yu, X.H. / Wang, C. / Zhang, Q. / Liu, W. / McSweeney, S. / Shanklin, J. / Lam, E. / Liu, Q.
Funding support United States, 1items
OrganizationGrant numberCountry
Department of Energy (DOE, United States) United States
CitationJournal: Nat Commun / Year: 2020
Title: Structural basis for Ca2+-dependent activation of a plant metacaspase.
Authors: Zhu, P. / Yu, X.H. / Wang, C. / Zhang, Q. / Liu, W. / McSweeney, S. / Shanklin, J. / Lam, E. / Liu, Q.
History
DepositionMar 21, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 20, 2020Provider: repository / Type: Initial release
Revision 1.1Oct 18, 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: Metacaspase-4
B: Metacaspase-4
C: Metacaspase-4
D: Metacaspase-4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)187,15612
Polymers186,3874
Non-polymers7698
Water00
1
A: Metacaspase-4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,8854
Polymers46,5971
Non-polymers2883
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Metacaspase-4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,6932
Polymers46,5971
Non-polymers961
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Metacaspase-4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,8854
Polymers46,5971
Non-polymers2883
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Metacaspase-4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,6932
Polymers46,5971
Non-polymers961
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)125.910, 284.440, 57.680
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21212
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11(chain A and (resseq 2:15 or resseq 17:50 or resseq...
21(chain B and (resseq 2:15 or resseq 17:50 or resseq...
31(chain C and (resseq 2:15 or resseq 17:50 or resseq...
41(chain D and (resseq 2:15 or resseq 17:50 or resseq...

NCS domain segments:
Dom-IDComponent-IDEns-IDSelection detailsAuth asym-IDAuth seq-ID
111(chain A and (resseq 2:15 or resseq 17:50 or resseq...A2 - 15
121(chain A and (resseq 2:15 or resseq 17:50 or resseq...A17 - 50
131(chain A and (resseq 2:15 or resseq 17:50 or resseq...A0
141(chain A and (resseq 2:15 or resseq 17:50 or resseq...A0
151(chain A and (resseq 2:15 or resseq 17:50 or resseq...A2 - 420
161(chain A and (resseq 2:15 or resseq 17:50 or resseq...A2 - 420
171(chain A and (resseq 2:15 or resseq 17:50 or resseq...A2 - 420
181(chain A and (resseq 2:15 or resseq 17:50 or resseq...A2 - 420
191(chain A and (resseq 2:15 or resseq 17:50 or resseq...A2 - 420
1101(chain A and (resseq 2:15 or resseq 17:50 or resseq...A2 - 420
1111(chain A and (resseq 2:15 or resseq 17:50 or resseq...A2 - 420
211(chain B and (resseq 2:15 or resseq 17:50 or resseq...B2 - 15
221(chain B and (resseq 2:15 or resseq 17:50 or resseq...B17 - 50
231(chain B and (resseq 2:15 or resseq 17:50 or resseq...B52
241(chain B and (resseq 2:15 or resseq 17:50 or resseq...B54 - 140
251(chain B and (resseq 2:15 or resseq 17:50 or resseq...B212
261(chain B and (resseq 2:15 or resseq 17:50 or resseq...B214
271(chain B and (resseq 2:15 or resseq 17:50 or resseq...B2 - 420
281(chain B and (resseq 2:15 or resseq 17:50 or resseq...B2 - 420
291(chain B and (resseq 2:15 or resseq 17:50 or resseq...B2 - 420
2101(chain B and (resseq 2:15 or resseq 17:50 or resseq...B2 - 420
2111(chain B and (resseq 2:15 or resseq 17:50 or resseq...B2 - 420
2121(chain B and (resseq 2:15 or resseq 17:50 or resseq...B2 - 420
311(chain C and (resseq 2:15 or resseq 17:50 or resseq...C2 - 15
321(chain C and (resseq 2:15 or resseq 17:50 or resseq...C17 - 50
331(chain C and (resseq 2:15 or resseq 17:50 or resseq...C52
341(chain C and (resseq 2:15 or resseq 17:50 or resseq...C54
351(chain C and (resseq 2:15 or resseq 17:50 or resseq...C2 - 420
361(chain C and (resseq 2:15 or resseq 17:50 or resseq...C214
371(chain C and (resseq 2:15 or resseq 17:50 or resseq...C2 - 420
381(chain C and (resseq 2:15 or resseq 17:50 or resseq...C2 - 420
391(chain C and (resseq 2:15 or resseq 17:50 or resseq...C2 - 420
411(chain D and (resseq 2:15 or resseq 17:50 or resseq...D2 - 15
421(chain D and (resseq 2:15 or resseq 17:50 or resseq...D17 - 50
431(chain D and (resseq 2:15 or resseq 17:50 or resseq...D52
441(chain D and (resseq 2:15 or resseq 17:50 or resseq...D54
451(chain D and (resseq 2:15 or resseq 17:50 or resseq...D2 - 420
461(chain D and (resseq 2:15 or resseq 17:50 or resseq...D214
471(chain D and (resseq 2:15 or resseq 17:50 or resseq...D2 - 420
481(chain D and (resseq 2:15 or resseq 17:50 or resseq...D2 - 420
491(chain D and (resseq 2:15 or resseq 17:50 or resseq...D2 - 420

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Components

#1: Protein
Metacaspase-4 / AtMC4 / Metacaspase 2d / AtMCP2d / Metacaspase-7


Mass: 46596.809 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Gene: AMC4, AMC7, MCP2D, At1g79340, YUP8H12R.4
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
References: UniProt: O64517, Hydrolases; Acting on peptide bonds (peptidases); Cysteine endopeptidases
#2: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: SO4
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: 2.77 Å3/Da / Density % sol: 55.61 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.4
Details: 100 mM sodium cacodylate, pH 6.4, 2.1 M ammonium sulfate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: NSLS-II / Beamline: 17-ID-2 / Wavelength: 1.61 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Feb 24, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.61 Å / Relative weight: 1
ReflectionResolution: 3.47→40 Å / Num. obs: 27566 / % possible obs: 98.9 % / Redundancy: 44.3 % / CC1/2: 0.997 / Net I/σ(I): 8.1
Reflection shellResolution: 3.47→3.56 Å / Num. unique obs: 1761 / CC1/2: 0.605

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Processing

Software
NameVersionClassification
Aimlessdata scaling
PHENIX1.10.1_2155refinement
PDB_EXTRACT3.25data extraction
DIALSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6W8R

6w8r


Resolution: 3.484→38.804 Å / SU ML: 0.5 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 27.46
RfactorNum. reflection% reflection
Rfree0.2839 1242 5.09 %
Rwork0.2501 --
obs0.2518 24400 88.88 %
Solvent computationShrinkage radii: 0.8 Å / VDW probe radii: 1.1 Å
Displacement parametersBiso max: 235.01 Å2 / Biso min: 38.49 Å2
Refinement stepCycle: final / Resolution: 3.484→38.804 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10868 0 40 0 10908
Biso mean--131.95 --
Num. residues----1438
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00711065
X-RAY DIFFRACTIONf_angle_d1.41814926
X-RAY DIFFRACTIONf_dihedral_angle_d15.5186774
X-RAY DIFFRACTIONf_chiral_restr0.0761677
X-RAY DIFFRACTIONf_plane_restr0.0071983
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A6336X-RAY DIFFRACTION6.202TORSIONAL
12B6336X-RAY DIFFRACTION6.202TORSIONAL
13C6336X-RAY DIFFRACTION6.202TORSIONAL
14D6336X-RAY DIFFRACTION6.202TORSIONAL
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)
10.5086-0.145-0.05480.15420.00760.7079-0.0548-0.48420.4171-0.52760.03970.21830.2035-0.0821-0.01440.3703-0.10060.0260.4299-0.09360.574226.3987331.78541.8729
20.34410.23750.2890.72330.12930.21580.5019-0.1887-0.11620.2877-0.4911-0.3296-0.12920.33410.35930.1649-0.02440.430.7086-0.3161-0.157933.349333.145317.4077
30.44160.16360.06240.41620.31590.1989-0.28550.121-0.2389-0.22060.2021-0.1897-0.0731-0.0397-00.6678-0.17210.31040.5119-0.05790.635147.2908327.9241-10.1409
40.2756-0.05320.05220.19840.30340.3542-0.0776-0.33370.08-0.3762-0.149-0.7654-0.0973-0.2463-0.01290.6329-0.1350.13610.6009-0.06120.69931.718335.745210.3936
50.6825-0.046-0.29160.00440.03970.17090.2176-1.03981.12320.14120.09560.3075-0.62340.43550.05920.5905-0.0050.23330.5201-0.10630.872620.8472342.129917.1042
60.3651-0.07130.10860.40180.23710.0651-0.14110.1456-0.08690.2315-0.05310.297-0.1626-0.17-00.6140.1429-0.05490.53970.0060.609321.1654374.3782-8.6876
7-0.0193-0.11950.01020.20810.24310.2149-0.1259-0.026-0.5158-0.0047-0.2423-0.41450.05160.1071-0.01760.76410.066-0.00210.6372-0.10280.651528.2654370.4097-14.6083
80.3213-0.1304-0.23710.58060.34030.26750.1755-0.23450.18680.12020.1205-0.6418-0.16810.23960.64610.55180.2549-0.37540.8225-0.02970.746744.8909381.51740.0536
90.0399-0.02590.05780.05960.00610.09-0.2744-0.5731-0.2348-0.0242-0.09160.34940.1706-0.04710.01930.66520.1306-0.14460.62740.13760.970839.2728368.46713.8812
100.20630.0479-0.23470.1101-0.03530.04910.18910.1286-0.3038-0.631-0.2195-0.0950.2787-0.0961-00.86480.1052-0.09410.4707-0.09120.651219.5042364.9514-22.7809
110.02350.06350.27080.9769-1.0322.36350.4685-0.2785-0.23920.66330.30750.655-0.18760.06462.14730.60430.2638-0.43310.43460.1098-0.05248.3554405.232-12.5113
12-0.02750.0705-0.00140.16290.01530.1185-0.0070.18510.1560.03320.1575-0.1237-0.06270.30950.00010.53290.0386-0.02240.569-0.02340.467111.424411.2675-19.7949
130.06010.1739-0.29150.63050.17071.05930.2558-0.0222-0.017-0.72740.08860.3308-0.21850.17980.14080.3605-0.0137-0.76270.3646-0.0050.6242-0.5438403.0751-32.5744
140.4548-0.0452-0.61380.0010.04730.7990.01470.19710.43290.23990.3464-0.513-0.1890.19740.24620.59870.0308-0.30460.6496-0.23760.732521.529415.9432-11.1186
150.0912-0.00540.20250.46980.13560.15320.2149-0.1813-0.21170.27910.1894-0.1862-0.25810.08840.00190.76430.0401-0.03820.56610.07170.539771.0067404.9153-24.8353
160.03340.0110.06130.9284-0.08190.780.19060.0640.0265-0.3163-0.02880.11650.0155-0.01440.39560.37740.033-0.18620.61520.05770.52464.8282403.2251-39.7773
170.0830.0607-0.17320.0262-0.18220.8128-0.2491-0.00130.0694-0.935-0.5370.36340.09750.4856-0.08960.67890.1431-0.46950.4562-0.08711.228159.9948415.9875-38.0981
180.0704-0.0147-0.20430.1799-0.19590.347-0.37650.25350.7295-0.12480.28370.1392-0.42710.6824-0.00190.67910.08-0.15350.6458-0.11481.08984.7665415.7607-25.5645
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 2 through 137 )A2 - 137
2X-RAY DIFFRACTION2chain 'A' and (resid 138 through 228 )A138 - 228
3X-RAY DIFFRACTION3chain 'A' and (resid 229 through 323 )A229 - 323
4X-RAY DIFFRACTION4chain 'A' and (resid 324 through 364 )A324 - 364
5X-RAY DIFFRACTION5chain 'A' and (resid 365 through 420 )A365 - 420
6X-RAY DIFFRACTION6chain 'B' and (resid 2 through 101 )B2 - 101
7X-RAY DIFFRACTION7chain 'B' and (resid 102 through 228 )B102 - 228
8X-RAY DIFFRACTION8chain 'B' and (resid 229 through 304 )B229 - 304
9X-RAY DIFFRACTION9chain 'B' and (resid 305 through 338 )B305 - 338
10X-RAY DIFFRACTION10chain 'B' and (resid 339 through 420 )B339 - 420
11X-RAY DIFFRACTION11chain 'C' and (resid 2 through 101 )C2 - 101
12X-RAY DIFFRACTION12chain 'C' and (resid 102 through 217 )C102 - 217
13X-RAY DIFFRACTION13chain 'C' and (resid 218 through 338 )C218 - 338
14X-RAY DIFFRACTION14chain 'C' and (resid 339 through 420 )C339 - 420
15X-RAY DIFFRACTION15chain 'D' and (resid 2 through 101 )D2 - 101
16X-RAY DIFFRACTION16chain 'D' and (resid 102 through 313 )D102 - 313
17X-RAY DIFFRACTION17chain 'D' and (resid 314 through 342 )D314 - 342
18X-RAY DIFFRACTION18chain 'D' and (resid 343 through 420 )D343 - 420

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