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- PDB-6w8t: Crystal structure of metacaspase 4 from Arabidopsis (microcrystal... -

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Basic information

Entry
Database: PDB / ID: 6w8t
TitleCrystal structure of metacaspase 4 from Arabidopsis (microcrystals treated with calcium)
ComponentsMetacaspase-4
KeywordsPLANT PROTEIN / HYDROLASE / metacaspase / protease / Ca2+-dependent activation / microcrystals / 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: 3.2 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 / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)93,2903
Polymers93,1942
Non-polymers961
Water00
1
A: 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
2
B: Metacaspase-4


Theoretical massNumber of molelcules
Total (without water)46,5971
Polymers46,5971
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)49.345, 58.059, 300.697
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number17
Space group name H-MP2221
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11(chain A and (resseq 2:26 or resseq 28:35 or resseq...
21(chain B and (resseq 2:26 or resseq 28:35 or resseq...

NCS domain segments:

Ens-ID: 1

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11THRTHRVALVAL(chain A and (resseq 2:26 or resseq 28:35 or resseq...AA2 - 262 - 26
12ARGARGGLUGLU(chain A and (resseq 2:26 or resseq 28:35 or resseq...AA28 - 3528 - 35
13TYRTYRHISHIS(chain A and (resseq 2:26 or resseq 28:35 or resseq...AA37 - 14037 - 140
14THRTHRCYSCYS(chain A and (resseq 2:26 or resseq 28:35 or resseq...AA2 - 4182 - 418
15ASPASPASPASP(chain A and (resseq 2:26 or resseq 28:35 or resseq...AA243243
16THRTHRCYSCYS(chain A and (resseq 2:26 or resseq 28:35 or resseq...AA2 - 4182 - 418
17THRTHRCYSCYS(chain A and (resseq 2:26 or resseq 28:35 or resseq...AA2 - 4182 - 418
18THRTHRCYSCYS(chain A and (resseq 2:26 or resseq 28:35 or resseq...AA2 - 4182 - 418
19THRTHRCYSCYS(chain A and (resseq 2:26 or resseq 28:35 or resseq...AA2 - 4182 - 418
110THRTHRCYSCYS(chain A and (resseq 2:26 or resseq 28:35 or resseq...AA2 - 4182 - 418
111THRTHRCYSCYS(chain A and (resseq 2:26 or resseq 28:35 or resseq...AA2 - 4182 - 418
21THRTHRVALVAL(chain B and (resseq 2:26 or resseq 28:35 or resseq...BB2 - 262 - 26
22ARGARGGLUGLU(chain B and (resseq 2:26 or resseq 28:35 or resseq...BB28 - 3528 - 35
23TYRTYRHISHIS(chain B and (resseq 2:26 or resseq 28:35 or resseq...BB37 - 14037 - 140
24THRTHRCYSCYS(chain B and (resseq 2:26 or resseq 28:35 or resseq...BB2 - 4182 - 418
25ASPASPASPASP(chain B and (resseq 2:26 or resseq 28:35 or resseq...BB243243
26THRTHRCYSCYS(chain B and (resseq 2:26 or resseq 28:35 or resseq...BB2 - 4182 - 418
27THRTHRCYSCYS(chain B and (resseq 2:26 or resseq 28:35 or resseq...BB2 - 4182 - 418
28THRTHRCYSCYS(chain B and (resseq 2:26 or resseq 28:35 or resseq...BB2 - 4182 - 418
29THRTHRCYSCYS(chain B and (resseq 2:26 or resseq 28:35 or resseq...BB2 - 4182 - 418
210THRTHRCYSCYS(chain B and (resseq 2:26 or resseq 28:35 or resseq...BB2 - 4182 - 418
211THRTHRCYSCYS(chain B and (resseq 2:26 or resseq 28:35 or resseq...BB2 - 4182 - 418

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Components

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


Mass: 46596.809 Da / Num. of mol.: 2
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.: 1 / 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: 2.31 Å3/Da / Density % sol: 46.78 %
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: 2.0664 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: May 30, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 2.0664 Å / Relative weight: 1
ReflectionResolution: 3.2→40 Å / Num. obs: 13981 / % possible obs: 93.6 % / Redundancy: 3.5 % / CC1/2: 0.98 / Net I/σ(I): 6.6
Reflection shellResolution: 3.2→3.28 Å / Num. unique obs: 1027 / CC1/2: 0.791

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Processing

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

6w8r


Resolution: 3.2→38 Å / SU ML: 0.57 / Cross valid method: THROUGHOUT / σ(F): 0 / Phase error: 35.6
RfactorNum. reflection% reflection
Rfree0.3211 1328 5.2 %
Rwork0.2858 --
obs0.2878 13869 92.76 %
Solvent computationShrinkage radii: 0.8 Å / VDW probe radii: 1.1 Å
Displacement parametersBiso max: 247.29 Å2 / Biso mean: 79.2663 Å2 / Biso min: 5.89 Å2
Refinement stepCycle: final / Resolution: 3.2→38 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5228 0 5 0 5233
Biso mean--104.8 --
Num. residues----693
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0035307
X-RAY DIFFRACTIONf_angle_d0.5697157
X-RAY DIFFRACTIONf_dihedral_angle_d14.1053249
X-RAY DIFFRACTIONf_chiral_restr0.043804
X-RAY DIFFRACTIONf_plane_restr0.004953
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A3033X-RAY DIFFRACTION6.167TORSIONAL
12B3033X-RAY DIFFRACTION6.167TORSIONAL
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)
10.55270.36140.14920.4053-0.07310.7437-0.3991-0.209-0.2748-0.39650.1177-0.3511-0.0018-0.6782-0.4085-0.1943-0.1313-0.07330.0438-0.07580.104-7.2211-6.2618-20.4305
20.03140.0065-0.05960.0698-0.01920.1001-0.09080.0343-0.08560.039-0.0027-0.14430.066-0.0041-0.11690.4428-0.04010.4333-0.14990.12440.34590.7797-20.6281-17.4469
30.7911-0.2615-0.09060.3891-0.06410.4405-0.59050.21370.0814-0.1977-0.3091-0.2865-0.23050.1892-0.7759-0.8854-1.2801-0.4623-0.8679-0.3189-0.060512.28076.2276-29.5804
40.00780.01630.01160.0249-0.0110.0067-0.0267-0.0697-0.01130.0851-0.1287-0.1204-0.07940.0499-0.06390.1753-0.0064-0.14460.3042-0.00190.32116.54965.3812-11.3005
50.2748-0.13070.1790.1177-0.04370.1303-0.2301-0.2831-0.03520.10520.0755-0.08920.0192-0.2577-0.10020.4531-0.1820.13490.1388-0.09310.1543-7.9778-21.0588-11.6764
60.0727-0.0219-0.04890.0104-0.0190.19010.3343-0.2919-0.04230.0271-0.2531-0.0274-0.28920.4960.11291.2471-0.5774-0.16320.65790.16660.0689-18.27-15.7601-52.9093
70.0718-0.03260.07450.0207-0.03630.1042-0.015-0.0596-0.0316-0.0561-0.1966-0.081-0.14740.1926-0.10420.6197-0.4648-0.07750.79390.21450.1116-20.7323-22.7436-58.8709
80.02140.00070.00780.01610.00250.0026-0.0242-0.0346-0.0296-0.0107-0.0550.0664-0.04420.0304-00.362-0.2442-0.08761.09910.3680.4012-12.1268-30.2004-49.0628
90.0099-0.0013-0.00790.0023-0.00010.0063-0.0054-0.0978-0.05930.0355-0.073-0.00260.03710.0663-0.00350.2452-0.3910.19520.38840.04820.3419-23.9248-35.4586-43.8885
100.0086-0.0030.00090.07060.01410.0042-0.13590.00450.2223-0.00450.03410.04810.01450.0911-0.04030.3674-0.05470.03710.059-0.0380.3673-29.1814-45.1353-51.2288
110.0337-0.0065-0.00930.0233-0.00140.03010.0681-0.1723-0.07420.0033-0.08330.1153-0.0377-0.0733-0.01530.3272-0.4087-0.05260.2793-0.06460.415-34.6311-39.5589-49.21
12-0.0047-0.003-0.00220.00270.01030.0118-0.03750.057-0.04280.0732-0.00630.04310.08250.029900.4642-0.12920.02860.57260.04540.336-16.9296-27.6265-65.8427
130.00290-0.00080.00070.00340.0039-0.12980.0835-0.05520.0325-0.0199-0.0298-0.0143-0.034900.5557-0.2442-0.0950.59690.06440.7602-0.823-14.2136-47.9505
140.06150.02070.0180.00520.00910.02370.00060.0909-0.0123-0.02640.0226-0.1324-0.0688-0.01280.00680.5367-0.5478-0.11141.01880.39090.5929-2.1479-9.6573-64.9154
150.02130.05630.03220.18030.14370.1192-0.0842-0.0089-0.0585-0.1371-0.1821-0.1289-0.07520.0801-0.14090.2268-0.1822-0.10971.07960.27890.2225-9.016-15.6275-68.7955
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 313 )A229 - 313
4X-RAY DIFFRACTION4chain 'A' and (resid 314 through 338 )A314 - 338
5X-RAY DIFFRACTION5chain 'A' and (resid 339 through 418 )A339 - 418
6X-RAY DIFFRACTION6chain 'B' and (resid 2 through 101 )B2 - 101
7X-RAY DIFFRACTION7chain 'B' and (resid 102 through 137 )B102 - 137
8X-RAY DIFFRACTION8chain 'B' and (resid 138 through 239 )B138 - 239
9X-RAY DIFFRACTION9chain 'B' and (resid 240 through 263 )B240 - 263
10X-RAY DIFFRACTION10chain 'B' and (resid 264 through 293 )B264 - 293
11X-RAY DIFFRACTION11chain 'B' and (resid 294 through 323 )B294 - 323
12X-RAY DIFFRACTION12chain 'B' and (resid 324 through 347 )B324 - 347
13X-RAY DIFFRACTION13chain 'B' and (resid 348 through 364 )B348 - 364
14X-RAY DIFFRACTION14chain 'B' and (resid 365 through 397 )B365 - 397
15X-RAY DIFFRACTION15chain 'B' and (resid 398 through 418 )B398 - 418

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