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- PDB-9n3d: Crystal structure of Arabidopsis metacaspase 9 C147G at pH 4.2 -

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Basic information

Entry
Database: PDB / ID: 9n3d
TitleCrystal structure of Arabidopsis metacaspase 9 C147G at pH 4.2
ComponentsMetacaspase-9
KeywordsPLANT PROTEIN / Plant immunity / Metacaspase / pH-dependent activation / cysteine protease
Function / homology
Function and homology information


apoplast / cysteine-type peptidase activity / Hydrolases; Acting on peptide bonds (peptidases); Cysteine endopeptidases / cysteine-type endopeptidase activity / proteolysis
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: 1.7 Å
AuthorsLiu, H. / Liu, Q.
Funding support United States, 1items
OrganizationGrant numberCountry
Department of Energy (DOE, United States) United States
CitationJournal: Nat Commun / Year: 2025
Title: Structural determinants for pH-dependent activation of a plant metacaspase.
Authors: Liu, H. / Henderson, M. / Pang, Z. / Zhang, Q. / Lam, E. / Liu, Q.
History
DepositionJan 30, 2025Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 11, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Metacaspase-9


Theoretical massNumber of molelcules
Total (without water)35,5031
Polymers35,5031
Non-polymers00
Water5,332296
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)72.829, 54.516, 81.010
Angle α, β, γ (deg.)90.000, 97.094, 90.000
Int Tables number5
Space group name H-MI121
Space group name HallC2y(x,y,-x+z)
Components on special symmetry positions
IDModelComponents
11A-648-

HOH

21A-689-

HOH

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Components

#1: Protein Metacaspase-9 / AtMC9


Mass: 35503.340 Da / Num. of mol.: 1 / Mutation: C147G
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Gene: AMC9, MCP2F, At5g04200, F21E1.120 / Production host: Escherichia coli (E. coli)
References: UniProt: Q9FYE1, Hydrolases; Acting on peptide bonds (peptidases); Cysteine endopeptidases
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 296 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationN

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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: 2.25 Å3/Da / Density % sol: 45.27 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: Sodium chloride, Phosphate/citrate, PEG 8000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: NSLS-II / Beamline: 17-ID-1 / Wavelength: 0.92 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Jan 29, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.92 Å / Relative weight: 1
ReflectionResolution: 1.7→36.14 Å / Num. obs: 45945 / % possible obs: 76.7 % / Redundancy: 6.97 % / CC1/2: 0.997 / Net I/σ(I): 17
Reflection shellResolution: 1.7→1.74 Å / Num. unique obs: 2358 / CC1/2: 0.983

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Processing

Software
NameVersionClassification
PHENIX1.18.2refinement
DIALSdata reduction
Aimlessdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.7→36.14 Å / SU ML: 0.1749 / Cross valid method: FREE R-VALUE / σ(F): 1.39 / Phase error: 22.8251
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2188 1651 4.89 %
Rwork0.2003 32138 -
obs0.2013 33789 97.08 %
Solvent computationShrinkage radii: 1 Å / VDW probe radii: 1.2 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 19.88 Å2
Refinement stepCycle: LAST / Resolution: 1.7→36.14 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2362 0 0 296 2658
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00162398
X-RAY DIFFRACTIONf_angle_d0.40313231
X-RAY DIFFRACTIONf_chiral_restr0.0402370
X-RAY DIFFRACTIONf_plane_restr0.0027423
X-RAY DIFFRACTIONf_dihedral_angle_d13.5164897
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.7-1.750.20831220.22862586X-RAY DIFFRACTION93.86
1.75-1.810.26541430.22142629X-RAY DIFFRACTION96.48
1.81-1.870.23131510.21562634X-RAY DIFFRACTION96.4
1.87-1.950.23121260.22432648X-RAY DIFFRACTION96.52
1.95-2.030.22671280.21282672X-RAY DIFFRACTION97.26
2.03-2.140.2391320.20912699X-RAY DIFFRACTION97.19
2.14-2.280.24421400.20582673X-RAY DIFFRACTION97.37
2.28-2.450.25761450.21022671X-RAY DIFFRACTION97.71
2.45-2.70.22571450.21232700X-RAY DIFFRACTION98.1
2.7-3.090.22471230.20582720X-RAY DIFFRACTION97.93
3.09-3.890.20521600.18262711X-RAY DIFFRACTION97.89
3.89-36.140.17331360.17482795X-RAY DIFFRACTION98.13
Refinement TLS params.Method: refined / Origin x: 4.77950832084 Å / Origin y: -26.57040179 Å / Origin z: -19.0302800018 Å
111213212223313233
T0.106050271585 Å2-0.00367918895998 Å20.00113654417817 Å2-0.0879290668098 Å20.000211562000032 Å2--0.103413389976 Å2
L1.01487320661 °2-0.00349740355486 °2-0.122119980357 °2-0.610161849786 °20.0556674250955 °2--1.40450130871 °2
S0.000649475764278 Å °-0.0533950946513 Å °0.0292669304201 Å °0.0262101594927 Å °0.00750622292056 Å °0.0100960782055 Å °0.0507414941647 Å °-0.0594988180895 Å °-0.0078840156436 Å °
Refinement TLS groupSelection details: all

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