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- PDB-9n3f: Crystal structure of Arabidopsis Metacaspase 9 C147G at pH 7.5 -

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Basic information

Entry
Database: PDB / ID: 9n3f
TitleCrystal structure of Arabidopsis Metacaspase 9 C147G at pH 7.5
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: 1.4 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
Water5,927329
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)73.347, 54.448, 81.075
Angle α, β, γ (deg.)90.000, 97.324, 90.000
Int Tables number5
Space group name H-MI121
Space group name HallC2y(x,y,-x+z)
Symmetry operation#1: x,y,z
#2: -x,y,-z
#3: x+1/2,y+1/2,z+1/2
#4: -x+1/2,y+1/2,-z+1/2

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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.: 329 / 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: 2.26 Å3/Da / Density % sol: 45.61 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: Ammonium sulfate, Tris, PEG 5000 MME

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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: 1.4→36.37 Å / Num. obs: 60144 / % possible obs: 96.5 % / Redundancy: 6.91 % / Biso Wilson estimate: 13.29 Å2 / CC1/2: 0.985 / Net I/σ(I): 6.9
Reflection shellResolution: 1.4→1.44 Å / Num. unique obs: 4135 / CC1/2: 0.79

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Processing

Software
NameVersionClassification
PHENIX1.18.2refinement
DIALSdata reduction
Aimlessdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.4→30.75 Å / SU ML: 0.1475 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 24.8477
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2316 3054 5.09 %
Rwork0.2201 56955 -
obs0.2207 60009 96.08 %
Solvent computationShrinkage radii: 0.7 Å / VDW probe radii: 1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 20.18 Å2
Refinement stepCycle: LAST / Resolution: 1.4→30.75 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2368 0 0 329 2697
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00182404
X-RAY DIFFRACTIONf_angle_d0.39363242
X-RAY DIFFRACTIONf_chiral_restr0.058373
X-RAY DIFFRACTIONf_plane_restr0.0027425
X-RAY DIFFRACTIONf_dihedral_angle_d12.897894
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.4-1.420.26451360.2912382X-RAY DIFFRACTION89.23
1.42-1.450.27691270.26752425X-RAY DIFFRACTION90.75
1.45-1.470.29391260.2672501X-RAY DIFFRACTION93.49
1.47-1.50.26221380.26162562X-RAY DIFFRACTION94.87
1.5-1.530.23571320.25232584X-RAY DIFFRACTION95.23
1.53-1.560.27851430.24512519X-RAY DIFFRACTION95.38
1.56-1.590.26281300.23492548X-RAY DIFFRACTION95.4
1.59-1.630.24921550.23842568X-RAY DIFFRACTION96.05
1.63-1.670.25551460.24532546X-RAY DIFFRACTION95.87
1.67-1.710.24781590.25342577X-RAY DIFFRACTION96.2
1.71-1.760.26341200.24022609X-RAY DIFFRACTION96.23
1.76-1.820.26311450.23872616X-RAY DIFFRACTION96.91
1.82-1.890.27811340.23392602X-RAY DIFFRACTION96.34
1.89-1.960.22271380.24012584X-RAY DIFFRACTION97.21
1.96-2.050.21671330.22062635X-RAY DIFFRACTION97.36
2.05-2.160.25511340.21732636X-RAY DIFFRACTION97.54
2.16-2.290.22681550.21952631X-RAY DIFFRACTION97.65
2.29-2.470.21531270.21782672X-RAY DIFFRACTION98.07
2.47-2.720.2371500.22792629X-RAY DIFFRACTION98.02
2.72-3.110.25661350.21842674X-RAY DIFFRACTION98.35
3.11-3.920.20741350.19452692X-RAY DIFFRACTION98.16
3.92-30.750.1861560.18782763X-RAY DIFFRACTION99.32
Refinement TLS params.Method: refined / Origin x: -0.37988360264 Å / Origin y: 0.801624256939 Å / Origin z: 21.1627698242 Å
111213212223313233
T0.127949050632 Å2-0.00538944084062 Å2-0.00911666319741 Å2-0.0867232998457 Å20.00283985921357 Å2--0.0884482943291 Å2
L1.01938142697 °20.0794061066381 °2-0.0405203516034 °2-0.729429372238 °20.12925263167 °2--1.4784328461 °2
S0.0275177636772 Å °-0.0711547777718 Å °0.0141823841185 Å °0.0941950211849 Å °-0.00657381387369 Å °-0.00306726481037 Å °0.0501317358773 Å °-0.0841723983614 Å °-0.0170880383858 Å °
Refinement TLS groupSelection details: all

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