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- PDB-9n3e: Crystal structure of Arabidopsis metacaspase 9 C147G at pH 5.5 -

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Basic information

Entry
Database: PDB / ID: 9n3e
TitleCrystal structure of Arabidopsis metacaspase 9 C147G at pH 5.5
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: 1.55 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

Downloads & links

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Assembly

Deposited unit
A: Metacaspase-9
B: Metacaspase-9


Theoretical massNumber of molelcules
Total (without water)71,0072
Polymers71,0072
Non-polymers00
Water7,188399
1
A: Metacaspase-9


Theoretical massNumber of molelcules
Total (without water)35,5031
Polymers35,5031
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Metacaspase-9


Theoretical massNumber of molelcules
Total (without water)35,5031
Polymers35,5031
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)58.627, 89.046, 64.693
Angle α, β, γ (deg.)90.000, 97.873, 90.000
Int Tables number4
Space group name H-MP1211
Space group name HallP2yb
Symmetry operation#1: x,y,z
#2: -x,y+1/2,-z
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
d_1ens_1chain "A"
d_2ens_1(chain "B" and (resid 6 through 164 or resid 171 through 325))

NCS domain segments:

Ens-ID: ens_1

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
d_11METMETPROPROAA6 - 3256 - 325
d_21METMETSERSERBB6 - 1646 - 164
d_22PROPROPROPROBB171 - 325171 - 325

NCS oper: (Code: givenMatrix: (0.574982981552, 0.753318022156, 0.31922801948), (-0.744310522914, 0.319620909313, 0.586382400664), (0.339700480431, -0.574764675171, 0.744479114395)Vector: -7. ...NCS oper: (Code: given
Matrix: (0.574982981552, 0.753318022156, 0.31922801948), (-0.744310522914, 0.319620909313, 0.586382400664), (0.339700480431, -0.574764675171, 0.744479114395)
Vector: -7.85598915367, -41.9809552135, -4.11087865804)

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Components

#1: Protein Metacaspase-9 / AtMC9


Mass: 35503.340 Da / Num. of mol.: 2 / 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.: 399 / 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: 2.36 Å3/Da / Density % sol: 47.79 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: PEG 5000 MME, sodium acetate, 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: 0.979 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Mar 22, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 1.55→36.77 Å / Num. obs: 93555 / % possible obs: 98.3 % / Redundancy: 6.63 % / CC1/2: 0.996 / Net I/σ(I): 7.8
Reflection shellResolution: 1.55→1.59 Å / Num. unique obs: 6273 / CC1/2: 0.319

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Processing

Software
NameVersionClassification
PHENIX1.18.2refinement
DIALSdata reduction
Aimlessdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.55→29.84 Å / SU ML: 0.2108 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 28.9078
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2404 4674 5.01 %
Rwork0.2326 88563 -
obs0.233 93237 97.85 %
Solvent computationShrinkage radii: 1 Å / VDW probe radii: 1.2 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 27.34 Å2
Refinement stepCycle: LAST / Resolution: 1.55→29.84 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4821 0 0 399 5220
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00164899
X-RAY DIFFRACTIONf_angle_d0.44916605
X-RAY DIFFRACTIONf_chiral_restr0.0418753
X-RAY DIFFRACTIONf_plane_restr0.0028867
X-RAY DIFFRACTIONf_dihedral_angle_d14.46181835
Refine LS restraints NCSType: Torsion NCS / Rms dev position: 0.796066148354 Å
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.55-1.570.41281430.37222470X-RAY DIFFRACTION82.56
1.57-1.590.37111500.36972752X-RAY DIFFRACTION91.49
1.59-1.610.36971510.36392821X-RAY DIFFRACTION95.1
1.61-1.630.39431580.34622918X-RAY DIFFRACTION96.25
1.63-1.650.36291860.33852897X-RAY DIFFRACTION97.66
1.65-1.670.37311850.33432916X-RAY DIFFRACTION97.79
1.67-1.690.33171500.32242948X-RAY DIFFRACTION97.3
1.69-1.720.27141670.31242944X-RAY DIFFRACTION98.14
1.72-1.750.3511640.30952936X-RAY DIFFRACTION98.07
1.75-1.770.2821480.30762951X-RAY DIFFRACTION97.95
1.77-1.80.30431680.29082915X-RAY DIFFRACTION98.06
1.8-1.840.29131500.29272988X-RAY DIFFRACTION98.52
1.84-1.870.30971450.28562940X-RAY DIFFRACTION98.63
1.87-1.910.30591480.27533000X-RAY DIFFRACTION98.47
1.91-1.950.291790.27382942X-RAY DIFFRACTION98.11
1.95-20.28911470.26292941X-RAY DIFFRACTION98.66
2-2.050.25841350.24793005X-RAY DIFFRACTION98.9
2.05-2.10.23021630.24783004X-RAY DIFFRACTION98.88
2.1-2.170.28831380.23923001X-RAY DIFFRACTION99.12
2.17-2.240.25341540.24632999X-RAY DIFFRACTION99.24
2.24-2.320.21211460.23943008X-RAY DIFFRACTION99.31
2.32-2.410.24111570.24152988X-RAY DIFFRACTION99.46
2.41-2.520.22621510.23293006X-RAY DIFFRACTION99.62
2.52-2.650.22871660.23512998X-RAY DIFFRACTION99.37
2.65-2.820.2421620.23323033X-RAY DIFFRACTION99.41
2.82-3.030.27081470.23223008X-RAY DIFFRACTION99.81
3.03-3.340.21841450.20673052X-RAY DIFFRACTION99.88
3.34-3.820.19161500.18963049X-RAY DIFFRACTION99.97
3.82-4.810.17121520.16553048X-RAY DIFFRACTION99.88
4.81-29.840.17691690.18323085X-RAY DIFFRACTION99.69
Refinement TLS params.Method: refined / Origin x: 11.0511055043 Å / Origin y: -20.7026441211 Å / Origin z: 16.1096258199 Å
111213212223313233
T0.149656581977 Å20.0186044885222 Å2-0.00367196208981 Å2-0.225947864235 Å2-0.013700338061 Å2--0.146266999936 Å2
L0.368356640276 °20.1724945969 °20.125877329942 °2-0.590663785297 °20.0508651634661 °2--0.193085027596 °2
S-0.0186830222928 Å °-0.0985407955643 Å °0.0436743891385 Å °-0.0289569982597 Å °0.00750904060218 Å °0.0489576760903 Å °-0.0206136642275 Å °-0.0710724296449 Å °0.0121608938742 Å °
Refinement TLS groupSelection details: all

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