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- PDB-7l7v: Crystal structure of Arabidopsis NRG1.1 CC-R domain K94E/K96E/R99... -

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Basic information

Entry
Database: PDB / ID: 7l7v
TitleCrystal structure of Arabidopsis NRG1.1 CC-R domain K94E/K96E/R99E/K100E/R103E/K106E/K110E mutant
ComponentsProbable disease resistance protein At5g66900
KeywordsIMMUNE SYSTEM / 4-helix bundle / cell death / membrane pore / calcium channel
Function / homology
Function and homology information


endomembrane system / defense response to fungus / ubiquitin binding / ADP binding / ATP binding / cytosol
Similarity search - Function
Powdery mildew resistance protein, RPW8 domain / Disease resistance protein, RPW8-like / Arabidopsis broad-spectrum mildew resistance protein RPW8 / RPW8 domain profile. / Apoptotic protease-activating factors, helical domain / NB-ARC / NB-ARC domain / Leucine rich repeat / Leucine-rich repeat / Leucine-rich repeat domain superfamily ...Powdery mildew resistance protein, RPW8 domain / Disease resistance protein, RPW8-like / Arabidopsis broad-spectrum mildew resistance protein RPW8 / RPW8 domain profile. / Apoptotic protease-activating factors, helical domain / NB-ARC / NB-ARC domain / Leucine rich repeat / Leucine-rich repeat / Leucine-rich repeat domain superfamily / Winged helix-like DNA-binding domain superfamily / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
Probable disease resistance protein At5g66900
Similarity search - Component
Biological speciesArabidopsis thaliana (thale cress)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.95 Å
AuthorsWalton, W.G. / Wan, L. / Lietzan, A.D. / Redinbo, M.R. / Dangl, J.L.
Funding support United States, 2items
OrganizationGrant numberCountry
National Science Foundation (NSF, United States)IOS-1758400 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)RO1GM107444 United States
CitationJournal: Science / Year: 2021
Title: Plant "helper" immune receptors are Ca 2+ -permeable nonselective cation channels.
Authors: Jacob, P. / Kim, N.H. / Wu, F. / El-Kasmi, F. / Chi, Y. / Walton, W.G. / Furzer, O.J. / Lietzan, A.D. / Sunil, S. / Kempthorn, K. / Redinbo, M.R. / Pei, Z.M. / Wan, L. / Dangl, J.L.
History
DepositionDec 30, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 16, 2021Provider: repository / Type: Initial release
Revision 1.1Jul 14, 2021Group: Database references / Category: citation / citation_author
Item: _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.name
Revision 1.2Jul 28, 2021Group: Database references / Category: citation_author / Item: _citation_author.identifier_ORCID
Revision 1.3Sep 1, 2021Group: Database references / Category: database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.4Sep 8, 2021Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Probable disease resistance protein At5g66900
B: Probable disease resistance protein At5g66900
C: Probable disease resistance protein At5g66900
D: Probable disease resistance protein At5g66900
E: Probable disease resistance protein At5g66900
F: Probable disease resistance protein At5g66900


Theoretical massNumber of molelcules
Total (without water)95,1676
Polymers95,1676
Non-polymers00
Water0
1
A: Probable disease resistance protein At5g66900
E: Probable disease resistance protein At5g66900
F: Probable disease resistance protein At5g66900


Theoretical massNumber of molelcules
Total (without water)47,5833
Polymers47,5833
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Probable disease resistance protein At5g66900
C: Probable disease resistance protein At5g66900
D: Probable disease resistance protein At5g66900


Theoretical massNumber of molelcules
Total (without water)47,5833
Polymers47,5833
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)84.332, 89.656, 149.398
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21221
Symmetry operation#1: x,y,z
#2: x+1/2,-y,-z+1/2
#3: -x,y,-z
#4: -x+1/2,-y,z+1/2

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Components

#1: Protein
Probable disease resistance protein At5g66900


Mass: 15861.127 Da / Num. of mol.: 6 / Mutation: K94E, K96E, R99E, K100E, R103E, K106E, K110E
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Gene: At5g66900, MUD21.16 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9FKZ1

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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: 2.95 Å3/Da / Density % sol: 58.32 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / Details: 0.1M MES (pH 5.5), 1 M Potassium Sodium Tartrate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-D / Wavelength: 1.03317 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Apr 4, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.03317 Å / Relative weight: 1
ReflectionResolution: 2.95→40 Å / Num. obs: 24727 / % possible obs: 99.8 % / Redundancy: 11.7 % / Rmerge(I) obs: 0.13 / Rpim(I) all: 0.039 / Rrim(I) all: 0.135 / Χ2: 0.727 / Net I/σ(I): 4.9 / Num. measured all: 289192
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
2.95-38.51.68712180.5060.5941.7930.412100
3-3.069.71.59112000.6120.5221.6770.42899.1
3.06-3.1110.31.28112270.7270.4081.3470.422100
3.11-3.1810.61.10812000.7960.3471.1630.41698.8
3.18-3.2511.70.97812090.8480.291.0210.419100
3.25-3.3211.50.75112220.8960.2240.7850.4499.4
3.32-3.4111.70.60912050.9270.1810.6360.45799.7
3.41-3.512.30.49912170.9540.1440.520.46399.8
3.5-3.612.30.36712200.9740.1070.3820.48499.6
3.6-3.7212.10.29912310.9820.0880.3120.54499.7
3.72-3.8511.60.20812280.9890.0640.2180.578100
3.85-412.30.16912140.9940.050.1760.6599.8
4-4.18120.12912400.9960.0390.1350.72799.8
4.18-4.4112.90.10812320.9960.0310.1130.84799.8
4.41-4.68130.09112420.9980.0260.0950.90199.9
4.68-5.0412.20.08612450.9980.0260.090.98599.8
5.04-5.5512.60.09212570.9970.0270.0960.933100
5.55-6.35130.08712570.9980.0250.090.96699.9
6.35-7.9912.10.06212920.9990.0190.0651.231100
7.99-4011.40.04513710.9990.0140.0471.76699.9

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Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
DENZOdata reduction
SCALEPACKdata scaling
AutoSolphasing
RefinementMethod to determine structure: SAD / Resolution: 2.95→39.61 Å / Cor.coef. Fo:Fc: 0.943 / Cor.coef. Fo:Fc free: 0.928 / SU B: 37.214 / SU ML: 0.294 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 1.015 / ESU R Free: 0.344 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.2403 1285 5.3 %RANDOM
Rwork0.2194 ---
obs0.2205 23168 99.63 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 227.15 Å2 / Biso mean: 84.591 Å2 / Biso min: 43.14 Å2
Baniso -1Baniso -2Baniso -3
1--1.43 Å20 Å2-0 Å2
2---1.71 Å20 Å2
3---3.14 Å2
Refinement stepCycle: final / Resolution: 2.95→39.61 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5239 0 0 0 5239
Num. residues----665
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0135321
X-RAY DIFFRACTIONr_bond_other_d0.0010.0174988
X-RAY DIFFRACTIONr_angle_refined_deg1.6281.6367198
X-RAY DIFFRACTIONr_angle_other_deg1.6511.57711480
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.3375658
X-RAY DIFFRACTIONr_dihedral_angle_2_deg29.2624.449272
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.67415955
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.731522
X-RAY DIFFRACTIONr_chiral_restr0.0920.2722
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.025937
X-RAY DIFFRACTIONr_gen_planes_other0.0020.021123
LS refinement shellResolution: 2.95→3.027 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.362 83 -
Rwork0.34 1670 -
all-1753 -
obs--98.21 %
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)
16.439-2.48963.06723.6111-1.066.11380.2307-0.1071-0.24130.0005-0.1441-0.15860.35360.4719-0.08660.0578-0.02470.03650.1752-0.01550.120917.4044-27.8633-11.8637
24.69241.66152.87566.00153.72245.4587-0.10210.4708-0.1694-0.73580.01350.05550.0407-0.10830.08860.23010.01440.04230.26050.04870.121927.2054-32.0908-38.0538
31.2348-3.1195-0.319613.83742.24510.6213-0.2458-0.13510.29560.39440.06470.6354-0.4013-0.17920.18111.01870.1850.02540.47530.01730.431533.64415.8475-14.4545
49.8776-2.99963.27243.1294-1.22333.76480.0883-0.0402-0.1845-0.03440.0039-0.27440.04960.4498-0.09220.0661-0.04650.04110.2593-0.09680.103361.8281-27.8257-13.9145
52.9743-3.7161-0.002414.02261.98950.5881-0.2598-0.17650.62660.35120.04730.4389-0.3347-0.1820.21240.79510.16220.01630.40780.03390.3151-11.94435.4023-17.8162
64.49111.86912.80777.85522.18134.6613-0.49740.5756-0.2966-1.80760.37990.46190.6143-0.24960.11750.9427-0.26340.02390.45170.02090.1432-14.4337-32.326-40.0175
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A2 - 122
2X-RAY DIFFRACTION2B18 - 126
3X-RAY DIFFRACTION3C19 - 127
4X-RAY DIFFRACTION4D17 - 121
5X-RAY DIFFRACTION5E19 - 126
6X-RAY DIFFRACTION6F2 - 117

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