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- PDB-7dvg: Crystal structure of rice immune receptor RGA5-HMA5 mutant. -

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Basic information

Entry
Database: PDB / ID: 7dvg
TitleCrystal structure of rice immune receptor RGA5-HMA5 mutant.
ComponentsDisease resistance protein RGA5
KeywordsPLANT PROTEIN / Immune receptor
Function / homology
Function and homology information


plant-type hypersensitive response / innate immune response-activating signaling pathway / ADP binding / : / defense response to bacterium / ATP binding / metal ion binding / cytoplasm
Similarity search - Function
Rx, N-terminal / Rx N-terminal domain / Disease resistance protein, plants / Apoptotic protease-activating factors, helical domain / NB-ARC / NB-ARC domain / Heavy-metal-associated domain profile. / Heavy metal-associated domain, HMA / Leucine-rich repeat domain superfamily / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
Disease resistance protein RGA5
Similarity search - Component
Biological speciesOryza sativa subsp. japonica (Japanese rice)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.8 Å
AuthorsZhang, X. / Liu, J.F.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)32030089 China
CitationJournal: To Be Published
Title: Crystal structure of rice immune receptor RGA5-HMA5.
Authors: Zhang, X. / Liu, J.F.
History
DepositionJan 13, 2021Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jan 19, 2022Provider: repository / Type: Initial release
Revision 1.1Nov 29, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Disease resistance protein RGA5
B: Disease resistance protein RGA5


Theoretical massNumber of molelcules
Total (without water)15,8132
Polymers15,8132
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1120 Å2
ΔGint-8 kcal/mol
Surface area7760 Å2
Unit cell
Length a, b, c (Å)65.995, 65.995, 132.142
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number96
Space group name H-MP43212
Space group name HallP4nw2abw

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Components

#1: Protein Disease resistance protein RGA5 / / Os11gRGA5 / SasRGA5


Mass: 7906.425 Da / Num. of mol.: 2 / Mutation: G1009D, M1016V, S1027V, V1039E
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Oryza sativa subsp. japonica (Japanese rice)
Gene: RGA5 / Production host: Escherichia coli (E. coli) / References: UniProt: F7J0N2

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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: 4.55 Å3/Da / Density % sol: 72.96 %
Description: THE ENTRY CONTAINS FRIEDEL PAIRS IN F_PLUS/MINUS COLUMNS.
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / Details: 0.2 M ammonium nitrate, 20 % (w/v) PEG 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.9786 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Jun 16, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9786 Å / Relative weight: 1
ReflectionResolution: 2.8→33.1 Å / Num. obs: 13666 / % possible obs: 99.52 % / Redundancy: 12.1 % / Biso Wilson estimate: 81.05 Å2 / CC1/2: 0.99 / Rmerge(I) obs: 0.11 / Rrim(I) all: 0.11 / Net I/σ(I): 13.2
Reflection shellResolution: 2.8→2.9 Å / Rmerge(I) obs: 0.84 / Num. unique obs: 736 / CC1/2: 0.86

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
PHENIX1.13_2998refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
PDB_EXTRACT3.27data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5ZNE

5zne


Resolution: 2.8→33.04 Å / SU ML: 0.2973 / Cross valid method: THROUGHOUT / σ(F): 0.39 / Phase error: 30.1598 / Stereochemistry target values: GeoStd + Monomer Library
RfactorNum. reflection% reflection
Rfree0.2333 654 4.79 %
Rwork0.1997 13010 -
obs0.2013 13664 99.61 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 91.55 Å2
Refinement stepCycle: LAST / Resolution: 2.8→33.04 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1098 0 0 0 1098
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00911102
X-RAY DIFFRACTIONf_angle_d1.04681484
X-RAY DIFFRACTIONf_chiral_restr0.0568192
X-RAY DIFFRACTIONf_plane_restr0.0044186
X-RAY DIFFRACTIONf_dihedral_angle_d13.9927700
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.8-3.020.38921520.32262587X-RAY DIFFRACTION99.35
3.02-3.320.35731390.28432576X-RAY DIFFRACTION99.63
3.32-3.80.34021190.22262611X-RAY DIFFRACTION99.53
3.8-4.790.16251270.1622604X-RAY DIFFRACTION99.74
4.79-33.040.20081170.18062632X-RAY DIFFRACTION99.78
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)
16.17717299849-1.949978657180.2376452219448.384454102513.431663895339.00905175841-0.2672606966960.165562564134-0.3665746307530.3863539812060.205606859385-0.4022428672410.750630574822-0.3068600179530.09430034031380.617378432372-0.07369180036570.04049047589210.7100501195020.09220282902230.538816680517-16.061207022-5.9557635238310.5721203371
29.26733641518-4.23784659129-2.602326260014.25512330587-1.81786618234.85205668795-0.4567004839410.1582283125350.360636634034-0.1008481526190.2667855594880.63999032356-0.600124409745-0.397567505220.1523849655130.657787077801-0.04388941539450.01026694396370.6527896978210.02252110606350.567042502217-20.1915171469-0.72429940982110.8356566539
38.60933834388-4.491117066260.008223971734975.87217381238-3.195779656462.88661218272-0.930570799886-0.6064070605541.545944156250.749263046359-0.109772261668-2.29791933454-0.3702374551170.5872330768230.6435229536830.708884683003-0.0556249414733-0.2310050681340.7118179669870.05984209674990.740619387189-8.42803074024-0.5469312417147.05736886738
42.146880560640.665494869382-1.82801528730.717536288011-0.7700439965253.70920877415-0.03185202548520.1502880054080.1450559941551.050459364850.0349832591364-0.0697060063607-0.521520517742-0.200656269465-0.05877116166380.910525250005-0.040048862311-0.1122035801730.6912782274-0.003463481477060.621694732884-19.36412169412.108832408412.90293686175
55.178586852462.3810573851-2.904100156473.9020571076-4.487644139477.87757304636-0.07754391921370.0801005753389-0.84011094758-0.592152811875-0.658088962176-0.5400778105950.3548558339410.7115462491230.7294937647980.8385896193340.1175436306680.08770615699480.7825683952050.03468174149820.632307149012-25.7711704356-16.410825714926.9780407772
63.423698031030.968897359262-1.33883546226.8656329653.025752162099.48912432166-0.005824149091721.288787542440.58814415614-0.530501337255-0.2129054119810.0238118997897-0.798678314511.05320062060.2916193447930.671930424332-0.005452033281680.07914702665010.7671744630210.09867311847120.697742649864-24.5031047213-9.6830569826527.0963680281
73.811678303223.81140025494-2.174661967413.88780467576-2.994149473778.14090081087-0.5091476893740.770605190665-0.874769411271-0.2253838769880.197072690807-1.707707537681.621679366431.762354067370.6328922421720.8967858790320.250999143480.1230735004351.111478019880.1952497190071.00965395172-16.2808576976-18.204798230423.3898121541
87.856800260480.2118945222190.3283692248770.109188864350.1298506985162.56060903494-0.2085736981820.605665188595-0.3842874632150.448738218885-0.14562154962-0.0087459758331-0.2752288739880.6754298937710.4140467682140.904563234604-0.03674193108310.02904127407630.9317628533690.06315669970160.523361212805-22.039632128-8.4205767572319.3184571548
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 997 through 1021 )
2X-RAY DIFFRACTION2chain 'A' and (resid 1022 through 1046 )
3X-RAY DIFFRACTION3chain 'A' and (resid 1047 through 1058 )
4X-RAY DIFFRACTION4chain 'A' and (resid 1059 through 1069 )
5X-RAY DIFFRACTION5chain 'B' and (resid 997 through 1021 )
6X-RAY DIFFRACTION6chain 'B' and (resid 1022 through 1046 )
7X-RAY DIFFRACTION7chain 'B' and (resid 1047 through 1058 )
8X-RAY DIFFRACTION8chain 'B' and (resid 1059 through 1069 )

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