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- PDB-9j7j: The crystal structure of RipG4 LRR domain -

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Basic information

Entry
Database: PDB / ID: 9j7j
TitleThe crystal structure of RipG4 LRR domain
ComponentsGALA protein
KeywordsIMMUNOSUPPRESSANT / Bacteria type3 secretion system / Bacteria effector protein / GALA family / Ralstonia solanacearum effector. LRR domain
Function / homology
Function and homology information


: / Leucine-rich repeat, cysteine-containing subtype / Leucine-rich repeat - CC (cysteine-containing) subfamily / Leucine rich repeat, ribonuclease inhibitor type / Leucine Rich repeat / Leucine rich repeat / Leucine-rich repeat profile. / Leucine-rich repeat / Leucine-rich repeat domain superfamily
Similarity search - Domain/homology
GALA4 type III effector
Similarity search - Component
Biological speciesRalstonia solanacearum UW551 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.35 Å
AuthorsJung, E.H. / Kim, M.S.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: To Be Published
Title: The crystal structure of RipG4 LRR domain
Authors: Jung, E.H. / Kim, M.S.
History
DepositionAug 19, 2024Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Sep 3, 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: GALA protein


Theoretical massNumber of molelcules
Total (without water)37,2431
Polymers37,2431
Non-polymers00
Water00
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)188.846, 188.846, 108.239
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number179
Space group name H-MP6522

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Components

#1: Protein GALA protein / GALA4 type III effector


Mass: 37242.652 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Ralstonia solanacearum UW551 (bacteria)
Gene: QQO21_16795 / Production host: Escherichia coli (E. coli) / References: UniProt: F5CT18
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: 7.48 Å3/Da / Density % sol: 83.56 %
Crystal growTemperature: 277.15 K / Method: vapor diffusion, hanging drop
Details: 0.1M BIS-TRIS propane pH 7.5, 1.5M ammonium tartrate dibasic

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: PAL/PLS / Beamline: 5C (4A) / Wavelength: 1 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Feb 29, 2024
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 3.35→50 Å / Num. obs: 16806 / % possible obs: 99.69 % / Redundancy: 19.9 % / CC1/2: 0.997 / Rmerge(I) obs: 0.097 / Rpim(I) all: 0.022 / Rrim(I) all: 0.099 / Rsym value: 0.041 / Net I/σ(I): 28.78
Reflection shellResolution: 3.35→3.41 Å / Num. unique obs: 16806 / CC1/2: 0.997

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Processing

Software
NameVersionClassification
PHENIX1.20.1-4487refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIX1.20.1-4487phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.35→38.25 Å / SU ML: 0.51 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 29.45 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2637 833 5.01 %
Rwork0.2239 --
obs0.2259 16806 99.69 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 3.35→38.25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2608 0 0 0 2608
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.35-3.560.34991330.30942531X-RAY DIFFRACTION98
3.56-3.830.31421350.26882583X-RAY DIFFRACTION99
3.83-4.220.27951380.24452599X-RAY DIFFRACTION99
4.22-4.830.26781380.21622635X-RAY DIFFRACTION100
4.83-6.080.26021410.25092664X-RAY DIFFRACTION99
6.08-38.250.23251480.18412796X-RAY DIFFRACTION99

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