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- PDB-22yz: Crystal structure of RipNE220A(82-474) from Ralstonia solanacearum -

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Basic information

Entry
Database: PDB / ID: 22yz
TitleCrystal structure of RipNE220A(82-474) from Ralstonia solanacearum
ComponentsType III effector protein
KeywordsHYDROLASE / Nudix effector Ralstonia solanacearum / RipN
Function / homologyNUDIX hydrolase, conserved site / Nudix box signature. / NUDIX hydrolase-like domain superfamily / hydrolase activity / ACETATE ION / Type III effector protein
Function and homology information
Biological speciesRalstonia nicotianae
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsGe, H.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC) China
CitationJournal: Biochem.Biophys.Res.Commun. / Year: 2026
Title: Structural basis of dinucleotide substrate recognition and catalysis by the Nudix effector RipN from Ralstonia solanacearum.
Authors: Chen, X. / Zhou, Z. / Lu, L. / Xiao, C. / Cao, L. / Cao, Y. / Ge, H. / Wang, W. / Gao, J.
History
DepositionJan 28, 2026Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Mar 11, 2026Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Type III effector protein
B: Type III effector protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)87,3835
Polymers87,1402
Non-polymers2433
Water11,367631
1
A: Type III effector protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,7213
Polymers43,5701
Non-polymers1512
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Type III effector protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,6622
Polymers43,5701
Non-polymers921
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)127.106, 127.106, 102.852
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221
Components on special symmetry positions
IDModelComponents
11A-763-

HOH

21B-633-

HOH

31B-739-

HOH

41B-745-

HOH

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Components

#1: Protein Type III effector protein / RipN


Mass: 43569.785 Da / Num. of mol.: 2 / Mutation: E220A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Ralstonia nicotianae (strain ATCC BAA-1114 / GMI1000) (bacteria)
Gene: RSp1130 / Production host: Escherichia coli (E. coli) / References: UniProt: Q8XQT8
#2: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#3: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H3O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 631 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
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: 2.75 Å3/Da / Density % sol: 55.31 %
Crystal growTemperature: 287 K / Method: vapor diffusion, hanging drop / Details: 0.2 M ammonium acetate, 28% (w/v) PEG 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL18U1 / Wavelength: 0.9793 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Oct 29, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
ReflectionResolution: 1.8→50 Å / Num. obs: 88786 / % possible obs: 100 % / Redundancy: 19.8 % / CC1/2: 1 / Net I/σ(I): 24
Reflection shellResolution: 1.8→1.85 Å / Num. unique obs: 6514 / CC1/2: 0.73

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Processing

Software
NameVersionClassification
REFMAC5.8.0415refinement
autoPXdata processing
PHASERphasing
autoPXdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.8→20 Å / Cor.coef. Fo:Fc: 0.971 / Cor.coef. Fo:Fc free: 0.959 / SU B: 7.081 / SU ML: 0.091 / Cross valid method: THROUGHOUT / ESU R: 0.139 / ESU R Free: 0.098 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.19802 4525 5.1 %RANDOM
Rwork0.16399 ---
obs0.16573 84139 99.77 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 35.337 Å2
Baniso -1Baniso -2Baniso -3
1--0.43 Å2-0.21 Å2-0 Å2
2---0.43 Å20 Å2
3---1.38 Å2
Refinement stepCycle: 1 / Resolution: 1.8→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5494 0 16 631 6141
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0125600
X-RAY DIFFRACTIONr_bond_other_d0.0010.0165336
X-RAY DIFFRACTIONr_angle_refined_deg1.311.6477592
X-RAY DIFFRACTIONr_angle_other_deg0.4521.57312232
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.7415718
X-RAY DIFFRACTIONr_dihedral_angle_2_deg4.787538
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.54110932
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.0640.2863
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.026799
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021277
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it2.1863.6512873
X-RAY DIFFRACTIONr_mcbond_other2.1863.652872
X-RAY DIFFRACTIONr_mcangle_it2.8376.5443587
X-RAY DIFFRACTIONr_mcangle_other2.8396.5463588
X-RAY DIFFRACTIONr_scbond_it2.6084.1072727
X-RAY DIFFRACTIONr_scbond_other2.6084.1062728
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other3.3947.324005
X-RAY DIFFRACTIONr_long_range_B_refined3.8536.196491
X-RAY DIFFRACTIONr_long_range_B_other3.76635.286324
X-RAY DIFFRACTIONr_rigid_bond_restr4.543310936
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.8→1.846 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.315 391 -
Rwork0.287 5961 -
obs--98.33 %

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