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- PDB-22za: crystal structures of RipN from Ralstonia solanacearum -

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Basic information

Entry
Database: PDB / ID: 22za
Titlecrystal structures of RipN 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 / Type III effector protein
Function and homology information
Biological speciesRalstonia nicotianae
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.278 Å
AuthorsGe, H.
Funding support China, 1items
OrganizationGrant numberCountry
National Science Foundation (NSF, China) 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)104,4548
Polymers104,3082
Non-polymers1466
Water4,306239
1
A: Type III effector protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)52,2274
Polymers52,1541
Non-polymers733
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Type III effector protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)52,2274
Polymers52,1541
Non-polymers733
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)127.355, 127.355, 104.917
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
11B-683-

HOH

21B-701-

HOH

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Components

#1: Protein Type III effector protein / RipN


Mass: 52154.199 Da / Num. of mol.: 2
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-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Mg / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 239 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
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: 2.35 Å3/Da / Density % sol: 47.76 %
Crystal growTemperature: 287 K / Method: vapor diffusion, hanging drop
Details: 0.1 M sodium cacodylate pH 6.1, 0.2 M magnesium acetate, 20% PEG 8000, 10 mM magnesium chloride

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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: Jun 5, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
ReflectionResolution: 2.278→50 Å / Num. obs: 45219 / % possible obs: 100 % / Redundancy: 11.9 % / CC1/2: 1 / Net I/σ(I): 16.8
Reflection shellResolution: 2.278→2.32 Å / Num. unique obs: 2251 / CC1/2: 0.96

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Processing

Software
NameVersionClassification
REFMAC5.8.0415refinement
autoPROCdata processing
autoPXdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.278→20 Å / Cor.coef. Fo:Fc: 0.867 / Cor.coef. Fo:Fc free: 0.837 / SU B: 18.889 / SU ML: 0.223 / Cross valid method: THROUGHOUT / ESU R: 0.386 / ESU R Free: 0.269 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.29018 2025 5 %RANDOM
Rwork0.26426 ---
obs0.26555 38540 89.66 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 36.751 Å2
Baniso -1Baniso -2Baniso -3
1-0.65 Å20.32 Å2-0 Å2
2--0.65 Å2-0 Å2
3----2.1 Å2
Refinement stepCycle: 1 / Resolution: 2.278→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5505 0 6 239 5750
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0125593
X-RAY DIFFRACTIONr_bond_other_d0.0010.0165313
X-RAY DIFFRACTIONr_angle_refined_deg1.5431.6487587
X-RAY DIFFRACTIONr_angle_other_deg0.5811.57212183
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.0695718
X-RAY DIFFRACTIONr_dihedral_angle_2_deg2.939538
X-RAY DIFFRACTIONr_dihedral_angle_3_deg21.18110928
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.070.2861
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.026795
X-RAY DIFFRACTIONr_gen_planes_other0.0020.021273
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_it2.6122.0712878
X-RAY DIFFRACTIONr_mcbond_other2.6072.0712878
X-RAY DIFFRACTIONr_mcangle_it3.9343.7153594
X-RAY DIFFRACTIONr_mcangle_other3.9333.7163595
X-RAY DIFFRACTIONr_scbond_it2.5812.2342715
X-RAY DIFFRACTIONr_scbond_other2.5812.2342716
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other4.034.0063994
X-RAY DIFFRACTIONr_long_range_B_refined6.68520.26366
X-RAY DIFFRACTIONr_long_range_B_other6.66520.116346
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.278→2.337 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.345 96 -
Rwork0.284 2027 -
obs--65.54 %
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)
11.01080.2239-0.08190.27970.08140.0513-0.10410.0873-0.00130.00280.07310.04260.01310.00250.0310.07350.04720.00430.23940.02360.22229.326759.97270.1634
20.6863-0.2223-0.01920.56940.03380.0251-0.05450.1512-0.1590.01210.03280.1527-0.02170.02160.02180.05220.02130.00830.1998-0.0350.2831-3.8147.39090.5863
31.5938-0.58150.10550.9410.11240.0463-0.0748-0.1536-0.04570.11250.02750.08160.0055-0.04490.04730.05160.07530.02140.1923-0.03840.223-5.528252.69757.1704
42.215-3.4427-4.403710.18555.44549.1653-0.0127-0.0105-0.1739-0.043-0.27030.59380.0320.11860.28290.00470.0089-0.02970.10820.03580.3115-6.25174.78933.4934
50.75830.3788-0.72243.2528-1.8051.3754-0.2013-0.0733-0.35610.65510.20350.5268-0.1335-0.0013-0.00220.3110.17370.19290.2048-0.04720.461115.213891.60537.3626
60.3748-0.19640.06291.0472-0.02410.0128-0.0192-0.02020.07970.124-0.0087-0.0329-0.0012-0.01150.02790.1440.107-0.0020.16010.01030.243126.392393.3047-0.6143
71.8438-0.1054-0.02470.569-0.15130.05890.01310.14460.32480.0314-0.0335-0.17730.00520.01030.02040.07840.0752-0.07240.092-0.01780.372435.6302112.9861-2.5453
81.07931.30830.03111.70270.20171.7354-0.17940.1271-0.1187-0.13320.08260.0353-0.06520.01060.09690.13220.07940.02580.1542-0.12630.332813.2185100.0426-10.5936
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A102 - 209
2X-RAY DIFFRACTION2A210 - 351
3X-RAY DIFFRACTION3A352 - 451
4X-RAY DIFFRACTION4A452 - 460
5X-RAY DIFFRACTION5B100 - 120
6X-RAY DIFFRACTION6B121 - 283
7X-RAY DIFFRACTION7B284 - 408
8X-RAY DIFFRACTION8B409 - 460

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