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- PDB-8zjb: Oomycete Nudix effectors display WY-Nudix conformations with mRNA... -

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Basic information

Entry
Database: PDB / ID: 8zjb
TitleOomycete Nudix effectors display WY-Nudix conformations with mRNA decapping activity
ComponentsNudix hydrolase domain-containing protein
KeywordsHYDROLASE / Avr3b / effector protein
Function / homology
Function and homology information


endopolyphosphatase activity / bis(5'-adenosyl)-hexaphosphatase activity / diphosphoinositol polyphosphate metabolic process / diadenosine pentaphosphate catabolic process / diadenosine hexaphosphate catabolic process / adenosine 5'-(hexahydrogen pentaphosphate) catabolic process / diphosphoinositol-polyphosphate diphosphatase activity / bis(5'-adenosyl)-pentaphosphatase activity / nucleus / metal ion binding / cytoplasm
Similarity search - Function
NUDIX hydrolase, conserved site / Nudix box signature. / NUDIX domain / NUDIX hydrolase domain / NUDIX hydrolase-like domain superfamily
Similarity search - Domain/homology
Nudix hydrolase domain-containing protein
Similarity search - Component
Biological speciesPhytophthora sojae strain P6497 (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.19 Å
AuthorsXing, W. / Xing, W.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC) China
CitationJournal: J Integr Plant Biol / Year: 2024
Title: Oomycete Nudix effectors display WY-Nudix conformation and mRNA decapping activity.
Authors: Guo, B. / Hu, Q. / Wang, B. / Yao, D. / Wang, H. / Kong, G. / Han, C. / Dong, S. / Liu, F. / Xing, W. / Wang, Y.
History
DepositionMay 14, 2024Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Jul 3, 2024Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Nudix hydrolase domain-containing protein
B: Nudix hydrolase domain-containing protein
C: Nudix hydrolase domain-containing protein
D: Nudix hydrolase domain-containing protein
E: Nudix hydrolase domain-containing protein
F: Nudix hydrolase domain-containing protein


Theoretical massNumber of molelcules
Total (without water)163,1446
Polymers163,1446
Non-polymers00
Water00
1
A: Nudix hydrolase domain-containing protein


Theoretical massNumber of molelcules
Total (without water)27,1911
Polymers27,1911
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Nudix hydrolase domain-containing protein


Theoretical massNumber of molelcules
Total (without water)27,1911
Polymers27,1911
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Nudix hydrolase domain-containing protein


Theoretical massNumber of molelcules
Total (without water)27,1911
Polymers27,1911
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Nudix hydrolase domain-containing protein


Theoretical massNumber of molelcules
Total (without water)27,1911
Polymers27,1911
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
5
E: Nudix hydrolase domain-containing protein


Theoretical massNumber of molelcules
Total (without water)27,1911
Polymers27,1911
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
6
F: Nudix hydrolase domain-containing protein


Theoretical massNumber of molelcules
Total (without water)27,1911
Polymers27,1911
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)73.364, 164.496, 169.545
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein
Nudix hydrolase domain-containing protein


Mass: 27190.645 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Details: The first 4 amino acids, the last two amino acids and the amino acids between 102 and 114 are all disordered.
Source: (gene. exp.) Phytophthora sojae strain P6497 (eukaryote)
Gene: PHYSODRAFT_285308 / Production host: Escherichia coli (E. coli) / References: UniProt: G4Z7E8

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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: 3.14 Å3/Da / Density % sol: 60.77 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 8.3
Details: 0.2 M sodium citrate trisbase dihydrate (pH 8.3), 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: BL17U1 / Wavelength: 0.9864 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: May 14, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9864 Å / Relative weight: 1
ReflectionResolution: 3.19→50 Å / Num. obs: 34822 / % possible obs: 99.8 % / Redundancy: 6 % / Biso Wilson estimate: 31.92 Å2 / CC1/2: 0.978 / CC star: 0.994 / Rmerge(I) obs: 0.139 / Rpim(I) all: 0.065 / Rrim(I) all: 0.154 / Net I/σ(I): 21.8
Reflection shellResolution: 3.19→3.26 Å / Redundancy: 6.5 % / Rmerge(I) obs: 1.24 / Num. unique obs: 1668 / CC1/2: 0.604 / CC star: 0.868 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX(1.18.2_3874: ???)refinement
HKL-2000data scaling
DIALSdata reduction
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.19→39.35 Å / SU ML: 0.5 / Cross valid method: THROUGHOUT / σ(F): 0 / Phase error: 30.17 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.3108 1941 5.77 %
Rwork0.2555 --
obs0.2587 33616 96.33 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 3.19→39.35 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9168 0 0 0 9168
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0129302
X-RAY DIFFRACTIONf_angle_d1.36312567
X-RAY DIFFRACTIONf_dihedral_angle_d18.2853338
X-RAY DIFFRACTIONf_chiral_restr0.2321454
X-RAY DIFFRACTIONf_plane_restr0.0071603
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.19-3.270.40521140.32861944X-RAY DIFFRACTION85
3.27-3.360.39651400.32472066X-RAY DIFFRACTION90
3.36-3.460.37741230.30162137X-RAY DIFFRACTION92
3.46-3.570.35141300.2942164X-RAY DIFFRACTION94
3.57-3.70.32511480.25922279X-RAY DIFFRACTION97
3.7-3.850.31161320.25122260X-RAY DIFFRACTION98
3.85-4.020.31311420.26042293X-RAY DIFFRACTION99
4.02-4.230.30821460.25472297X-RAY DIFFRACTION99
4.23-4.50.25791360.22722334X-RAY DIFFRACTION99
4.5-4.840.25381440.21422336X-RAY DIFFRACTION99
4.84-5.330.27821440.21712342X-RAY DIFFRACTION100
5.33-6.10.32481430.25882367X-RAY DIFFRACTION99
6.1-7.670.29331480.25822384X-RAY DIFFRACTION99
7.68-39.350.27491510.22652472X-RAY DIFFRACTION98
Refinement TLS params.Method: refined / Origin x: 11.2895 Å / Origin y: 88.1064 Å / Origin z: 89.7012 Å
111213212223313233
T0.2272 Å20.0062 Å20.1465 Å2-0.1845 Å2-0.0533 Å2--0.1524 Å2
L0.0371 °20.0308 °20.0281 °2-0.3229 °20.3431 °2--0.2315 °2
S0.0136 Å °0.033 Å °0.1281 Å °-0.0368 Å °-0.0941 Å °-0.0047 Å °-0.1857 Å °0.0963 Å °0.0125 Å °
Refinement TLS groupSelection details: all

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