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- PDB-7dnt: mRNA-decapping enzyme g5Rp -

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Basic information

Entry
Database: PDB / ID: 7dnt
TitlemRNA-decapping enzyme g5Rp
ComponentsmRNA-decapping protein g5R
KeywordsVIRAL PROTEIN / mRNA-decapping enzyme
Function / homology
Function and homology information


AMP biosynthetic process / diphosphoinositol-polyphosphate diphosphatase activity / bis(5'-nucleosyl)-tetraphosphatase (asymmetrical) activity / diphosphoinositol-polyphosphate diphosphatase / host cell rough endoplasmic reticulum / ATP biosynthetic process / Hydrolases; Acting on ester bonds; Phosphoric-monoester hydrolases / symbiont-mediated suppression of host gene expression / RNA binding / metal ion binding
Similarity search - Function
: / NUDIX hydrolase, conserved site / Nudix box signature. / NUDIX domain / Nudix hydrolase domain profile. / NUDIX hydrolase domain / NUDIX hydrolase-like domain superfamily
Similarity search - Domain/homology
mRNA-decapping protein g5R
Similarity search - Component
Biological speciesAfrican swine fever virus
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.5 Å
AuthorsYang, Y. / Chen, C. / Li, L. / Li, X.H. / Su, D.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)31370735 China
CitationJournal: J.Virol. / Year: 2022
Title: Structural Insight into Molecular Inhibitory Mechanism of InsP 6 on African Swine Fever Virus mRNA-Decapping Enzyme g5Rp.
Authors: Yang, Y. / Zhang, C. / Li, X. / Li, L. / Chen, Y. / Yang, X. / Zhao, Y. / Chen, C. / Wang, W. / Zhong, Z. / Yang, C. / Huang, Z. / Su, D.
History
DepositionDec 10, 2020Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Mar 9, 2022Provider: repository / Type: Initial release
Revision 1.1Dec 28, 2022Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: mRNA-decapping protein g5R


Theoretical massNumber of molelcules
Total (without water)30,4311
Polymers30,4311
Non-polymers00
Water50428
1
A: mRNA-decapping protein g5R

A: mRNA-decapping protein g5R


Theoretical massNumber of molelcules
Total (without water)60,8632
Polymers60,8632
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_665-x+1,-y+1,z1
Buried area3050 Å2
ΔGint1 kcal/mol
Surface area23930 Å2
MethodPISA
Unit cell
Length a, b, c (Å)56.083, 105.113, 49.523
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21212
Components on special symmetry positions
IDModelComponents
11A-309-

HOH

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Components

#1: Protein mRNA-decapping protein g5R / g5Rp / ASFV-DP / Diphosphoinositol polyphosphate phosphohydrolase / DIPP


Mass: 30431.457 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) African swine fever virus (strain Badajoz 1971 Vero-adapted)
Gene: Ba71V-102, D250R / Production host: Escherichia coli (E. coli)
References: UniProt: P32092, Hydrolases; Acting on ester bonds; Phosphoric-monoester hydrolases, diphosphoinositol-polyphosphate diphosphatase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 28 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.44 Å3/Da / Density % sol: 49.58 %
Crystal growTemperature: 289.15 K / Method: vapor diffusion, hanging drop / pH: 5.8
Details: 0.1M sodium citrate tribasic dihydrate (pH 5.8), 0.54M magnesium formate dihydrate, 10% (v/v) 1,2-butanediol as an additive reagent

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Data collection

DiffractionMean temperature: 80 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.9785 Å
DetectorType: RAYONIX MX300HE / Detector: CCD / Date: Jul 11, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9785 Å / Relative weight: 1
ReflectionResolution: 2.499→50 Å / Num. obs: 17165 / % possible obs: 91.7 % / Redundancy: 9.1 % / Rmerge(I) obs: 0.127 / Rpim(I) all: 0.041 / Rrim(I) all: 0.134 / Χ2: 2.049 / Net I/σ(I): 7.9
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
2.5-2.543.40.3052480.920.1570.3460.72748.8
2.54-2.593.60.4283160.8920.2080.480.60360.3
2.59-2.6440.4353720.8970.20.4830.6270.7
2.64-2.694.30.3953960.8470.20.4480.90577
2.69-2.7550.3774510.9710.1530.410.63987.2
2.75-2.825.20.3454600.9610.140.3750.67890.7
2.82-2.897.10.345200.9770.1240.3640.60598.1
2.89-2.968.80.3565180.9830.1210.3770.6899.6
2.96-3.0510.20.3625180.9770.1160.3810.642100
3.05-3.1510.90.2775230.9850.0870.2910.779100
3.15-3.2611.50.2545230.9930.0770.2650.856100
3.26-3.3911.30.1935250.9940.060.2020.99399.8
3.39-3.5511.20.1725250.990.0540.181.28199.8
3.55-3.739.70.1415320.9930.0470.1491.68599.4
3.73-3.9712.20.1175240.9950.0350.1231.91100
3.97-4.2712.20.0965310.9970.0290.12.2899.8
4.27-4.711.70.0885380.9980.0270.0922.67999.8
4.7-5.3810.10.0835450.9980.0270.0873.01499.6
5.38-6.7811.40.1055530.9970.0320.114.499.6
6.78-509.50.0766030.9970.0250.0817.74299.2

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Processing

Software
NameVersionClassification
PHENIX1.15.2_3472refinement
HKL-2000data scaling
PDB_EXTRACT3.27data extraction
HKL-2000data reduction
PHENIXphasing
RefinementMethod to determine structure: SAD / Resolution: 2.5→29.715 Å / SU ML: 0.36 / Cross valid method: THROUGHOUT / σ(F): 1.37 / Phase error: 32.33 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2851 1738 10.13 %
Rwork0.1939 15427 -
obs0.2029 17165 87.66 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 156.48 Å2 / Biso mean: 59.5894 Å2 / Biso min: 19.77 Å2
Refinement stepCycle: final / Resolution: 2.5→29.715 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2026 0 0 28 2054
Biso mean---48.7 -
Num. residues----243
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.5-2.57290.3897650.29755037
2.5729-2.65590.4465980.314184659
2.6559-2.75070.33781290.2844107874
2.7507-2.86080.31691390.2517127286
2.8608-2.99090.31151590.2871146098
2.9909-3.14840.34361640.24911453100
3.1484-3.34540.33581590.22171451100
3.3454-3.60330.29171650.19061471100
3.6033-3.96510.23991660.17681463100
3.9651-4.53720.26051640.1471476100
4.5372-5.70970.27311630.15031452100
5.7097-29.7150.24541670.1782145599
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)
12.39732.06740.87683.03582.50254.1235-0.02120.19760.44280.1013-0.37010.61210.0501-0.17340.12010.14010.0043-0.04280.27550.00620.299321.575240.970213.7124
21.899-1.42741.00243.2026-0.91772.5241-0.372100.03051.6272-0.1038-0.53860.23270.12460.1550.90020.0006-0.10390.30670.0310.334.339141.308332.2987
32.79721.2371-1.18524.93580.24454.8453-0.0514-0.01430.1682-0.23390.04120.63640.45890.0443-0.04550.17810.0012-0.04970.2324-0.01890.381817.731138.380810.4457
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 6 through 42 )A6 - 42
2X-RAY DIFFRACTION2chain 'A' and (resid 43 through 139 )A43 - 139
3X-RAY DIFFRACTION3chain 'A' and (resid 140 through 248 )A140 - 248

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