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- PDB-8iib: Crystal structure of Israeli acute paralysis virus RNA-dependent ... -

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Basic information

Entry
Database: PDB / ID: 8iib
TitleCrystal structure of Israeli acute paralysis virus RNA-dependent RNA polymerase delta85 mutant (residues 86-546)
ComponentsPolymerase polyprotein
KeywordsTRANSFERASE / RNA-dependent RNA polymerase
Function / homology:
Function and homology information
Biological speciesIsraeli acute paralysis virus
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.69 Å
AuthorsFang, X. / Lu, G. / Hou, C. / Gong, P.
Funding support China, 2items
OrganizationGrant numberCountry
Ministry of Science and Technology (MoST, China)2018YFA0507200 China
National Natural Science Foundation of China (NSFC)31802147 China
CitationJournal: Virol Sin / Year: 2023
Title: Unusual substructure conformations observed in crystal structures of a dicistrovirus RNA-dependent RNA polymerase suggest contribution of the N-terminal extension in proper folding.
Authors: Fang, X. / Lu, G. / Deng, Y. / Yang, S. / Hou, C. / Gong, P.
History
DepositionFeb 24, 2023Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jun 7, 2023Provider: repository / Type: Initial release
Revision 1.1Aug 30, 2023Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Polymerase polyprotein
B: Polymerase polyprotein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)110,66921
Polymers109,7772
Non-polymers89219
Water2,882160
1
A: Polymerase polyprotein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)55,41610
Polymers54,8881
Non-polymers5289
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Polymerase polyprotein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)55,25311
Polymers54,8881
Non-polymers36510
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)150.510, 150.510, 104.626
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number152
Space group name H-MP3121
Components on special symmetry positions
IDModelComponents
11A-725-

HOH

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Components

#1: Protein Polymerase polyprotein


Mass: 54888.414 Da / Num. of mol.: 2 / Mutation: N510D
Source method: isolated from a genetically manipulated source
Details: GB:MG599488.1 / Source: (gene. exp.) Israeli acute paralysis virus / Production host: Escherichia coli (E. coli)
#2: Chemical
ChemComp-CD / CADMIUM ION


Mass: 112.411 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Cd / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Mg
#4: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: Cl / Feature type: SUBJECT OF INVESTIGATION
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 160 / 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: 3.12 Å3/Da / Density % sol: 60.53 %
Crystal growTemperature: 289 K / Method: evaporation / pH: 8.5 / Details: PEG 4000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U1 / Wavelength: 0.9792 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Dec 6, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 2.69→23.8 Å / Num. obs: 38083 / % possible obs: 100 % / Redundancy: 10.1 % / Rmerge(I) obs: 0.041 / Rpim(I) all: 0.014 / Rrim(I) all: 0.043 / Χ2: 0.922 / Net I/σ(I): 16.2
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
2.69-2.810.60.71337460.9310.2290.7490.966100
2.8-2.9110.50.46737930.9630.1510.490.971100
2.91-3.0410.30.29737480.9860.0970.3130.973100
3.04-3.29.90.18337880.9930.0610.1940.949100
3.2-3.49.70.10737880.9960.0360.1130.9399.9
3.4-3.6610.60.07237830.9980.0230.0760.907100
3.66-4.0310.40.04938020.9990.0160.0510.795100
4.03-4.619.90.03638260.9990.0120.0380.989100
4.61-5.799.90.02938550.9990.010.0310.75199.9
5.79-23.89.60.0239540.9990.0070.0210.99599.6

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Processing

Software
NameVersionClassification
PHENIX1.17refinement
HKL-2000data scaling
PDB_EXTRACT3.27data extraction
HKL-2000data reduction
PHENIXphasing
RefinementMethod to determine structure: SAD / Resolution: 2.69→23.41 Å / SU ML: 0.31 / Cross valid method: THROUGHOUT / σ(F): 1.37 / Phase error: 25.13 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2539 1819 4.91 %
Rwork0.2127 35262 -
obs0.2147 37081 97.41 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 94.46 Å2 / Biso mean: 40.2077 Å2 / Biso min: 10.8 Å2
Refinement stepCycle: final / Resolution: 2.69→23.41 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5339 0 18 160 5517
Biso mean--48.03 35.47 -
Num. residues----707
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 13

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.69-2.770.30611120.25361910202270
2.77-2.850.30261460.26762651279796
2.85-2.940.31191450.250627512896100
2.94-3.040.28431550.235827462901100
3.04-3.170.24271380.226727732911100
3.17-3.310.24541740.216127252899100
3.31-3.480.27091160.214927992915100
3.48-3.70.27081290.201927772906100
3.7-3.980.22651370.192128052942100
3.99-4.380.21591140.192228122926100
4.38-5.010.23091430.186228002943100
5.01-6.290.261580.223528102968100
6.3-23.410.24741520.21412903305599

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