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- PDB-5x71: Crystal structure of Rice Dwarf Virus P5 in space group P212121 -

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Basic information

Entry
Database: PDB / ID: 5x71
TitleCrystal structure of Rice Dwarf Virus P5 in space group P212121
ComponentsmRNA capping enzyme P5
KeywordsTRANSFERASE / mRNA 5'-capping enzyme / guanylyltransferase / methyltransferase
Function / homology
Function and homology information


7-methylguanosine mRNA capping / virion component / mRNA guanylyltransferase activity / mRNA guanylyltransferase / host cell cytoplasm / GTP binding / RNA binding
Similarity search - Function
mRNA-capping enzyme P5, phytoreovirus
Similarity search - Domain/homology
GUANOSINE-5'-MONOPHOSPHATE / Putative mRNA-capping enzyme P5
Similarity search - Component
Biological speciesRice dwarf virus
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.568 Å
AuthorsNakamichi, Y. / Higashiura, A. / Nakagawa, A.
Funding support Japan, 1items
OrganizationGrant numberCountry
JSPSJP25251009 Japan
CitationJournal: To Be Published
Title: Crystal structure of the capping enzyme P5 from Rice Dwarf Virus
Authors: Nakamichi, Y. / Higashiura, A. / Narita, H. / Hagiwara, K. / Uehara-Ichiki, T. / Omura, T. / Nakagawa, A.
History
DepositionFeb 23, 2017Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Feb 28, 2018Provider: repository / Type: Initial release
Revision 1.1Nov 22, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: mRNA capping enzyme P5
B: mRNA capping enzyme P5
hetero molecules


Theoretical massNumber of molelcules
Total (without water)182,3314
Polymers181,6052
Non-polymers7262
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7310 Å2
ΔGint-35 kcal/mol
Surface area57860 Å2
MethodPISA
Unit cell
Length a, b, c (Å)76.814, 122.631, 192.262
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 mRNA capping enzyme P5


Mass: 90802.461 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rice dwarf virus (isolate O) / Strain: isolate O / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: P14583*PLUS, mRNA guanylyltransferase
#2: Chemical ChemComp-5GP / GUANOSINE-5'-MONOPHOSPHATE


Mass: 363.221 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H14N5O8P
Sequence detailsTHE SEQUENCE OF THIS PROTEIN WAS NOT AVAILABLE AT THE UNIPROT KNOWLEDGEBASE DATABASE (UNIPROTKB) AT ...THE SEQUENCE OF THIS PROTEIN WAS NOT AVAILABLE AT THE UNIPROT KNOWLEDGEBASE DATABASE (UNIPROTKB) AT THE TIME OF DEPOSITION. N-TERMINAL GGS ARE EXPRESSION TAGS.

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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: 2.49 Å3/Da / Density % sol: 50.66 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 1mM GpppG, 5mM Magnesium chloride, 16% PEG 3350, 0.1M MES, pH 6.0

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL44XU / Wavelength: 0.9 Å
DetectorType: RAYONIX MX300HE / Detector: CCD / Date: Dec 18, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9 Å / Relative weight: 1
ReflectionResolution: 2.55→50 Å / Num. obs: 57936 / % possible obs: 100 % / Redundancy: 7.3 % / Rmerge(I) obs: 0.101 / Net I/σ(I): 18.9
Reflection shellResolution: 2.55→2.59 Å / Redundancy: 6.8 % / Rmerge(I) obs: 0.507 / Mean I/σ(I) obs: 3.8 / Num. unique obs: 2839 / % possible all: 99.9

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Processing

Software
NameVersionClassification
PHENIX(dev_2614: ???)refinement
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5X6X

5x6x


Resolution: 2.568→44.304 Å / SU ML: 0.29 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 23.6
RfactorNum. reflection% reflectionSelection details
Rfree0.2353 2938 5.08 %Random
Rwork0.1907 ---
obs0.193 57792 98.38 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.568→44.304 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms12657 0 48 0 12705
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00413049
X-RAY DIFFRACTIONf_angle_d0.6517721
X-RAY DIFFRACTIONf_dihedral_angle_d6.41610749
X-RAY DIFFRACTIONf_chiral_restr0.0462004
X-RAY DIFFRACTIONf_plane_restr0.0042208
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.5683-2.61040.3296930.24121752X-RAY DIFFRACTION68
2.6104-2.65540.31761340.23272629X-RAY DIFFRACTION99
2.6554-2.70370.30531370.22672584X-RAY DIFFRACTION99
2.7037-2.75570.31851380.22432613X-RAY DIFFRACTION100
2.7557-2.81190.26761680.22272576X-RAY DIFFRACTION100
2.8119-2.8730.29841460.22852631X-RAY DIFFRACTION100
2.873-2.93990.25341320.22812641X-RAY DIFFRACTION100
2.9399-3.01340.29671470.22872609X-RAY DIFFRACTION100
3.0134-3.09480.28891270.23152658X-RAY DIFFRACTION100
3.0948-3.18590.26611310.2212644X-RAY DIFFRACTION100
3.1859-3.28870.26881580.20782609X-RAY DIFFRACTION100
3.2887-3.40620.28041510.21832636X-RAY DIFFRACTION100
3.4062-3.54250.26861420.20622645X-RAY DIFFRACTION100
3.5425-3.70360.24311450.19742659X-RAY DIFFRACTION100
3.7036-3.89880.23421470.18132639X-RAY DIFFRACTION100
3.8988-4.14290.2041370.1672662X-RAY DIFFRACTION100
4.1429-4.46250.19261360.15132682X-RAY DIFFRACTION100
4.4625-4.91110.18251420.14332691X-RAY DIFFRACTION100
4.9111-5.62050.18111420.15872702X-RAY DIFFRACTION100
5.6205-7.07650.18871490.18952734X-RAY DIFFRACTION100
7.0765-44.31070.18411360.17062858X-RAY DIFFRACTION99

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