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- PDB-5x6x: Crystal structure of the capping enzyme P5 from Rice Dwarf Virus -

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Basic information

Entry
Database: PDB / ID: 5x6x
TitleCrystal structure of the capping enzyme P5 from Rice Dwarf Virus
ComponentsmRNA capping enzyme P5
KeywordsTRANSFERASE / mRNA 5'-capping / guanylyltransferase / methyltransferase
Function / homologymRNA-capping enzyme P5, phytoreovirus / 7-methylguanosine mRNA capping / virion component / mRNA guanylyltransferase activity / mRNA guanylyltransferase / host cell cytoplasm / GTP binding / RNA binding / Putative mRNA-capping enzyme P5
Function and homology information
Biological speciesRice dwarf virus
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.1 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 1.1Mar 27, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)363,58210
Polymers363,2104
Non-polymers3726
Water22,3031238
1
C: mRNA capping enzyme P5
D: mRNA capping enzyme P5
hetero molecules


Theoretical massNumber of molelcules
Total (without water)181,7915
Polymers181,6052
Non-polymers1863
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6520 Å2
ΔGint-20 kcal/mol
Surface area56670 Å2
MethodPISA
2
A: mRNA capping enzyme P5
B: mRNA capping enzyme P5
hetero molecules


Theoretical massNumber of molelcules
Total (without water)181,7915
Polymers181,6052
Non-polymers1863
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6300 Å2
ΔGint-20 kcal/mol
Surface area57290 Å2
MethodPISA
Unit cell
Length a, b, c (Å)77.230, 83.854, 143.250
Angle α, β, γ (deg.)103.41, 102.47, 95.37
Int Tables number1
Space group name H-MP1

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Components

#1: Protein
mRNA capping enzyme P5


Mass: 90802.461 Da / Num. of mol.: 4
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-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C2H6O2
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 1238 / Source method: isolated from a natural source / Formula: H2O
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: 2.4 Å3/Da / Density % sol: 48.71 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6 / Details: 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: Jun 4, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9 Å / Relative weight: 1
ReflectionResolution: 2.1→50 Å / Num. obs: 194125 / % possible obs: 98.5 % / Redundancy: 4 % / Rmerge(I) obs: 0.073 / Rpim(I) all: 0.042 / Net I/σ(I): 24.5
Reflection shellResolution: 2.1→2.14 Å / Redundancy: 4 % / Rmerge(I) obs: 0.55 / Mean I/σ(I) obs: 3.2 / Num. unique obs: 9600 / CC1/2: 0.853 / Rpim(I) all: 0.32 / % possible all: 97.7

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Processing

Software
NameVersionClassification
PHENIX(dev_2614: ???)refinement
HKL-2000data reduction
HKL-2000data scaling
AutoSolphasing
RefinementMethod to determine structure: SAD / Resolution: 2.1→44.504 Å / SU ML: 0.24 / Cross valid method: FREE R-VALUE / σ(F): 1.96 / Phase error: 26.85
RfactorNum. reflection% reflectionSelection details
Rfree0.2374 9483 4.89 %Random
Rwork0.1883 ---
obs0.1908 193899 98.46 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.1→44.504 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms24746 0 24 1238 26008
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00825409
X-RAY DIFFRACTIONf_angle_d0.82234471
X-RAY DIFFRACTIONf_dihedral_angle_d8.4518047
X-RAY DIFFRACTIONf_chiral_restr0.0523900
X-RAY DIFFRACTIONf_plane_restr0.0054305
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.1-2.12390.31033080.25386044X-RAY DIFFRACTION97
2.1239-2.14880.2933390.25386108X-RAY DIFFRACTION98
2.1488-2.17510.29533250.22976026X-RAY DIFFRACTION98
2.1751-2.20260.27953020.22746160X-RAY DIFFRACTION98
2.2026-2.23160.27753150.22876043X-RAY DIFFRACTION98
2.2316-2.26210.29953470.22886107X-RAY DIFFRACTION98
2.2621-2.29450.30072970.22966095X-RAY DIFFRACTION98
2.2945-2.32870.31022800.22016232X-RAY DIFFRACTION98
2.3287-2.36510.28992870.21526058X-RAY DIFFRACTION98
2.3651-2.40390.27243250.20956168X-RAY DIFFRACTION98
2.4039-2.44530.27483160.21496099X-RAY DIFFRACTION98
2.4453-2.48980.27523250.21326172X-RAY DIFFRACTION98
2.4898-2.53770.28273150.2136097X-RAY DIFFRACTION98
2.5377-2.58940.28223250.20466148X-RAY DIFFRACTION98
2.5894-2.64570.2763280.20316183X-RAY DIFFRACTION98
2.6457-2.70730.26583350.19736095X-RAY DIFFRACTION99
2.7073-2.7750.25833220.20146127X-RAY DIFFRACTION99
2.775-2.850.27183050.20026202X-RAY DIFFRACTION99
2.85-2.93380.27553130.2066137X-RAY DIFFRACTION99
2.9338-3.02850.26572930.19936172X-RAY DIFFRACTION99
3.0285-3.13670.24263000.20076200X-RAY DIFFRACTION99
3.1367-3.26230.24952620.20126197X-RAY DIFFRACTION99
3.2623-3.41070.26032920.20436261X-RAY DIFFRACTION99
3.4107-3.59040.2423100.19426180X-RAY DIFFRACTION99
3.5904-3.81530.22753120.18296214X-RAY DIFFRACTION99
3.8153-4.10970.22563590.16386152X-RAY DIFFRACTION99
4.1097-4.52290.1753420.1466172X-RAY DIFFRACTION99
4.5229-5.17650.17453570.14736188X-RAY DIFFRACTION99
5.1765-6.51860.20783270.16856208X-RAY DIFFRACTION100
6.5186-44.51440.17713200.15786171X-RAY DIFFRACTION99

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