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- PDB-5x6y: Crystal structure of Rice Dwarf Virus P5 in complex with S-adenos... -

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Basic information

Entry
Database: PDB / ID: 5x6y
TitleCrystal structure of Rice Dwarf Virus P5 in complex with S-adenosylmethionine
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
CITRATE ANION / S-ADENOSYLMETHIONINE / Putative mRNA-capping enzyme P5
Similarity search - Component
Biological speciesRice dwarf virus
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / 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 1.1Nov 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
C: mRNA capping enzyme P5
D: mRNA capping enzyme P5
hetero molecules


Theoretical massNumber of molelcules
Total (without water)366,32821
Polymers363,2104
Non-polymers3,11817
Water9,404522
1
A: mRNA capping enzyme P5
B: mRNA capping enzyme P5
hetero molecules


Theoretical massNumber of molelcules
Total (without water)183,55113
Polymers181,6052
Non-polymers1,94611
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7890 Å2
ΔGint-3 kcal/mol
Surface area53820 Å2
MethodPISA
2
C: mRNA capping enzyme P5
D: mRNA capping enzyme P5
hetero molecules


Theoretical massNumber of molelcules
Total (without water)182,7778
Polymers181,6052
Non-polymers1,1726
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5960 Å2
ΔGint-22 kcal/mol
Surface area55520 Å2
MethodPISA
Unit cell
Length a, b, c (Å)60.182, 122.778, 129.257
Angle α, β, γ (deg.)73.80, 87.14, 86.08
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-SAM / S-ADENOSYLMETHIONINE


Mass: 398.437 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C15H22N6O5S
#3: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: C2H6O2
#4: Chemical ChemComp-FLC / CITRATE ANION


Mass: 189.100 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C6H5O7
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 522 / 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: 2.52 Å3/Da / Density % sol: 51.26 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 16% PEG 3350, 0.03M sodium citrate, 0.07M bis-tris propane, 0.2M sodium chloride, 0.01M tris(2-carboxyethyl)phosphine, 5mM S-adenosylmethionine, 1mM GpppG, 5mM magnesium chloride

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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: Jul 23, 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: 198192 / % possible obs: 96 % / Redundancy: 2.1 % / Rmerge(I) obs: 0.04 / Net I/σ(I): 24
Reflection shellResolution: 2.1→2.14 Å / Redundancy: 2 % / Rmerge(I) obs: 0.389 / Mean I/σ(I) obs: 2.1 / Num. unique obs: 9820 / % possible all: 95

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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: 2.1→38.226 Å / SU ML: 0.26 / Cross valid method: FREE R-VALUE / σ(F): 1.97 / Phase error: 25.18
RfactorNum. reflection% reflectionSelection details
Rfree0.2452 9512 5.03 %Random
Rwork0.202 ---
obs0.2041 189254 91.5 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.1→38.226 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms23457 0 210 522 24189
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00824259
X-RAY DIFFRACTIONf_angle_d0.90832906
X-RAY DIFFRACTIONf_dihedral_angle_d7.78918608
X-RAY DIFFRACTIONf_chiral_restr0.0543752
X-RAY DIFFRACTIONf_plane_restr0.0064077
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.1-2.12390.35682360.25353707X-RAY DIFFRACTION57
2.1239-2.14880.28792710.24524486X-RAY DIFFRACTION69
2.1488-2.17510.30352470.23144775X-RAY DIFFRACTION74
2.1751-2.20260.2642850.22735068X-RAY DIFFRACTION78
2.2026-2.23160.28632980.22465435X-RAY DIFFRACTION82
2.2316-2.26210.2783030.23235636X-RAY DIFFRACTION87
2.2621-2.29440.3013250.23145847X-RAY DIFFRACTION90
2.2944-2.32870.26483620.23335957X-RAY DIFFRACTION92
2.3287-2.36510.30023370.22846178X-RAY DIFFRACTION95
2.3651-2.40380.28463100.21886286X-RAY DIFFRACTION95
2.4038-2.44530.26013480.21266175X-RAY DIFFRACTION96
2.4453-2.48970.26563090.21776284X-RAY DIFFRACTION95
2.4897-2.53760.31183210.21566273X-RAY DIFFRACTION96
2.5376-2.58940.2543290.21316257X-RAY DIFFRACTION95
2.5894-2.64570.25962900.20846345X-RAY DIFFRACTION96
2.6457-2.70720.25723020.21046278X-RAY DIFFRACTION96
2.7072-2.77490.25823180.21016260X-RAY DIFFRACTION96
2.7749-2.84990.27673420.21576311X-RAY DIFFRACTION96
2.8499-2.93370.26443350.21686253X-RAY DIFFRACTION97
2.9337-3.02840.273380.21196424X-RAY DIFFRACTION97
3.0284-3.13660.26823460.22286308X-RAY DIFFRACTION97
3.1366-3.26210.2593120.21546419X-RAY DIFFRACTION98
3.2621-3.41050.27173140.21286494X-RAY DIFFRACTION98
3.4105-3.59020.24643360.21036477X-RAY DIFFRACTION99
3.5902-3.81490.23053260.19736490X-RAY DIFFRACTION99
3.8149-4.10910.2223690.18026408X-RAY DIFFRACTION99
4.1091-4.52210.16773230.15546445X-RAY DIFFRACTION98
4.5221-5.17510.18383390.166468X-RAY DIFFRACTION99
5.1751-6.51480.23143510.18496452X-RAY DIFFRACTION99
6.5148-38.23240.20862900.19365546X-RAY DIFFRACTION85

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