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- PDB-7d8u: Crystal structure of the C-terminal domain of pNP868R from Africa... -

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Basic information

Entry
Database: PDB / ID: 7d8u
TitleCrystal structure of the C-terminal domain of pNP868R from African swine fever virus
ComponentsGTP--RNA guanylyltransferase
KeywordsTRANSFERASE / ASFV / RNA capping / methyltransferase
Function / homology
Function and homology information


mRNA 5'-triphosphate monophosphatase activity / mRNA 5'-phosphatase / polynucleotide 5'-phosphatase activity / virion component / mRNA guanylyltransferase activity / mRNA guanylyltransferase / mRNA (guanine-N7)-methyltransferase / mRNA 5'-cap (guanine-N7-)-methyltransferase activity / GTP binding / RNA binding
Similarity search - Function
mRNA cap guanine-N7 methyltransferase / mRNA (guanine-N(7))-methyltransferase domain / mRNA (guanine-N(7))-methyltransferase domain / mRNA (guanine-N(7)-)-methyltransferase (EC 2.1.1.56) domain profile. / CYTH-like domain superfamily / S-adenosyl-L-methionine-dependent methyltransferase superfamily
Similarity search - Domain/homology
FORMIC ACID / S-ADENOSYLMETHIONINE / mRNA-capping enzyme / mRNA-capping enzyme
Similarity search - Component
Biological speciesAfrican swine fever virus
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.7 Å
AuthorsDu, X. / Geng, Z. / Zhang, H.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)31970152 China
CitationJournal: J.Virol. / Year: 2020
Title: Structure and Biochemical Characteristic of the Methyltransferase (MTase) Domain of RNA Capping Enzyme from African Swine Fever Virus.
Authors: Du, X. / Gao, Z.Q. / Geng, Z. / Dong, Y.H. / Zhang, H.
History
DepositionOct 10, 2020Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Dec 2, 2020Provider: repository / Type: Initial release
Revision 1.1Jun 16, 2021Group: 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.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Nov 29, 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: GTP--RNA guanylyltransferase
B: GTP--RNA guanylyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)67,39112
Polymers66,1142
Non-polymers1,27710
Water72140
1
A: GTP--RNA guanylyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,5804
Polymers33,0571
Non-polymers5233
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: GTP--RNA guanylyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,8128
Polymers33,0571
Non-polymers7557
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)127.315, 127.315, 208.198
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number179
Space group name H-MP6522

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Components

#1: Protein GTP--RNA guanylyltransferase / Polynucleotide 5'-triphosphatase / Probable mRNA-capping enzyme / mRNA (guanine-N(7)-)- ...Polynucleotide 5'-triphosphatase / Probable mRNA-capping enzyme / mRNA (guanine-N(7)-)-methyltransferase / mRNA 5'-triphosphatase / mRNA guanylyltransferase


Mass: 33056.953 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) African swine fever virus / Gene: NP868R / Production host: Escherichia coli (E. coli)
References: UniProt: A0A0A1DYG7, UniProt: P32094*PLUS, mRNA (guanine-N7)-methyltransferase, mRNA guanylyltransferase, polynucleotide 5'-phosphatase
#2: Chemical ChemComp-SAM / S-ADENOSYLMETHIONINE


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


Mass: 62.068 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: C2H6O2 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-FMT / FORMIC ACID


Mass: 46.025 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: CH2O2 / Feature type: SUBJECT OF INVESTIGATION
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 40 / 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: 3.67 Å3/Da / Density % sol: 66.5 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.6 / Details: 4.3M sodium formate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U1 / Wavelength: 0.9788 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jan 5, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9788 Å / Relative weight: 1
ReflectionResolution: 2.7→50 Å / Num. obs: 28114 / % possible obs: 100 % / Redundancy: 35.9 % / CC1/2: 1 / Rmerge(I) obs: 0.131 / Rpim(I) all: 0.022 / Rrim(I) all: 0.133 / Net I/σ(I): 27
Reflection shellResolution: 2.7→2.75 Å / Redundancy: 25.8 % / Rmerge(I) obs: 0.752 / Mean I/σ(I) obs: 3 / Num. unique obs: 1364 / CC1/2: 0.87 / Rpim(I) all: 0.145 / Rrim(I) all: 0.766 / % possible all: 99.7

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Processing

Software
NameVersionClassification
PHENIX1.10.1_2155refinement
PDB_EXTRACT3.25data extraction
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1RI1

1ri1


Resolution: 2.7→47.068 Å / SU ML: 0.33 / Cross valid method: THROUGHOUT / σ(F): 1.4 / Phase error: 21.54 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2255 3671 7.1 %
Rwork0.1841 48020 -
obs0.187 27986 99.7 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 115.03 Å2 / Biso mean: 49.0837 Å2 / Biso min: 20 Å2
Refinement stepCycle: final / Resolution: 2.7→47.068 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4619 0 85 40 4744
Biso mean--41.29 45.82 -
Num. residues----566
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0114793
X-RAY DIFFRACTIONf_angle_d1.0096461
X-RAY DIFFRACTIONf_chiral_restr0.06708
X-RAY DIFFRACTIONf_plane_restr0.005806
X-RAY DIFFRACTIONf_dihedral_angle_d17.8622807
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.7004-2.73590.27331430.26179997
2.7359-2.77340.34831410.24241855100
2.7734-2.8130.29781400.23151839100
2.813-2.8550.32641450.23511851100
2.855-2.89960.27891400.23171864100
2.8996-2.94720.2661480.22751836100
2.9472-2.9980.29391420.2351828100
2.998-3.05250.27871480.21351876100
3.0525-3.11120.2631410.21851848100
3.1112-3.17470.22261400.22291850100
3.1747-3.24370.32751420.22881861100
3.2437-3.31910.30271340.22041834100
3.3191-3.40210.27021450.22881870100
3.4021-3.4940.25451420.21641828100
3.494-3.59680.2651420.18951867100
3.5968-3.71290.22611420.18221844100
3.7129-3.84550.24191400.17781866100
3.8455-3.99940.17011370.16841874100
3.9994-4.18130.19561400.16961818100
4.1813-4.40160.16151440.13971880100
4.4016-4.67720.17821440.14311836100
4.6772-5.03790.18061400.1551851100
5.0379-5.54420.21541450.1731853100
5.5442-6.34480.24261340.1861843100
6.3448-7.98740.2071340.1862185199
7.9874-470.19771380.1589179897

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