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- PDB-1vp3: VACCINIA VIRUS PROTEIN VP39 IN COMPLEX WITH S-ADENOSYLHOMOCYSTEINE -

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ID or keywords:

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Basic information

Entry
Database: PDB / ID: 1vp3
TitleVACCINIA VIRUS PROTEIN VP39 IN COMPLEX WITH S-ADENOSYLHOMOCYSTEINE
ComponentsVP39
KeywordsMETHYLTRANSFERASE / RNA CAP / POLY(A) POLYMERASE / VACCINIA / MRNA PROCESSING / TRANSCRIPTION
Function / homology
Function and homology information


regulation of mRNA 3'-end processing / 7-methylguanosine mRNA capping / virion component / methylation / methyltransferase cap1 / methyltransferase cap1 activity / RNA binding
Similarity search - Function
mRNA methyltransferase-like / Poxvirus/kinetoplastid-type cap-specific nucleoside 2-O-methyltransferase / Poxvirus cap-specific nucleoside 2-O-methyltransferase / Poly A polymerase regulatory subunit / Poxvirus/kinetoplastid-type ribose 2'-O-methyltransferase (EC 2.1.1.57) family profile. / Vaccinia Virus protein VP39 / S-adenosyl-L-methionine-dependent methyltransferase superfamily / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
S-ADENOSYL-L-HOMOCYSTEINE / Cap-specific mRNA (nucleoside-2'-O-)-methyltransferase
Similarity search - Component
Biological speciesVaccinia virus
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsHodel, A.E. / Gershon, P.D. / Quiocho, F.A.
Citation
Journal: Nat.Struct.Biol. / Year: 1997
Title: Specific protein recognition of an mRNA cap through its alkylated base.
Authors: Hodel, A.E. / Gershon, P.D. / Shi, X. / Wang, S.M. / Quiocho, F.A.
#1: Journal: Cell(Cambridge,Mass.) / Year: 1996
Title: The 1.85 A Structure of Vaccinia Protein Vp39: A Bifunctional Enzyme that Participates in the Modification of Both Mrna Ends
Authors: Hodel, A.E. / Gershon, P.D. / Shi, X. / Quiocho, F.A.
History
DepositionNov 21, 1996Processing site: BNL
Revision 1.0Sep 17, 1997Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Source and taxonomy / Version format compliance
Revision 1.3Nov 16, 2011Group: Atomic model
Revision 1.4Aug 9, 2023Group: Database references / Derived calculations ...Database references / Derived calculations / Other / Refinement description
Category: database_2 / pdbx_database_status ...database_2 / pdbx_database_status / pdbx_initial_refinement_model / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.process_site / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.5May 22, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: VP39
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,5412
Polymers40,1561
Non-polymers3841
Water3,081171
1
A: VP39
hetero molecules

A: VP39
hetero molecules


Theoretical massNumber of molelcules
Total (without water)81,0814
Polymers80,3122
Non-polymers7692
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,y,-z1
Unit cell
Length a, b, c (Å)84.600, 67.300, 79.600
Angle α, β, γ (deg.)90.00, 117.30, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-556-

HOH

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Components

#1: Protein VP39 / POLY(A) POLYMERASE REGULATORY SUBUNIT


Mass: 40156.227 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Vaccinia virus / Genus: Orthopoxvirus / Strain: WR / Cell line: BL21 / Plasmid: BL21 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21 (DE3)
References: UniProt: P07617, polynucleotide adenylyltransferase
#2: Chemical ChemComp-SAH / S-ADENOSYL-L-HOMOCYSTEINE


Type: L-peptide linking / Mass: 384.411 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C14H20N6O5S
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 171 / Source method: isolated from a natural source / Formula: H2O

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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: 2.51 Å3/Da / Density % sol: 53 %
Crystal growpH: 4.5 / Details: pH 4.5
Crystal grow
*PLUS
Details: macro-seeding, Hodel, A.E., (1996) Cell(Cambridge,Mass.), 85, 247.
Method: other
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
110 %PEG800011
20.125 M11AmSO4
30.1 Mcitrate11

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Data collection

DiffractionMean temperature: 103 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RUH2R / Wavelength: 1.5418
DetectorType: MACSCIENCE / Detector: IMAGE PLATE / Date: Apr 12, 1996 / Details: MIRROR
RadiationMonochromator: NI FILTER / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.9→15 Å / Num. obs: 24966 / % possible obs: 79 % / Observed criterion σ(I): 2 / Redundancy: 3 % / Rmerge(I) obs: 0.057 / Net I/σ(I): 18.2
Reflection shellResolution: 1.9→1.97 Å / Redundancy: 1 % / Rmerge(I) obs: 0.21 / Mean I/σ(I) obs: 2.2 / % possible all: 27
Reflection shell
*PLUS
% possible obs: 27 %

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Processing

Software
NameVersionClassification
X-PLOR3.1model building
X-PLOR3.1refinement
DENZOdata reduction
SCALEPACKdata scaling
X-PLOR3.1phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1VPT

1vpt


Resolution: 1.9→8 Å / Data cutoff high absF: 100000 / Data cutoff low absF: 0.0001 / Isotropic thermal model: RESTRAINED / σ(F): 2
RfactorNum. reflection% reflection
Rwork0.215 --
obs0.215 24966 79 %
Displacement parametersBiso mean: 26.9 Å2
Refinement stepCycle: LAST / Resolution: 1.9→8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2402 0 26 171 2599
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONx_bond_d0.01
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg1.8
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it1.5
X-RAY DIFFRACTIONx_mcangle_it2
X-RAY DIFFRACTIONx_scbond_it2
X-RAY DIFFRACTIONx_scangle_it2
Software
*PLUS
Name: X-PLOR / Version: 3.1 / Classification: refinement
Refinement
*PLUS
Solvent computation
*PLUS
Displacement parameters
*PLUS

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