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- PDB-1bky: VACCINIA METHYLTRANSFERASE VP39 COMPLEXED WITH M1CYT AND S-ADENOS... -

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Basic information

Entry
Database: PDB / ID: 1bky
TitleVACCINIA METHYLTRANSFERASE VP39 COMPLEXED WITH M1CYT AND S-ADENOSYLHOMOCYSTEINE
ComponentsVP39
KeywordsMRNA PROCESSING / METHYLATED CYTOSINE / METHYLTRANSFERASE / RNA CAP ANALOG / POLY(A) POLYMERASE / VACCINIA / TRANSCRIPTION / COMPLEX (TRANSFERASE-RNA CAP ANALOG)
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
1-METHYLCYTOSINE / S-ADENOSYL-L-HOMOCYSTEINE / Cap-specific mRNA (nucleoside-2'-O-)-methyltransferase
Similarity search - Component
Biological speciesVaccinia virus
MethodX-RAY DIFFRACTION / OTHER / Resolution: 2 Å
AuthorsHu, G. / Hodel, A.E. / Gershon, P.D. / Quiocho, F.A.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 1999
Title: mRNA cap recognition: dominant role of enhanced stacking interactions between methylated bases and protein aromatic side chains.
Authors: Hu, G. / Gershon, P.D. / Hodel, A.E. / Quiocho, F.A.
History
DepositionJul 13, 1998Processing site: BNL
Revision 1.0Jul 22, 1999Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 7, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: VP39
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,4313
Polymers35,9211
Non-polymers5102
Water2,126118
1
A: VP39
hetero molecules

A: VP39
hetero molecules


Theoretical massNumber of molelcules
Total (without water)72,8626
Polymers71,8432
Non-polymers1,0194
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,y,-z1
Unit cell
Length a, b, c (Å)84.500, 67.210, 79.560
Angle α, β, γ (deg.)90.00, 117.30, 90.00
Int Tables number5
Space group name H-MC121

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Components

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


Mass: 35921.438 Da / Num. of mol.: 1 / Mutation: C-TERMINAL DELETION OF 26 RESIDUES
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Vaccinia virus / Genus: Orthopoxvirus / 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: Chemical ChemComp-1MC / 1-METHYLCYTOSINE


Mass: 125.129 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C5H7N3O
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 118 / 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: 2.77 Å3/Da / Density % sol: 56 %
Crystal growpH: 6.5 / Details: pH 6.5
Crystal grow
*PLUS
pH: 4.5 / Method: other
Details: used macroseeding, Hodel, A.E., (1996) Cell, 85, 247.
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: SIEMENS / Detector: CCD / Date: Oct 22, 1997 / Details: GOBEL MIRROR
RadiationMonochromator: NI FILTER / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2→20 Å / Num. obs: 30509 / % possible obs: 100 % / Observed criterion σ(I): 2 / Redundancy: 3 % / Rsym value: 0.084 / Net I/σ(I): 15
Reflection shellResolution: 2→2.1 Å / Redundancy: 2.9 % / Mean I/σ(I) obs: 8.9 / Rsym value: 0.23 / % possible all: 99.7
Reflection
*PLUS
Highest resolution: 1.86 Å / % possible obs: 90.7 % / Rmerge(I) obs: 0.088

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Processing

Software
NameVersionClassification
X-PLOR3.851model building
X-PLOR3.851refinement
SMARTdata reduction
SAINTdata scaling
X-PLOR3.851phasing
RefinementMethod to determine structure: OTHER / Resolution: 2→8 Å / Data cutoff high absF: 100000 / Data cutoff low absF: 0.0001 / Cross valid method: FREE-R / σ(F): 2
RfactorNum. reflection% reflectionSelection details
Rfree0.261 -10 %RANDOM
Rwork0.227 ---
obs0.227 30509 99.7 %-
Refinement stepCycle: LAST / Resolution: 2→8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2394 0 35 0 2429
Refine LS restraints
Refine-IDTypeDev ideal
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_deg1.6
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_it
X-RAY DIFFRACTIONx_mcangle_it
X-RAY DIFFRACTIONx_scbond_it
X-RAY DIFFRACTIONx_scangle_it
Xplor file
Refine-IDSerial noParam file
X-RAY DIFFRACTION1PARAM19X.PRO
X-RAY DIFFRACTION2
Software
*PLUS
Name: X-PLOR / Version: 3.851 / Classification: refinement
Refinement
*PLUS
Rfactor Rfree: 0.265
Solvent computation
*PLUS
Displacement parameters
*PLUS

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