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- PDB-1ri5: Structure and mechanism of mRNA cap (guanine N-7) methyltransferase -

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Basic information

Entry
Database: PDB / ID: 1ri5
TitleStructure and mechanism of mRNA cap (guanine N-7) methyltransferase
ComponentsmRNA CAPPING ENZYME
KeywordsTRANSFERASE / methyltransferase / rna / cap / m7G / messenger rna cap / Structural Genomics / PSI / Protein Structure Initiative / New York SGX Research Center for Structural Genomics / NYSGXRC
Function / homology
Function and homology information


mRNA (guanine-N7)-methyltransferase / mRNA 5'-cap (guanine-N7-)-methyltransferase activity / RNA binding / nucleus
Similarity search - Function
mRNA cap guanine-N7 methyltransferase, eukaryotes / 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. / Vaccinia Virus protein VP39 / S-adenosyl-L-methionine-dependent methyltransferase superfamily / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
mRNA cap guanine-N(7) methyltransferase
Similarity search - Component
Biological speciesEncephalitozoon cuniculi (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD, MIR / Resolution: 2.1 Å
AuthorsFabrega, C. / Hausmann, S. / Shen, V. / Shuman, S. / Lima, C.D. / Burley, S.K. / New York SGX Research Center for Structural Genomics (NYSGXRC)
CitationJournal: Mol.Cell / Year: 2004
Title: Structure and mechanism of mRNA cap (Guanine-n7) methyltransferase
Authors: Fabrega, C. / Hausmann, S. / Shen, V. / Shuman, S. / Lima, C.D.
History
DepositionNov 16, 2003Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 3, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 3, 2021Group: Structure summary / Category: audit_author / Item: _audit_author.identifier_ORCID
Revision 1.4Feb 14, 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
A: mRNA CAPPING ENZYME


Theoretical massNumber of molelcules
Total (without water)34,8241
Polymers34,8241
Non-polymers00
Water2,864159
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)63.773, 63.773, 112.778
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121

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Components

#1: Protein mRNA CAPPING ENZYME / mRNA cap (guanine N-7) methyltransferase Ecm1


Mass: 34823.684 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Encephalitozoon cuniculi (fungus) / Gene: ECU10_0380 / Plasmid: pSUMO/SMT3 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21 DE3 / References: UniProt: Q8SR66
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 159 / 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: 1.9 Å3/Da / Density % sol: 35.29 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 6.25
Details: 1.2M Na/K tartrate, 50mM BIS/TRIS, 20mM DTT, pH 6.25, VAPOR DIFFUSION, HANGING DROP, temperature 291K
Crystal grow
*PLUS
pH: 8 / Method: vapor diffusion
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formulaDetails
16.5 mg/mlprotein1drop
2220 mM1dropNaCl
320 mMTris-HCl1droppH8.0
41 mMbeta-mercaptoethanol1drop
51.2 Msodium/pootassium tartrate1reservoir
650 mMbis-tris1reservoirpH6.0
720 mMdithiothreitol1reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 31-ID / Wavelength: 0.979 Å
DetectorType: MARRESEARCH / Detector: CCD
RadiationMonochromator: SI / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2.05→20 Å / Num. all: 17150 / Num. obs: 16224 / % possible obs: 94.6 % / Observed criterion σ(F): -1 / Observed criterion σ(I): -1 / Biso Wilson estimate: 35.6 Å2 / Rmerge(I) obs: 0.074 / Net I/σ(I): 16.4
Reflection shellResolution: 2.05→2.15 Å / % possible all: 89
Reflection
*PLUS
Num. measured all: 151528
Reflection shell
*PLUS
% possible obs: 89 % / Rmerge(I) obs: 0.193 / Mean I/σ(I) obs: 6.5

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Processing

Software
NameVersionClassification
CNS1.1refinement
DENZOdata reduction
SCALEPACKdata scaling
SHARPphasing
RefinementMethod to determine structure: SAD, MIR / Resolution: 2.1→19.73 Å / Rfactor Rfree error: 0.009 / Data cutoff high absF: 1707195.19 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber / Details: BULK SOLVENT MODEL USED
RfactorNum. reflection% reflectionSelection details
Rfree0.263 775 5.1 %RANDOM
Rwork0.23 ---
obs0.23 15203 94.7 %-
all-16053 --
Solvent computationSolvent model: FLAT MODEL / Bsol: 61.3136 Å2 / ksol: 0.420799 e/Å3
Displacement parametersBiso mean: 41.8 Å2
Baniso -1Baniso -2Baniso -3
1-2.85 Å22.08 Å20 Å2
2--2.85 Å20 Å2
3----5.69 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.33 Å0.27 Å
Luzzati d res low-6 Å
Luzzati sigma a0.28 Å0.2 Å
Refinement stepCycle: LAST / Resolution: 2.1→19.73 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2061 0 0 159 2220
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.008
X-RAY DIFFRACTIONc_angle_deg0.8
X-RAY DIFFRACTIONc_dihedral_angle_d22.7
X-RAY DIFFRACTIONc_improper_angle_d0.56
X-RAY DIFFRACTIONc_mcbond_it1.151.5
X-RAY DIFFRACTIONc_mcangle_it2.032
X-RAY DIFFRACTIONc_scbond_it1.442
X-RAY DIFFRACTIONc_scangle_it2.372.5
LS refinement shellResolution: 2.1→2.23 Å / Rfactor Rfree error: 0.028 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.315 128 5.4 %
Rwork0.271 2238 -
obs--89.9 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2
X-RAY DIFFRACTION3WATER_REP.PARAMWATER.TOP
X-RAY DIFFRACTION4ION.PARAMION.TOP
Refinement
*PLUS
Highest resolution: 2.1 Å / Lowest resolution: 20 Å / % reflection Rfree: 5 % / Rfactor Rfree: 0.26
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_angle_deg0.75
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg22.7
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.56
LS refinement shell
*PLUS
Rfactor Rfree: 0.32 / Rfactor Rwork: 0.27

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