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- PDB-1z3c: Encephalitozooan cuniculi mRNA Cap (Guanine-N7) Methyltransferase... -

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Basic information

Entry
Database: PDB / ID: 1z3c
TitleEncephalitozooan cuniculi mRNA Cap (Guanine-N7) Methyltransferasein complexed with AzoAdoMet
ComponentsmRNA CAPPING ENZYME
KeywordsTRANSFERASE / METHYLTRANSFERASE / RNA / CAP / M7G / MESSENGER RNA CAP / AZOADOMET
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
S-5'-AZAMETHIONINE-5'-DEOXYADENOSINE / mRNA cap guanine-N7 methyltransferase
Similarity search - Component
Biological speciesEncephalitozoon cuniculi (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsHausmann, S. / Zhang, S. / Fabrega, C. / Schneller, S.W. / Lima, C.D. / Shuman, S.
CitationJournal: J.Biol.Chem. / Year: 2005
Title: Encephalitozoon cuniculi mRNA cap (guanine N-7) methyltransferase: methyl acceptor specificity, inhibition BY S-adenosylmethionine analogs, and structure-guided mutational analysis.
Authors: Hausmann, S. / Zheng, S. / Fabrega, C. / Schneller, S.W. / Lima, C.D. / Shuman, S.
History
DepositionMar 11, 2005Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 22, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Aug 23, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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 / _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

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Assembly

Deposited unit
A: mRNA CAPPING ENZYME
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,2052
Polymers34,8241
Non-polymers3811
Water2,378132
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)63.253, 63.253, 111.841
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


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, mRNA (guanine-N7)-methyltransferase
#2: Chemical ChemComp-SA8 / S-5'-AZAMETHIONINE-5'-DEOXYADENOSINE / 5'-[N-[(3S)-3-AMINO-3-CARBOXYPROPYL]-N-METHYLAMINO]-5'-DEOXYADENOSINE


Mass: 381.387 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C15H23N7O5
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 132 / 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: 1.85 Å3/Da / Density % sol: 33.68 %
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, 1mM azoadomet, VAPOR DIFFUSION, HANGING DROP, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X4A / Wavelength: 0.979 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Mar 31, 2003
RadiationMonochromator: SAGITALLY FOCUSED Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2.2→20 Å / Num. all: 13740 / Num. obs: 13451 / % possible obs: 97.9 % / Observed criterion σ(F): -0.5 / Observed criterion σ(I): -0.5 / Biso Wilson estimate: 44.7 Å2 / Rmerge(I) obs: 0.084 / Net I/σ(I): 10.9
Reflection shellResolution: 2.2→2.3 Å / Rmerge(I) obs: 0.333 / Mean I/σ(I) obs: 4.9 / % possible all: 95.7

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Processing

Software
NameVersionClassification
CNS1.1refinement
DENZOdata reduction
SCALEPACKdata scaling
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: pdb entry 1RI5

1ri5


Resolution: 2.2→19.57 Å / Rfactor Rfree error: 0.01 / Data cutoff high absF: 233191.89 / 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
Rfree0.27 675 5.1 %RANDOM
Rwork0.222 ---
obs0.222 13288 97.2 %-
all-13740 --
Solvent computationSolvent model: FLAT MODEL / Bsol: 52.6668 Å2 / ksol: 0.347217 e/Å3
Displacement parametersBiso mean: 50.8 Å2
Baniso -1Baniso -2Baniso -3
1-4.77 Å27.96 Å20 Å2
2--4.77 Å20 Å2
3----9.54 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.38 Å0.31 Å
Luzzati d res low-8 Å
Luzzati sigma a0.57 Å0.53 Å
Refinement stepCycle: LAST / Resolution: 2.2→19.57 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2061 0 27 132 2220
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.006
X-RAY DIFFRACTIONc_angle_deg1.1
X-RAY DIFFRACTIONc_dihedral_angle_d22
X-RAY DIFFRACTIONc_improper_angle_d0.73
X-RAY DIFFRACTIONc_mcbond_it1.451.5
X-RAY DIFFRACTIONc_mcangle_it2.452
X-RAY DIFFRACTIONc_scbond_it2.122
X-RAY DIFFRACTIONc_scangle_it3.242.5
LS refinement shellResolution: 2.2→2.34 Å / Rfactor Rfree error: 0.048 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.454 91 4.3 %
Rwork0.424 2012 -
obs--93.6 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION3WATER_REP.PARAMWATER.TOP
X-RAY DIFFRACTION4ION.PARAMION.TOP
X-RAY DIFFRACTION5INH.PARINH.TOP

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