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- PDB-2qze: Monoclinic Mimivirus Capping Enzyme Triphosphatase. -

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Basic information

Entry
Database: PDB / ID: 2qze
TitleMonoclinic Mimivirus Capping Enzyme Triphosphatase.
ComponentsProbable mRNA-capping enzyme
KeywordsHYDROLASE / VIRAL PROTEIN / Mimivirus / capping / tunnel / triphosphatase / monoclinic / mRNA capping / mRNA processing / Multifunctional enzyme / Nucleotidyltransferase / S-adenosyl-L-methionine / Transferase
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 triphosphatase Cet1-like / mRNA triphosphatase Cet1-like / mRNA triphosphatase Cet1-like superfamily / mRNA Triphosphatase Cet1; Chain A / mRNA (guanine-N(7))-methyltransferase domain / mRNA cap guanine-N7 methyltransferase / 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 ...mRNA triphosphatase Cet1-like / mRNA triphosphatase Cet1-like / mRNA triphosphatase Cet1-like superfamily / mRNA Triphosphatase Cet1; Chain A / mRNA (guanine-N(7))-methyltransferase domain / mRNA cap guanine-N7 methyltransferase / 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 / Nucleic acid-binding, OB-fold / Alpha-Beta Barrel / Alpha Beta
Similarity search - Domain/homology
Probable mRNA-capping enzyme
Similarity search - Component
Biological speciesMimivirus
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.9 Å
AuthorsBenarroch, D. / Smith, P. / Shuman, S.
CitationJournal: Structure / Year: 2008
Title: Characterization of a trifunctional mimivirus mRNA capping enzyme and crystal structure of the RNA triphosphatase domain.
Authors: Benarroch, D. / Smith, P. / Shuman, S.
History
DepositionAug 16, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 1, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Aug 30, 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 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Probable mRNA-capping enzyme
B: Probable mRNA-capping enzyme


Theoretical massNumber of molelcules
Total (without water)55,2952
Polymers55,2952
Non-polymers00
Water1,63991
1
A: Probable mRNA-capping enzyme


Theoretical massNumber of molelcules
Total (without water)27,6471
Polymers27,6471
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Probable mRNA-capping enzyme


Theoretical massNumber of molelcules
Total (without water)27,6471
Polymers27,6471
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)39.184, 92.401, 72.809
Angle α, β, γ (deg.)90.00, 102.60, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Probable mRNA-capping enzyme


Mass: 27647.377 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mimivirus / Genus: Mimivirus / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)Codon+ / References: UniProt: Q5UQX1
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 91 / 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: 2.33 Å3/Da / Density % sol: 47.13 %
Crystal growTemperature: 300 K / Method: vapor diffusion, hanging drop
Details: 20-30% PEG 4000, 100mM Na Citrate, 200mM Na Acetate, pH 5.0-6.0, VAPOR DIFFUSION, HANGING DROP, temperature 300K

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Data collection

DiffractionMean temperature: 130 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X12C / Wavelength: 1.601 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Feb 7, 2007 / Details: Si(111) channel-cut crystal monochromator
RadiationMonochromator: Si(111) channel-cut crystal monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.601 Å / Relative weight: 1
ReflectionResolution: 2.9→50 Å / Num. all: 11266 / Num. obs: 10635 / % possible obs: 94.4 % / Observed criterion σ(I): -1 / Redundancy: 4.43 % / Biso Wilson estimate: 56.2 Å2 / Rsym value: 0.084 / Net I/σ(I): 14.91
Reflection shellResolution: 2.9→2.97 Å / Redundancy: 2.5 % / Mean I/σ(I) obs: 2.32 / Num. unique all: 646 / Rsym value: 0.314 / % possible all: 84.6

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Processing

Software
NameVersionClassification
CNS1.1refinement
HKL-2000data collection
HKL-2000data reduction
SCALEPACKdata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 2QY2

2qy2


Resolution: 2.9→46.2 Å / Rfactor Rfree error: 0.012 / Data cutoff high absF: 9449185.29 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 1 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.268 479 4.8 %RANDOM
Rwork0.223 ---
obs0.223 9878 87.7 %-
all-11316 --
Solvent computationSolvent model: FLAT MODEL / Bsol: 14.0354 Å2 / ksol: 0.345 e/Å3
Displacement parametersBiso mean: 51.7 Å2
Baniso -1Baniso -2Baniso -3
1-9.53 Å20 Å22.14 Å2
2--15.12 Å20 Å2
3----24.65 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.45 Å0.36 Å
Luzzati d res low-6 Å
Luzzati sigma a0.52 Å0.4 Å
Refinement stepCycle: LAST / Resolution: 2.9→46.2 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3636 0 0 91 3727
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.015
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.8
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d26.1
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d1.69
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it1.411.5
X-RAY DIFFRACTIONc_mcangle_it2.482
X-RAY DIFFRACTIONc_scbond_it2.112
X-RAY DIFFRACTIONc_scangle_it3.52.5
LS refinement shellResolution: 2.9→3 Å / Rfactor Rfree error: 0.052 / Total num. of bins used: 10
RfactorNum. reflection% reflection
Rfree0.319 37 5.2 %
Rwork0.31 671 -
obs--61.7 %

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