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- PDB-2qy2: Characterization of a trifunctional mimivirus mRNA capping enzyme... -

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Basic information

Entry
Database: PDB / ID: 2qy2
TitleCharacterization of a trifunctional mimivirus mRNA capping enzyme and crystal structure of the RNA triphosphatase domainm.
ComponentsProbable mRNA-capping enzyme
KeywordsHYDROLASE / VIRAL PROTEIN / mRNA capping / phosphatase / beta tunnel / 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
ACETATE ION / CITRATE ANION / Probable mRNA-capping enzyme
Similarity search - Component
Biological speciesMimivirus
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2 Å
AuthorsShuman, S. / Benarroch, D. / Smith, P.
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 13, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 1, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Feb 21, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _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: Probable mRNA-capping enzyme
B: Probable mRNA-capping enzyme
hetero molecules


Theoretical massNumber of molelcules
Total (without water)55,6025
Polymers55,2952
Non-polymers3073
Water6,215345
1
A: Probable mRNA-capping enzyme
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,7653
Polymers27,6471
Non-polymers1182
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Probable mRNA-capping enzyme
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,8362
Polymers27,6471
Non-polymers1891
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)154.462, 154.462, 39.618
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number172
Space group name H-MP64
Components on special symmetry positions
IDModelComponents
11B-1338-

HOH

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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 / Gene: Refseq YP_142736 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) Codon+ / References: UniProt: Q5UQX1
#2: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H3O2
#3: Chemical ChemComp-FLC / CITRATE ANION


Mass: 189.100 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H5O7
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 345 / 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: 2

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Sample preparation

CrystalDensity Matthews: 2.47 Å3/Da / Density % sol: 50.15 %
Crystal growTemperature: 300 K / Method: vapor diffusion, hanging drop
Details: 20-30% PEG 4000 (less than 1 mo. old), 0.1M Sodium Citrate, 0.2M Ammonium 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: X29A / Wavelength: 0.9793, 1.1
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Sep 30, 2006
Details: 54-pole harmonic emission undulator with a vertically focusing mirror and a horizontally focusing monochromator (Si111).
RadiationMonochromator: Si111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.97931
21.11
ReflectionResolution: 2→40 Å / Num. all: 36953 / Num. obs: 36620 / % possible obs: 99.1 % / Observed criterion σ(I): -1 / Redundancy: 4.61 % / Biso Wilson estimate: 26.9 Å2 / Rsym value: 0.048 / Net I/σ(I): 31.4
Reflection shellResolution: 2→2.07 Å / Redundancy: 2.65 % / Mean I/σ(I) obs: 1.95 / Num. unique all: 3678 / Rsym value: 0.4 / % possible all: 95.18

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Processing

Software
NameVersionClassification
CNS1.1refinement
HKL-2000data collection
HKL-2000data reduction
SCALEPACKdata scaling
SOLVEphasing
RefinementMethod to determine structure: SAD / Resolution: 2→34.09 Å / Rfactor Rfree error: 0.004 / Data cutoff high absF: 2490485.66 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 1 / Stereochemistry target values: Engh & Huber
Details: BULK SOLVENT MODEL USED, Optimized via grid search. Ksol=0.325 with a probe radius of 0.8 angstroms.
RfactorNum. reflection% reflectionSelection details
Rfree0.252 3429 9.9 %RANDOM
Rwork0.212 ---
obs0.212 34612 93.4 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 35.9835 Å2 / ksol: 0.325 e/Å3
Displacement parametersBiso mean: 46.5 Å2
Baniso -1Baniso -2Baniso -3
1-2.37 Å22.35 Å20 Å2
2--2.56 Å20 Å2
3----4.92 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.3 Å0.25 Å
Luzzati d res low-5 Å
Luzzati sigma a0.26 Å0.24 Å
Refinement stepCycle: LAST / Resolution: 2→34.09 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3862 0 21 345 4228
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.014
X-RAY DIFFRACTIONc_angle_deg1.6
X-RAY DIFFRACTIONc_dihedral_angle_d25.7
X-RAY DIFFRACTIONc_improper_angle_d1.62
X-RAY DIFFRACTIONc_mcbond_it2.873
X-RAY DIFFRACTIONc_mcangle_it4.094
X-RAY DIFFRACTIONc_scbond_it4.414
X-RAY DIFFRACTIONc_scangle_it6.285
Refine LS restraints NCSNCS model details: NONE - NO NCS RESTRAINTS APPLIED
LS refinement shellResolution: 2→2.07 Å / Rfactor Rfree error: 0.017 / Total num. of bins used: 10
RfactorNum. reflection% reflection
Rfree0.298 296 10.5 %
Rwork0.277 2512 -
obs--76.2 %

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