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- PDB-3vkw: Crystal Structure of the Superfamily 1 Helicase from Tomato Mosai... -

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Basic information

Entry
Database: PDB / ID: 3vkw
TitleCrystal Structure of the Superfamily 1 Helicase from Tomato Mosaic Virus
ComponentsReplicase large subunit
KeywordsTRANSFERASE / alpha/beta domain / Helicase
Function / homology
Function and homology information


mRNA methyltransferase activity / mRNA modification / RNA processing / Transferases; Transferring one-carbon groups; Methyltransferases / Transferases; Transferring phosphorus-containing groups; Nucleotidyltransferases / RNA helicase activity / RNA helicase / symbiont-mediated suppression of host innate immune response / RNA-directed RNA polymerase / viral RNA genome replication ...mRNA methyltransferase activity / mRNA modification / RNA processing / Transferases; Transferring one-carbon groups; Methyltransferases / Transferases; Transferring phosphorus-containing groups; Nucleotidyltransferases / RNA helicase activity / RNA helicase / symbiont-mediated suppression of host innate immune response / RNA-directed RNA polymerase / viral RNA genome replication / RNA-dependent RNA polymerase activity / virus-mediated perturbation of host defense response / DNA-templated transcription / ATP hydrolysis activity / RNA binding / ATP binding
Similarity search - Function
Beta-Lactamase - #420 / : / Viral methyltransferase / Alphavirus-like methyltransferase (MT) domain / Alphavirus-like methyltransferase (MT) domain profile. / Tymovirus, RNA-dependent RNA polymerase / RNA dependent RNA polymerase / Viral (Superfamily 1) RNA helicase / Beta-Lactamase / (+) RNA virus helicase core domain ...Beta-Lactamase - #420 / : / Viral methyltransferase / Alphavirus-like methyltransferase (MT) domain / Alphavirus-like methyltransferase (MT) domain profile. / Tymovirus, RNA-dependent RNA polymerase / RNA dependent RNA polymerase / Viral (Superfamily 1) RNA helicase / Beta-Lactamase / (+) RNA virus helicase core domain / (+)RNA virus helicase core domain profile. / P-loop containing nucleotide triphosphate hydrolases / RNA-directed RNA polymerase, catalytic domain / RdRp of positive ssRNA viruses catalytic domain profile. / DNA/RNA polymerase superfamily / Rossmann fold / P-loop containing nucleoside triphosphate hydrolase / 2-Layer Sandwich / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Replicase large subunit
Similarity search - Component
Biological speciesTomato mosaic virus
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.9 Å
AuthorsNishikiori, M. / Sugiyama, S. / Xiang, H. / Niiyama, M. / Ishibashi, K. / Inoue, T. / Ishikawa, M. / Matsumura, H. / Katoh, E.
CitationJournal: J.Virol. / Year: 2012
Title: Crystal structure of the superfamily 1 helicase from tomato mosaic virus
Authors: Nishikiori, M. / Sugiyama, S. / Xiang, H. / Niiyama, M. / Ishibashi, K. / Inoue, T. / Ishikawa, M. / Matsumura, H. / Katoh, E.
History
DepositionNov 22, 2011Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jul 11, 2012Provider: repository / Type: Initial release
Revision 1.1Mar 20, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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: Replicase large subunit
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,7018
Polymers50,0291
Non-polymers6727
Water10,215567
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)85.441, 128.817, 40.742
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Replicase large subunit / 183 kDa protein / RNA-directed RNA polymerase / Replicase small subunit / 126 kDa protein / ...183 kDa protein / RNA-directed RNA polymerase / Replicase small subunit / 126 kDa protein / Methyltransferase/RNA helicase / MT/HEL


Mass: 50028.535 Da / Num. of mol.: 1 / Fragment: helicase contained domain, UNP residues 666-1111
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Tomato mosaic virus / Strain: L / Production host: Escherichia coli (E. coli)
References: UniProt: P03587, Transferases; Transferring one-carbon groups; Methyltransferases, Transferases; Transferring phosphorus-containing groups; Nucleotidyltransferases, RNA helicase
#2: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 567 / 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: 2.24 Å3/Da / Density % sol: 45.11 %
Crystal growTemperature: 285 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 0.1M NaH2PO4-NaOH pH 6.5, 1.7M (NH4)2SO4, VAPOR DIFFUSION, HANGING DROP, temperature 285K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-17A / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Feb 15, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.9→40 Å / Num. all: 36315 / Num. obs: 36315 / % possible obs: 99.8 % / Observed criterion σ(I): -3 / Biso Wilson estimate: 10.2 Å2
Reflection shellResolution: 1.9→1.93 Å / % possible all: 97.8

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Processing

Software
NameVersionClassification
HKL-2000data collection
SHELXSphasing
CNS1.2refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: SAD / Resolution: 1.9→31.94 Å / Rfactor Rfree error: 0.005 / Data cutoff high absF: 57079.26 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Details: BULK SOLVENT MODEL USED
RfactorNum. reflection% reflectionSelection details
Rfree0.227 1752 5 %RANDOM
Rwork0.181 ---
obs0.181 35277 97 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 53.4476 Å2 / ksol: 0.4 e/Å3
Displacement parametersBiso mean: 19.7 Å2
Baniso -1Baniso -2Baniso -3
1--4.11 Å20 Å20 Å2
2--4.99 Å20 Å2
3----0.88 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.24 Å0.19 Å
Luzzati d res low-5 Å
Luzzati sigma a0.15 Å0.11 Å
Refinement stepCycle: LAST / Resolution: 1.9→31.94 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3455 0 35 567 4057
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.005
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_deg1.3
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d23.4
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.72
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it1.271.5
X-RAY DIFFRACTIONc_mcangle_it1.932
X-RAY DIFFRACTIONc_scbond_it2.212
X-RAY DIFFRACTIONc_scangle_it3.172.5
LS refinement shellResolution: 1.9→2.02 Å / Rfactor Rfree error: 0.016 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.262 279 5 %
Rwork0.205 5247 -
obs--92.7 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2water_rep.paramwater.top
X-RAY DIFFRACTION3ion.paramion.top
X-RAY DIFFRACTION4dna-rna_rep.paramdna-rna.top
X-RAY DIFFRACTION5tm1hel.paramtm1hel.top

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