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- PDB-3wrv: Crystal structure of NN domain of resistance protein -

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Basic information

Entry
Database: PDB / ID: 3wrv
TitleCrystal structure of NN domain of resistance protein
ComponentsTm-1 protein
KeywordsTRANSFERASE / alpha/beta domain / resistance
Function / homology
Function and homology information


host-mediated perturbation of viral RNA genome replication / catalytic activity / defense response to virus / protein homodimerization activity / ATP binding
Similarity search - Function
Uncharacterised protein family UPF0261, NN domain / TIM-barrel domain, IGPS-like / UPF0261 domain / : / Uncharacterised protein family (UPF0261) N-terminal domain / Phosphoenolpyruvate hydrolase-like / Uncharacterised protein family (UPF0261) C-terminal domain / : / Pyruvate/Phosphoenolpyruvate kinase-like domain superfamily / Aldolase-type TIM barrel ...Uncharacterised protein family UPF0261, NN domain / TIM-barrel domain, IGPS-like / UPF0261 domain / : / Uncharacterised protein family (UPF0261) N-terminal domain / Phosphoenolpyruvate hydrolase-like / Uncharacterised protein family (UPF0261) C-terminal domain / : / Pyruvate/Phosphoenolpyruvate kinase-like domain superfamily / Aldolase-type TIM barrel / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
ToMV resistance protein Tm-1(GCR237)
Similarity search - Component
Biological speciesSolanum lycopersicum (tomato)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.75 Å
AuthorsMatsumura, H. / Katoh, E.
Citation
Journal: Proc.Natl.Acad.Sci.USA / Year: 2014
Title: Structural basis for the recognition-evasion arms race between Tomato mosaic virus and the resistance gene Tm-1
Authors: Ishibashi, K. / Kezuka, Y. / Kobayashi, C. / Kato, M. / Inoue, T. / Nonaka, T. / Ishikawa, M. / Matsumura, H. / Katoh, E.
#1: Journal: Protein Expr.Purif. / Year: 2013
Title: Expression, purification, and functional characterization of an N-terminal fragment of the tomato mosaic virus resistance protein Tm-1
Authors: Kato, M. / Ishibashi, K. / Kobayashi, C. / Ishikawa, M. / Katoh, E.
#2: Journal: Acta Crystallogr.,Sect.F / Year: 2013
Title: Crystallization and preliminary X-ray crystallographic analysis of the inhibitory domain of the tomato mosaic virus resistance protein Tm-1
Authors: Kato, M. / Kezuka, Y. / Kobayashi, C. / Ishibashi, K. / Nonaka, T. / Ishikawa, M. / Katoh, E.
History
DepositionFeb 27, 2014Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Aug 13, 2014Provider: repository / Type: Initial release
Revision 1.1Nov 16, 2016Group: Database references
Revision 1.2Mar 20, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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

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Assembly

Deposited unit
A: Tm-1 protein
B: Tm-1 protein


Theoretical massNumber of molelcules
Total (without water)42,0362
Polymers42,0362
Non-polymers00
Water1267
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2320 Å2
ΔGint-15 kcal/mol
Surface area15510 Å2
MethodPISA
Unit cell
Length a, b, c (Å)74.573, 101.396, 46.927
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 Tm-1 protein / Resistance protein


Mass: 21017.758 Da / Num. of mol.: 2 / Fragment: NN domain, UNP residues 1-201 / Mutation: T91I
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Solanum lycopersicum (tomato) / Gene: Tm-1 / Production host: Escherichia coli (E. coli) / References: UniProt: A7M6E7
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 7 / 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: 2.11 Å3/Da / Density % sol: 41.71 %
Crystal growTemperature: 293 K / Method: vapor diffusion / pH: 6
Details: 4% Tacsimate (v/v), 12% (w/v) PEG3500, pH 6.0, VAPOR DIFFUSION, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-5A / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Nov 30, 2011 / Details: mirrors
RadiationMonochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.75→41.96 Å / Num. all: 9706 / Num. obs: 9706 / % possible obs: 95.3 % / Observed criterion σ(F): -3 / Observed criterion σ(I): -3
Reflection shellResolution: 2.75→2.8 Å / Rmerge(I) obs: 0.273 / Mean I/σ(I) obs: 2.6 / % possible all: 97.5

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Processing

Software
NameVersionClassification
HKL-2000data collection
MOLREPphasing
REFMAC5.7.0029refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.75→41.96 Å / Cor.coef. Fo:Fc: 0.945 / Cor.coef. Fo:Fc free: 0.913 / SU B: 12.938 / SU ML: 0.26 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.386 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.24591 442 4.8 %RANDOM
Rwork0.18836 ---
all0.191 9706 --
obs0.19109 8811 95.22 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 54.873 Å2
Baniso -1Baniso -2Baniso -3
1-4.43 Å20 Å2-0 Å2
2---4.57 Å20 Å2
3---0.15 Å2
Refinement stepCycle: LAST / Resolution: 2.75→41.96 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2682 0 0 7 2689
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0192714
X-RAY DIFFRACTIONr_bond_other_d0.0020.022624
X-RAY DIFFRACTIONr_angle_refined_deg1.531.9663672
X-RAY DIFFRACTIONr_angle_other_deg0.85736040
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.1575359
X-RAY DIFFRACTIONr_dihedral_angle_2_deg40.4824.57494
X-RAY DIFFRACTIONr_dihedral_angle_3_deg19.70515455
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.7321511
X-RAY DIFFRACTIONr_chiral_restr0.090.2452
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.023053
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02578
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.75→2.821 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.344 37 -
Rwork0.257 636 -
obs--98.39 %

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