[English] 日本語
Yorodumi
- PDB-3wrv: Crystal structure of NN domain of resistance protein -

+
Open data


ID or keywords:

Loading...

-
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


modulation by host 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 / UPF0261 domain / Uncharacterised protein family (UPF0261) N-terminal domain / Uncharacterised protein family (UPF0261) C-terminal domain / TIM-barrel domain, IGPS-like / : / Phosphoenolpyruvate hydrolase-like / Pyruvate/Phosphoenolpyruvate kinase-like domain superfamily / Aldolase-type TIM barrel / Rossmann fold ...Uncharacterised protein family UPF0261, NN domain / UPF0261 domain / Uncharacterised protein family (UPF0261) N-terminal domain / Uncharacterised protein family (UPF0261) C-terminal domain / TIM-barrel domain, IGPS-like / : / Phosphoenolpyruvate hydrolase-like / 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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
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

-
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

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
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

-
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

-
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 %

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more