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- PDB-3ozi: Crystal structure of the TIR domain from the flax disease resista... -

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Basic information

Entry
Database: PDB / ID: 3ozi
TitleCrystal structure of the TIR domain from the flax disease resistance protein L6
ComponentsL6tr
KeywordsPLANT PROTEIN / plant TIR domain / Signal transduction
Function / homology
Function and homology information


NADP+ nucleosidase activity / ADP-ribosyl cyclase/cyclic ADP-ribose hydrolase / NAD+ nucleotidase, cyclic ADP-ribose generating / ADP binding / signal transduction
Similarity search - Function
Toll/interleukin-1 receptor homology (TIR) domain / NB-ARC / NB-ARC domain / TIR domain / Toll - interleukin 1 - resistance / TIR domain profile. / Toll/interleukin-1 receptor homology (TIR) domain / Toll/interleukin-1 receptor homology (TIR) domain superfamily / Leucine-rich repeat domain superfamily / Winged helix DNA-binding domain superfamily ...Toll/interleukin-1 receptor homology (TIR) domain / NB-ARC / NB-ARC domain / TIR domain / Toll - interleukin 1 - resistance / TIR domain profile. / Toll/interleukin-1 receptor homology (TIR) domain / Toll/interleukin-1 receptor homology (TIR) domain superfamily / Leucine-rich repeat domain superfamily / Winged helix DNA-binding domain superfamily / Rossmann fold / P-loop containing nucleoside triphosphate hydrolase / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
: / ADP-ribosyl cyclase/cyclic ADP-ribose hydrolase / ADP-ribosyl cyclase/cyclic ADP-ribose hydrolase
Similarity search - Component
Biological speciesLinum usitatissimum (flax)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.3 Å
AuthorsVe, T. / Bernoux, M. / Williams, S. / Valkov, E. / Warren, C. / Hatters, D. / Ellis, J.G. / Dodds, P.N. / Kobe, B.
CitationJournal: Cell Host Microbe / Year: 2011
Title: Structural and Functional Analysis of a Plant Resistance Protein TIR Domain Reveals Interfaces for Self-Association, Signaling, and Autoregulation.
Authors: Bernoux, M. / Ve, T. / Williams, S. / Warren, C. / Hatters, D. / Valkov, E. / Zhang, X. / Ellis, J.G. / Kobe, B. / Dodds, P.N.
History
DepositionSep 25, 2010Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Apr 27, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 1, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / 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 / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _struct_conn.pdbx_dist_value / _struct_conn.ptnr2_auth_seq_id / _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: L6tr
B: L6tr
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,9133
Polymers46,8542
Non-polymers591
Water3,297183
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: L6tr
hetero molecules

B: L6tr


Theoretical massNumber of molelcules
Total (without water)46,9133
Polymers46,8542
Non-polymers591
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation1_554x,y,z-11
Buried area1570 Å2
ΔGint-10 kcal/mol
Surface area16300 Å2
MethodPISA
Unit cell
Length a, b, c (Å)65.941, 102.241, 58.300
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21212
Components on special symmetry positions
IDModelComponents
11A-205-

CO

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Components

#1: Protein L6tr


Mass: 23427.186 Da / Num. of mol.: 2 / Fragment: TIR domain (UNP RESIDUES 29-229)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Linum usitatissimum (flax) / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q40254, UniProt: Q9XEH0*PLUS
#2: Chemical ChemComp-CO / COBALT (II) ION


Mass: 58.933 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Co
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 183 / 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: 2.1 Å3/Da / Density % sol: 41.35 % / Mosaicity: 0 °
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.2
Details: 36% PEG 200, 0.1M sodium acetate, pH 5.2, 10mM hexammine cobalt(III) chloride, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.953693 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Sep 20, 2009
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.953693 Å / Relative weight: 1
ReflectionResolution: 2.3→55.415 Å / Num. all: 18088 / Num. obs: 18088 / % possible obs: 99.7 % / Redundancy: 7.2 % / Rsym value: 0.093 / Net I/σ(I): 16.7
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) allRmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRpim(I) allRrim(I) allRsym valueNet I/σ(I) obs% possible all
2.3-2.4270.3470.3212.31830926060.1290.3470.3216.799.8
2.42-2.577.40.2850.2652.81800724450.1040.2850.2658.199.7
2.57-2.757.40.2090.1943.81711823280.0760.2090.19410.499.8
2.75-2.977.30.1610.154.91570721450.0590.1610.1512.699.9
2.97-3.257.30.1160.1086.71462420050.0430.1160.10816.1100
3.25-3.647.20.0770.0719.71328518340.0290.0770.07122.299.9
3.64-4.27.10.060.05611.81155816220.0230.060.0562899.8
4.2-5.1470.0510.04712.4960713810.0190.0510.04732.8100
5.14-7.276.70.0560.05212748411090.0220.0560.05226.999.9
7.27-19.5316.50.0360.03315.439786130.0140.0360.03332.594.9

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Phasing

PhasingMethod: molecular replacement
Phasing MRRfactor: 75.13 / Model details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation2.5 Å19.53 Å
Translation2.5 Å19.53 Å

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Processing

Software
NameVersionClassificationNB
SCALA3.3.9data scaling
PHASER2.1.4phasing
PHENIX1.6.4_486refinement
PDB_EXTRACT3.1data extraction
Blu-Icedata collection
XSCALEdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3JRN

3jrn


Resolution: 2.3→19.296 Å / Occupancy max: 1 / Occupancy min: 1 / SU ML: 0.24 / σ(F): 1.36 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2297 918 5.09 %
Rwork0.1738 --
obs0.1766 18032 99.61 %
Solvent computationShrinkage radii: 0.72 Å / VDW probe radii: 1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 40.416 Å2 / ksol: 0.38 e/Å3
Displacement parametersBiso max: 71.81 Å2 / Biso mean: 23.8765 Å2 / Biso min: 7.7 Å2
Baniso -1Baniso -2Baniso -3
1-0.0834 Å20 Å2-0 Å2
2--0.3705 Å20 Å2
3----0.4539 Å2
Refinement stepCycle: LAST / Resolution: 2.3→19.296 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2796 0 1 183 2980
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0082862
X-RAY DIFFRACTIONf_angle_d1.0013851
X-RAY DIFFRACTIONf_chiral_restr0.067398
X-RAY DIFFRACTIONf_plane_restr0.004495
X-RAY DIFFRACTIONf_dihedral_angle_d15.6771089
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 7

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.3001-2.42120.23941320.177324122544100
2.4212-2.57250.25351350.18472377251299
2.5725-2.77060.24011460.182224032549100
2.7706-3.04850.24511200.184324222542100
3.0485-3.48740.23031290.172424452574100
3.4874-4.38520.20381450.155224542599100
4.3852-19.29640.23061110.17882601271299

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