+Open data
-Basic information
Entry | Database: PDB / ID: 2qvt | ||||||
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Title | Structure of Melampsora lini avirulence protein, AvrL567-D | ||||||
Components | AvrL567-D | ||||||
Keywords | UNKNOWN FUNCTION / AvrL567-A / AvrL567-D / plant disease resistance | ||||||
Function / homology | Immunoglobulin-like - #2510 / Melampsora lini avirulence protein AvrL567 / Melampsora avirulence protein AvrL567 superfamily / Melampsora lini avirulence protein AvrL567-A / Immunoglobulin-like / Sandwich / Mainly Beta / AvrL567-D Function and homology information | ||||||
Biological species | Melampsora lini (flax rust) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.26 Å | ||||||
Authors | Guncar, G. / Wang, C.I. / Forwood, J.K. / Teh, T. / Catanzariti, A.M. / Lawrence, G. / Schirra, H.J. / Anderson, P.A. / Ellis, J.G. / Dodds, P.N. / Kobe, B. | ||||||
Citation | Journal: Plant Cell / Year: 2007 Title: Crystal structures of flax rust avirulence proteins AvrL567-A and -D reveal details of the structural basis for flax disease resistance specificity. Authors: Wang, C.I. / Guncar, G. / Forwood, J.K. / Teh, T. / Catanzariti, A.M. / Lawrence, G.J. / Loughlin, F.E. / Mackay, J.P. / Schirra, H.J. / Anderson, P.A. / Ellis, J.G. / Dodds, P.N. / Kobe, B. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2qvt.cif.gz | 37.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2qvt.ent.gz | 25.6 KB | Display | PDB format |
PDBx/mmJSON format | 2qvt.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/qv/2qvt ftp://data.pdbj.org/pub/pdb/validation_reports/qv/2qvt | HTTPS FTP |
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-Related structure data
Related structure data | 2opcS S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 16896.322 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Melampsora lini (flax rust) / Strain: Bs1 / Plasmid: pHUE / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q1HBK6 |
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#2: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 2.25 Å3/Da / Density % sol: 45.4 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: 0.1 M HEPES, 1.66 M ammonium sulfate, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.5418 Å |
Detector | Type: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Mar 1, 2005 |
Radiation | Monochromator: Mirrors / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2.26→50 Å / Num. obs: 7619 / % possible obs: 99.7 % / Redundancy: 7.4 % / Rmerge(I) obs: 0.113 / Net I/σ(I): 11.9 |
Reflection shell | Resolution: 2.26→2.32 Å / Redundancy: 6.7 % / Rmerge(I) obs: 0.497 / Mean I/σ(I) obs: 8.35 / Num. unique all: 7619 / % possible all: 98.5 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 2opc Resolution: 2.26→40.26 Å / Cor.coef. Fo:Fc: 0.939 / Cor.coef. Fo:Fc free: 0.901 / SU B: 5.007 / SU ML: 0.127 / Cross valid method: THROUGHOUT / ESU R: 0.259 / ESU R Free: 0.223 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 29.332 Å2
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Refinement step | Cycle: LAST / Resolution: 2.26→40.26 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.26→2.32 Å / Total num. of bins used: 20
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