+Open data
-Basic information
Entry | Database: PDB / ID: 3ulz | ||||||
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Title | Crystal structure of apo BAK1 | ||||||
Components | BRASSINOSTEROID INSENSITIVE 1-associated receptor kinase 1 | ||||||
Keywords | TRANSFERASE / Kinase | ||||||
Function / homology | Function and homology information receptor serine/threonine kinase binding / transmembrane receptor protein tyrosine kinase activity / receptor protein-tyrosine kinase / defense response / endosome membrane / non-specific serine/threonine protein kinase / phosphorylation / signaling receptor binding / protein serine kinase activity / protein serine/threonine kinase activity ...receptor serine/threonine kinase binding / transmembrane receptor protein tyrosine kinase activity / receptor protein-tyrosine kinase / defense response / endosome membrane / non-specific serine/threonine protein kinase / phosphorylation / signaling receptor binding / protein serine kinase activity / protein serine/threonine kinase activity / ATP binding / identical protein binding / plasma membrane Similarity search - Function | ||||||
Biological species | Arabidopsis thaliana (thale cress) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.6 Å | ||||||
Authors | Lou, Z.Y. / Yan, L.M. / Ma, Y.Y. | ||||||
Citation | Journal: To be Published Title: Structural basis for BAK1 activation Authors: Lou, Z.Y. / Yan, L.M. / Ma, Y.Y. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3ulz.cif.gz | 142.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3ulz.ent.gz | 111.4 KB | Display | PDB format |
PDBx/mmJSON format | 3ulz.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ul/3ulz ftp://data.pdbj.org/pub/pdb/validation_reports/ul/3ulz | HTTPS FTP |
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-Related structure data
Related structure data | 2nryS S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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2 |
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Unit cell |
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Components on special symmetry positions |
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-Components
#1: Protein | Mass: 37515.266 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Gene: BAK1 / Production host: Escherichia coli (E. coli) References: UniProt: Q94F62, receptor protein-tyrosine kinase, non-specific serine/threonine protein kinase |
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#2: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.54 Å3/Da / Density % sol: 51.61 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: PEG 3350, sodium citrate, ammonium sulfate, HEPES, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 291K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 1 Å |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Jul 4, 2011 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.6→50 Å / Num. all: 11460 / Num. obs: 11442 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Biso Wilson estimate: 55.71 Å2 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 2NRY Resolution: 2.6→41.052 Å / Occupancy max: 1 / Occupancy min: 1 / FOM work R set: 0.7382 / SU ML: 0.73 / σ(F): 1.34 / Phase error: 31.94 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 78.591 Å2 / ksol: 0.319 e/Å3 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 206.75 Å2 / Biso mean: 81.9181 Å2 / Biso min: 20 Å2
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Refinement step | Cycle: LAST / Resolution: 2.6→41.052 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 3
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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