+Open data
-Basic information
Entry | Database: PDB / ID: 3kdi | ||||||
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Title | Structure of (+)-ABA bound PYL2 | ||||||
Components | Putative uncharacterized protein At2g26040 | ||||||
Keywords | HORMONE RECEPTOR / ABA / PYL2 | ||||||
Function / homology | Function and homology information protein phosphatase inhibitor complex / abscisic acid binding / abscisic acid-activated signaling pathway / protein phosphatase inhibitor activity / signaling receptor activity / protein homodimerization activity / identical protein binding / nucleus / plasma membrane / cytoplasm Similarity search - Function | ||||||
Biological species | Arabidopsis thaliana (thale cress) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.379 Å | ||||||
Authors | Yin, P. / Fan, H. / Hao, Q. / Yuan, X. / Yan, N. | ||||||
Citation | Journal: Nat.Struct.Mol.Biol. / Year: 2009 Title: Structural insights into the mechanism of abscisic acid signaling by PYL proteins Authors: Yin, P. / Fan, H. / Hao, Q. / Yuan, X. / Wu, D. / Pang, Y. / Yan, C. / Li, W. / Wang, J. / Yan, N. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3kdi.cif.gz | 86.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3kdi.ent.gz | 65.3 KB | Display | PDB format |
PDBx/mmJSON format | 3kdi.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3kdi_validation.pdf.gz | 730.9 KB | Display | wwPDB validaton report |
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Full document | 3kdi_full_validation.pdf.gz | 735.7 KB | Display | |
Data in XML | 3kdi_validation.xml.gz | 9.7 KB | Display | |
Data in CIF | 3kdi_validation.cif.gz | 11.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/kd/3kdi ftp://data.pdbj.org/pub/pdb/validation_reports/kd/3kdi | HTTPS FTP |
-Related structure data
Related structure data | 3kdhSC 3kdjC S: Starting model for refinement C: citing same article (ref.) |
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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 on special symmetry positions |
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-Components
#1: Protein | Mass: 21309.938 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Plasmid: pET-15b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: O80992 |
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#2: Chemical | ChemComp-A8S / ( |
#3: 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: 3.18 Å3/Da / Density % sol: 61.38 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, hanging drop / pH: 8.5 Details: 1M sodium citrate tribasic, 100mM Tris, pH8.5, 79mM MEGA-8 (Octanoyl-N-methylglucamide), VAPOR DIFFUSION, HANGING DROP, temperature 291K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SPring-8 / Beamline: BL41XU / Wavelength: 1 Å |
Detector | Type: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Oct 16, 2009 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.379→32.97 Å / Num. obs: 11603 / % possible obs: 95.5 % / Redundancy: 6.6 % / Biso Wilson estimate: 65.15 Å2 / Rmerge(I) obs: 0.062 / Net I/σ(I): 27 |
Reflection shell | Resolution: 2.379→2.47 Å / Rmerge(I) obs: 0.842 / Mean I/σ(I) obs: 2.3 / % possible all: 97.6 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 3KDH Resolution: 2.379→32.97 Å / Occupancy max: 1 / Occupancy min: 0.85 / FOM work R set: 0.798 / SU ML: 0.42 / Isotropic thermal model: TLS / σ(F): 1.34 / Phase error: 25.52 / 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: 61.548 Å2 / ksol: 0.392 e/Å3 | ||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 172.93 Å2 / Biso mean: 72.51 Å2 / Biso min: 40.93 Å2
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Refinement step | Cycle: LAST / Resolution: 2.379→32.97 Å
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Refine LS restraints |
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LS refinement shell |
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Refinement TLS params. | Method: refined / Origin x: -0.8065 Å / Origin y: 23.7398 Å / Origin z: 9.5054 Å
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Refinement TLS group | Selection details: resid 7:187 |