+Open data
-Basic information
Entry | Database: PDB / ID: 2p1q | ||||||
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Title | Mechanism of Auxin Perception by the TIR1 ubiquitin ligase | ||||||
Components |
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Keywords | SIGNALING PROTEIN / F-box / leucine rich repeat | ||||||
Function / homology | Function and homology information auxin receptor activity / auxin binding / lateral root formation / pollen maturation / stamen development / phragmoplast / gravitropism / jasmonic acid mediated signaling pathway / ethylene-activated signaling pathway / response to jasmonic acid ...auxin receptor activity / auxin binding / lateral root formation / pollen maturation / stamen development / phragmoplast / gravitropism / jasmonic acid mediated signaling pathway / ethylene-activated signaling pathway / response to jasmonic acid / response to auxin / auxin-activated signaling pathway / inositol hexakisphosphate binding / response to water deprivation / negative regulation of DNA recombination / cellular response to phosphate starvation / SCF ubiquitin ligase complex / chromosome segregation / defense response / response to wounding / microtubule cytoskeleton organization / spindle / ubiquitin-protein transferase activity / ubiquitin-dependent protein catabolic process / transcription cis-regulatory region binding / protein ubiquitination / DNA-binding transcription factor activity / mitochondrion / nucleus / cytosol Similarity search - Function | ||||||
Biological species | Arabidopsis thaliana (thale cress) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.91 Å | ||||||
Authors | Tan, X. / Calderon-Villalobos, L.I.A. / Sharon, M. / Robinson, C.V. / Estelle, M. / Zheng, N. | ||||||
Citation | Journal: Nature / Year: 2007 Title: Mechanism of auxin perception by the TIR1 ubiquitin ligase. Authors: Tan, X. / Calderon-Villalobos, L.I. / Sharon, M. / Zheng, C. / Robinson, C.V. / Estelle, M. / Zheng, N. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2p1q.cif.gz | 172.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2p1q.ent.gz | 131.9 KB | Display | PDB format |
PDBx/mmJSON format | 2p1q.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2p1q_validation.pdf.gz | 990.9 KB | Display | wwPDB validaton report |
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Full document | 2p1q_full_validation.pdf.gz | 996.9 KB | Display | |
Data in XML | 2p1q_validation.xml.gz | 16.7 KB | Display | |
Data in CIF | 2p1q_validation.cif.gz | 29.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/p1/2p1q ftp://data.pdbj.org/pub/pdb/validation_reports/p1/2p1q | HTTPS FTP |
-Related structure data
Related structure data | 2p1mSC 2p1nC 2p1oC 2p1pC 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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2 |
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Unit cell |
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Components on special symmetry positions |
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-Components
-Protein , 2 types, 2 molecules AB
#1: Protein | Mass: 17876.043 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Gene: SKP1A, ASK1, SKP1, UIP1 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: Q39255 |
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#2: Protein | Mass: 66875.438 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Gene: TIR1, FBL1, WEI1 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: Q570C0 |
-Protein/peptide , 1 types, 1 molecules C
#3: Protein/peptide | Mass: 1601.872 Da / Num. of mol.: 1 / Source method: obtained synthetically Details: IAA7 peptide and indole-3-acetic acid are from commercial sources. It naturally occurs in Arabidopsis thaliana References: UniProt: Q38825 |
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-Non-polymers , 3 types, 772 molecules
#4: Chemical | ChemComp-IHP / |
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#5: Chemical | ChemComp-IAC / |
#6: 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: 2.93 Å3/Da / Density % sol: 58.02 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6 Details: 100 mM BTP, 10% 14% PEG 20,000, 200 mM NaCl, and 5 mM DTT, pH 6, VAPOR DIFFUSION, HANGING DROP, temperature 298K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ALS / Beamline: 8.2.1 / Wavelength: 1 Å |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Sep 1, 2006 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.91→50 Å / Num. all: 69793 / Num. obs: 69793 / % possible obs: 99.9 % / Redundancy: 3.8 % / Rsym value: 0.039 / Net I/σ(I): 33 |
Reflection shell | Resolution: 1.91→2.03 Å / Redundancy: 3.6 % / Mean I/σ(I) obs: 4.9 / Rsym value: 0.249 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY: 2P1M Resolution: 1.91→50 Å / Cor.coef. Fo:Fc: 0.963 / Cor.coef. Fo:Fc free: 0.946 / SU B: 5.47 / SU ML: 0.086 / Cross valid method: THROUGHOUT / ESU R: 0.129 / ESU R Free: 0.128 / 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: 27.399 Å2
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Refinement step | Cycle: LAST / Resolution: 1.91→50 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.91→1.956 Å / Total num. of bins used: 20
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