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Yorodumi- PDB-2cjj: Crystal Structure of the MYB domain of the RAD transcription fact... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2cjj | ||||||
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Title | Crystal Structure of the MYB domain of the RAD transcription factor from Antirrhinum majus | ||||||
Components | RADIALIS | ||||||
Keywords | DNA BINDING PROTEIN / PLANT DEVELOPMENT / DNA-BINDING PROTEIN / MYB TRANSCRIPTION FACTOR / DNA-BINDING / NUCLEAR PROTEIN / FLORAL ASYMMETRY | ||||||
Function / homology | Function and homology information determination of dorsal/ventral asymmetry / flower development / nucleus Similarity search - Function | ||||||
Biological species | ANTIRRHINUM MAJUS (snapdragon) | ||||||
Method | X-RAY DIFFRACTION / SIRAS / Resolution: 1.9 Å | ||||||
Authors | Stevenson, C.E.M. / Burton, N. / Costa, M.M. / Nath, U. / Dixon, R.A. / Coen, E.S. / Lawson, D.M. | ||||||
Citation | Journal: Proteins: Struct., Funct., Bioinf. / Year: 2006 Title: Crystal Structure of the Myb Domain of the Rad Transcription Factor from Antirrhinum Majus. Authors: Stevenson, C.E.M. / Burton, N. / Costa, M.M. / Nath, U. / Dixon, R.A. / Coen, E.S. / Lawson, D.M. #1: Journal: Acta Crystallogr.,Sect.F / Year: 2005 Title: Crystallisation and Preliminary X-Ray Analysis of the Rad Protein from Antirrhinum Majus Authors: Stevenson, C.E.M. / Burton, N. / Costa, M. / Nath, U. / Dixon, R.A. / Coen, E.S. / Lawson, D.M. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2cjj.cif.gz | 26 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2cjj.ent.gz | 17 KB | Display | PDB format |
PDBx/mmJSON format | 2cjj.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/cj/2cjj ftp://data.pdbj.org/pub/pdb/validation_reports/cj/2cjj | HTTPS FTP |
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-Related structure data
Similar structure data |
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-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 10795.235 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Details: 8 KDA PROTEOLYTIC FRAGMENT, MYB DOMAIN / Source: (gene. exp.) ANTIRRHINUM MAJUS (snapdragon) / Plasmid: PRSET A / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q58FS3 |
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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: 2.3 Å3/Da / Density % sol: 46 % |
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Crystal grow | pH: 9.5 / Details: pH 9.50 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU RUH3R / Wavelength: 1.5418 |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE / Date: May 18, 2004 / Details: MIRRORS |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 1.9→37.9 Å / Num. obs: 6112 / % possible obs: 98.6 % / Observed criterion σ(I): 3 / Redundancy: 10.8 % / Biso Wilson estimate: 26.1 Å2 / Rmerge(I) obs: 0.07 / Net I/σ(I): 33.3 |
Reflection shell | Resolution: 1.9→1.97 Å / Rmerge(I) obs: 0.56 / Mean I/σ(I) obs: 3.6 / % possible all: 99.3 |
-Processing
Software |
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Refinement | Method to determine structure: SIRAS / Resolution: 1.9→37.9 Å / Cor.coef. Fo:Fc: 0.949 / Cor.coef. Fo:Fc free: 0.93 / SU B: 9.067 / SU ML: 0.125 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.168 / ESU R Free: 0.152 / 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: 1.4 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 24.04 Å2
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Refinement step | Cycle: LAST / Resolution: 1.9→37.9 Å
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Refine LS restraints |
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