+Open data
-Basic information
Entry | Database: PDB / ID: 3a03 | ||||||
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Title | Crystal structure of Hox11L1 homeodomain | ||||||
Components | T-cell leukemia homeobox protein 2 | ||||||
Keywords | GENE REGULATION / HOMEODOMAIN / Developmental protein / DNA-binding / Homeobox / Nucleus | ||||||
Function / homology | Function and homology information animal organ development / negative regulation of dendrite morphogenesis / enteric nervous system development / chromatin => GO:0000785 / mesoderm formation / sequence-specific double-stranded DNA binding / DNA-binding transcription activator activity, RNA polymerase II-specific / sequence-specific DNA binding / DNA-binding transcription factor activity, RNA polymerase II-specific / RNA polymerase II cis-regulatory region sequence-specific DNA binding ...animal organ development / negative regulation of dendrite morphogenesis / enteric nervous system development / chromatin => GO:0000785 / mesoderm formation / sequence-specific double-stranded DNA binding / DNA-binding transcription activator activity, RNA polymerase II-specific / sequence-specific DNA binding / DNA-binding transcription factor activity, RNA polymerase II-specific / RNA polymerase II cis-regulatory region sequence-specific DNA binding / regulation of transcription by RNA polymerase II / positive regulation of transcription by RNA polymerase II / nucleus / cytoplasm Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.54 Å | ||||||
Authors | Miyazono, K. / Nagata, K. / Saigo, K. / Kojima, T. / Tanokura, M. | ||||||
Citation | Journal: Embo J. / Year: 2010 Title: Cooperative DNA-binding and sequence-recognition mechanism of aristaless and clawless Authors: Miyazono, K. / Zhi, Y. / Takamura, Y. / Nagata, K. / Saigo, K. / Kojima, T. / Tanokura, M. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3a03.cif.gz | 25.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3a03.ent.gz | 16.8 KB | Display | PDB format |
PDBx/mmJSON format | 3a03.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/a0/3a03 ftp://data.pdbj.org/pub/pdb/validation_reports/a0/3a03 | HTTPS FTP |
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-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 6831.938 Da / Num. of mol.: 1 / Fragment: Homeobox, residues 162-216 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: TLX2, HOX11L1, NCX / Production host: Escherichia coli (E. coli) / References: UniProt: O43763 | ||
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#2: Chemical | ChemComp-NA / | ||
#3: Chemical | #4: 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: 2.97 Å3/Da / Density % sol: 58.56 % |
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: Photon Factory / Beamline: AR-NW12A |
Detector | Type: ADSC QUANTUM 210 / Detector: CCD |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Relative weight: 1 |
Reflection | Resolution: 1.54→20 Å / Num. obs: 11716 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.54→19.34 Å / Cor.coef. Fo:Fc: 0.959 / Cor.coef. Fo:Fc free: 0.952 / Occupancy max: 1 / Occupancy min: 0 / SU B: 1.142 / SU ML: 0.044 / Cross valid method: THROUGHOUT / ESU R: 0.081 / ESU R Free: 0.08 / 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 max: 65.1 Å2 / Biso mean: 26.966 Å2 / Biso min: 8.27 Å2
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Refinement step | Cycle: LAST / Resolution: 1.54→19.34 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.536→1.576 Å / Total num. of bins used: 20
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