+Open data
-Basic information
Entry | Database: PDB / ID: 3cmy | ||||||
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Title | Structure of a homeodomain in complex with DNA | ||||||
Components |
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Keywords | TRANSCRIPTION REGULATOR/DNA / DNA-BINDING PROTEIN / DNA / TRANSCRIPTION REGULATION / TRANSCRIPTION REGULATOR-DNA COMPLEX | ||||||
Function / homology | Function and homology information HMG box domain binding / chromatin => GO:0000785 / muscle organ development / sensory perception of sound / animal organ morphogenesis / sequence-specific double-stranded DNA binding / nervous system development / HATs acetylate histones / sequence-specific DNA binding / DNA-binding transcription factor activity, RNA polymerase II-specific ...HMG box domain binding / chromatin => GO:0000785 / muscle organ development / sensory perception of sound / animal organ morphogenesis / sequence-specific double-stranded DNA binding / nervous system development / HATs acetylate histones / sequence-specific DNA binding / DNA-binding transcription factor activity, RNA polymerase II-specific / DNA-binding transcription factor activity / apoptotic process / positive regulation of DNA-templated transcription / positive regulation of transcription by RNA polymerase II / nucleoplasm Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.95 Å | ||||||
Authors | Birrane, G. / Ladias, J.A.A. / Soni, A. | ||||||
Citation | Journal: Biochemistry / Year: 2009 Title: Structural Basis for DNA Recognition by the Human PAX3 Homeodomain. Authors: Birrane, G. / Soni, A. / Ladias, J.A. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3cmy.cif.gz | 58.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3cmy.ent.gz | 41.9 KB | Display | PDB format |
PDBx/mmJSON format | 3cmy.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/cm/3cmy ftp://data.pdbj.org/pub/pdb/validation_reports/cm/3cmy | 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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Number of models | 2 |
-Components
#1: Protein | Mass: 7540.420 Da / Num. of mol.: 1 / Fragment: HOMEODOMAIN (UNP residues 219-278) Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: PAX3 / Plasmid: PET-6H / Production host: Escherichia coli (E. coli) / Strain (production host): C41 / References: UniProt: P23760 |
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#2: DNA chain | Mass: 4247.805 Da / Num. of mol.: 1 / Source method: obtained synthetically |
#3: DNA chain | Mass: 4309.826 Da / Num. of mol.: 1 / Source method: obtained synthetically |
#4: Chemical | ChemComp-EDO / |
#5: Water | ChemComp-HOH / |
Compound details | THE DNA CAN PACK IN TWO ORIENTATIONS WHICH ARE NEARLY EQUIVALENT. ONLY 1/2 OF THE CRYSTALLIZED ...THE DNA CAN PACK IN TWO ORIENTATIO |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 1.94 Å3/Da / Density % sol: 36.53 % | ||||||||||||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.6 Details: 19-22% polyethylene glycol 8000, 100 mM ammonium sulphate, 20mM magnesium chloride, 15% 2-methyl-2,4-pentanediol, 50 mM 4-(2-hydroxyethyl)-1-piperazineethanesulfonic acid, pH 7.6, VAPOR ...Details: 19-22% polyethylene glycol 8000, 100 mM ammonium sulphate, 20mM magnesium chloride, 15% 2-methyl-2,4-pentanediol, 50 mM 4-(2-hydroxyethyl)-1-piperazineethanesulfonic acid, pH 7.6, VAPOR DIFFUSION, SITTING DROP, temperature 293K | ||||||||||||||||||||||||||||||||||||||||||||||||||||
Components of the solutions |
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: NSLS / Beamline: X12B / Wavelength: 1 Å |
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: Jan 25, 2008 / Details: MIRRORS |
Radiation | Monochromator: SAGITALLY FOCUSED Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.95→50 Å / Num. obs: 9726 / % possible obs: 99.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 7.6 % / Biso Wilson estimate: 38.3 Å2 / Rsym value: 0.064 / Net I/σ(I): 27 |
Reflection shell | Resolution: 1.95→2.02 Å / Redundancy: 6.7 % / Mean I/σ(I) obs: 3 / Num. unique all: 966 / Rsym value: 0.584 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: IFJL Resolution: 1.95→29.5 Å / Cor.coef. Fo:Fc: 0.971 / Cor.coef. Fo:Fc free: 0.96 / SU ML: 0.102 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.152 / ESU R Free: 0.14 / 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: BABINET MODEL WITH MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.95→29.5 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.95→2.001 Å / Total num. of bins used: 20
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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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