+Open data
-Basic information
Entry | Database: PDB / ID: 3ga1 | ||||||
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Title | Crystal Structure of the Human Nac1 POZ Domain | ||||||
Components | Nucleus accumbens-associated protein 1 | ||||||
Keywords | TRANSCRIPTION / BTB/POZ domain / Nucleus / Phosphoprotein / Repressor / Transcription regulation | ||||||
Function / homology | Function and homology information DNA-binding transcription repressor activity, RNA polymerase II-specific / histone deacetylase binding / cell junction / DNA-binding transcription factor activity, RNA polymerase II-specific / RNA polymerase II cis-regulatory region sequence-specific DNA binding / intracellular membrane-bounded organelle / negative regulation of DNA-templated transcription / positive regulation of cell population proliferation / regulation of transcription by RNA polymerase II / nucleoplasm ...DNA-binding transcription repressor activity, RNA polymerase II-specific / histone deacetylase binding / cell junction / DNA-binding transcription factor activity, RNA polymerase II-specific / RNA polymerase II cis-regulatory region sequence-specific DNA binding / intracellular membrane-bounded organelle / negative regulation of DNA-templated transcription / positive regulation of cell population proliferation / regulation of transcription by RNA polymerase II / nucleoplasm / nucleus / cytoplasm Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.1 Å | ||||||
Authors | Stead, M.A. / Carr, S.B. / Wright, S.C. | ||||||
Citation | Journal: Acta Crystallogr.,Sect.F / Year: 2009 Title: Structure of the human Nac1 POZ domain Authors: Stead, M.A. / Carr, S.B. / Wright, S.C. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3ga1.cif.gz | 62.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3ga1.ent.gz | 46.2 KB | Display | PDB format |
PDBx/mmJSON format | 3ga1.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ga/3ga1 ftp://data.pdbj.org/pub/pdb/validation_reports/ga/3ga1 | HTTPS FTP |
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-Related structure data
Related structure data | 2if5S S: Starting model for refinement |
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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
#1: Protein | Mass: 14270.242 Da / Num. of mol.: 2 / Fragment: POZ Domain, UNP residues 2-125 / Mutation: F98D Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: NAC1 / Plasmid: pGEX-6P-1 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3) pLysS / References: UniProt: Q96RE7 #2: Chemical | ChemComp-NO3 / #3: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.52 Å3/Da / Density % sol: 51.11 % / Mosaicity: 0.477 ° |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, sitting drop / pH: 7.5 Details: 6M ammonium nitrate, 0.1M bis-tris propane, pH7.5, VAPOR DIFFUSION, SITTING DROP, temperature 291K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.9763 Å |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Jan 21, 2009 / Details: Mirrors |
Radiation | Monochromator: Sigitally Focussed Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9763 Å / Relative weight: 1 |
Reflection | Redundancy: 6.75 % / Number: 120991 / Rmerge(I) obs: 0.103 / D res high: 2.1 Å / D res low: 47.96 Å |
Reflection | Resolution: 2.1→47.96 Å / Num. obs: 17928 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 6.7 % / Biso Wilson estimate: 26.855 Å2 / Rmerge(I) obs: 0.103 / Rsym value: 0.111 / Net I/σ(I): 13.5 |
Reflection shell | Resolution: 2.1→2.21 Å / Redundancy: 7 % / Rmerge(I) obs: 0.506 / Mean I/σ(I) obs: 4 / Num. measured all: 17832 / Num. unique all: 2542 / Rsym value: 0.546 / % possible all: 100 |
-Phasing
Phasing | Method: molecular replacement | |||||||||
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Phasing MR | Rfactor: 56.87 / Model details: Phaser MODE: MR_AUTO
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 2IF5 Resolution: 2.1→47.96 Å / Cor.coef. Fo:Fc: 0.936 / Cor.coef. Fo:Fc free: 0.927 / WRfactor Rfree: 0.243 / WRfactor Rwork: 0.208 / Occupancy max: 1 / Occupancy min: 0 / FOM work R set: 0.854 / SU B: 9.577 / SU ML: 0.118 / SU R Cruickshank DPI: 0.206 / SU Rfree: 0.176 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.206 / ESU R Free: 0.176 / 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: 55.26 Å2 / Biso mean: 18.089 Å2 / Biso min: 2 Å2
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Refinement step | Cycle: LAST / Resolution: 2.1→47.96 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.1→2.155 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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