+Open data
-Basic information
Entry | Database: PDB / ID: 3nxb | ||||||
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Title | Crystal Structure of the Bromodomain of human CECR2 | ||||||
Components | Cat eye syndrome critical region protein 2 | ||||||
Keywords | TRANSCRIPTION / Structural Genomics Consortium / SGC / CECR2 / cat eye syndrome chromosome region candidate 2 / bromodomain / structural genomics | ||||||
Function / homology | Function and homology information CERF complex / neural fold formation / inner ear receptor cell stereocilium organization / cytoskeleton-dependent cytokinesis / apoptotic DNA fragmentation / ATP-dependent chromatin remodeler activity / execution phase of apoptosis / cochlea development / single fertilization / cytoskeleton organization ...CERF complex / neural fold formation / inner ear receptor cell stereocilium organization / cytoskeleton-dependent cytokinesis / apoptotic DNA fragmentation / ATP-dependent chromatin remodeler activity / execution phase of apoptosis / cochlea development / single fertilization / cytoskeleton organization / vesicle-mediated transport / neural tube closure / euchromatin / chromatin remodeling / nucleus Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.83 Å | ||||||
Authors | Filippakopoulos, P. / Picaud, S. / Keates, T. / Muniz, J. / von Delft, F. / Arrowsmith, C.H. / Edwards, A. / Weigelt, J. / Bountra, C. / Knapp, S. / Structural Genomics Consortium (SGC) | ||||||
Citation | Journal: Cell(Cambridge,Mass.) / Year: 2012 Title: Histone recognition and large-scale structural analysis of the human bromodomain family. Authors: Filippakopoulos, P. / Picaud, S. / Mangos, M. / Keates, T. / Lambert, J.P. / Barsyte-Lovejoy, D. / Felletar, I. / Volkmer, R. / Muller, S. / Pawson, T. / Gingras, A.C. / Arrowsmith, C.H. / Knapp, S. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3nxb.cif.gz | 101.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3nxb.ent.gz | 77 KB | Display | PDB format |
PDBx/mmJSON format | 3nxb.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/nx/3nxb ftp://data.pdbj.org/pub/pdb/validation_reports/nx/3nxb | HTTPS FTP |
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-Related structure data
Related structure data | 2nxbC 2oo1SC 2ossSC 2ouoSC 2rfjC 3d7cSC 3daiSC 3dwySC 3gg3C 3hmeC 3hmfC 3hmhC 3i3jC 3iu5C 3iu6C 3lxjC 3mb3C 3mb4C 3mqmC 3p1cC 3p1dC 3q2eC 3rcwC 3tlpC 3uv2C 3uv4C 3uv5C 3uvdC 3uvwC 3uvxC 3uvyC 3uw9C 2grcS 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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1 |
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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 13856.856 Da / Num. of mol.: 2 / Fragment: BROMODOMAIN (unp residues 424-538) Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: CECR2, KIAA1740 / Plasmid: pNIC28-Bsa4 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)-R3 / References: UniProt: Q9BXF3 #2: Chemical | #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: 2.29 Å3/Da / Density % sol: 46.32 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, sitting drop / pH: 6.5 Details: 0.1M MES, 12% PEG 20,000, VAPOR DIFFUSION, SITTING DROP, temperature 277K, pH 6.5 |
-Data collection
Diffraction | Mean temperature: 100 K | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU FR-E SUPERBRIGHT / Wavelength: 1.542 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Jun 8, 2010 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 1.542 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Redundancy: 3.5 % / Av σ(I) over netI: 9.1 / Number: 77360 / Rsym value: 0.058 / D res high: 1.825 Å / D res low: 22.919 Å / Num. obs: 22346 / % possible obs: 99.3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Diffraction reflection shell |
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Reflection | Resolution: 1.83→29.25 Å / Num. all: 22503 / Num. obs: 22346 / % possible obs: 99.3 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.5 % / Biso Wilson estimate: 30.3 Å2 / Rmerge(I) obs: 0.058 / Rsym value: 0.058 / Net I/σ(I): 11.7 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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-Phasing
Phasing | Method: molecular replacement | |||||||||
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Phasing MR | Rfactor: 46.9 / 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: Ensemble of PDB entries 2OSS, 2OUO, 2GRC, 2OO1, 3DAI, 3D7C, 3DWY Resolution: 1.83→29.25 Å / Cor.coef. Fo:Fc: 0.964 / Cor.coef. Fo:Fc free: 0.954 / WRfactor Rfree: 0.21 / WRfactor Rwork: 0.1689 / Occupancy max: 1 / Occupancy min: 0.5 / FOM work R set: 0.8603 / SU B: 5.461 / SU ML: 0.086 / SU R Cruickshank DPI: 0.1225 / SU Rfree: 0.1189 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.119 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT U VALUES: WITH TLS ADDED
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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 max: 86.22 Å2 / Biso mean: 29.5597 Å2 / Biso min: 13.57 Å2
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Refinement step | Cycle: LAST / Resolution: 1.83→29.25 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.83→1.872 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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