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Open data
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Basic information
Entry | Database: PDB / ID: 3nxb | ||||||
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Title | Crystal Structure of the Bromodomain of human CECR2 | ||||||
![]() | Cat eye syndrome critical region protein 2 | ||||||
![]() | TRANSCRIPTION / Structural Genomics Consortium / SGC / CECR2 / cat eye syndrome chromosome region candidate 2 / bromodomain / structural genomics | ||||||
Function / homology | ![]() 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 / vesicle-mediated transport ...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 / vesicle-mediated transport / cytoskeleton organization / neural tube closure / euchromatin / chromatin remodeling / nucleus Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | 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) | ||||||
![]() | ![]() 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. | ||||||
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 101.6 KB | Display | ![]() |
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PDB format | ![]() | 77 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 449.1 KB | Display | ![]() |
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Full document | ![]() | 449.6 KB | Display | |
Data in XML | ![]() | 12.2 KB | Display | |
Data in CIF | ![]() | 17.2 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-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 ( |
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Similar structure data |
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Links
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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.) ![]() ![]() ![]() #2: Chemical | #3: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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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: ![]() | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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: ![]() | |||||||||
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Phasing MR | Rfactor: 46.9 / Model details: Phaser MODE: MR_AUTO
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Processing
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Refinement | Method to determine structure: ![]() 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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