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Yorodumi- PDB-5ene: Crystal structure of the second bromodomain of Pleckstrin homolog... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5ene | ||||||
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Title | Crystal structure of the second bromodomain of Pleckstrin homology domain interacting protein (PHIP) in complex with 5-Amino-2-benzyl-1,3-oxazole-4-carbonitrile (SGC - Diamond I04-1 fragment screening) | ||||||
Components | PH-interacting protein | ||||||
Keywords | SIGNALING PROTEIN / bromodomain / PHIP / crystallographic fragment screen / transcription / Structural Genomics / Structural Genomics Consortium / SGC | ||||||
Function / homology | Function and homology information regulation of cell morphogenesis / positive regulation of insulin-like growth factor receptor signaling pathway / RHOBTB2 GTPase cycle / cytoskeleton organization / positive regulation of mitotic nuclear division / negative regulation of extrinsic apoptotic signaling pathway / regulation of protein phosphorylation / lysine-acetylated histone binding / insulin receptor binding / insulin receptor signaling pathway ...regulation of cell morphogenesis / positive regulation of insulin-like growth factor receptor signaling pathway / RHOBTB2 GTPase cycle / cytoskeleton organization / positive regulation of mitotic nuclear division / negative regulation of extrinsic apoptotic signaling pathway / regulation of protein phosphorylation / lysine-acetylated histone binding / insulin receptor binding / insulin receptor signaling pathway / regulation of cell shape / positive regulation of cell population proliferation / regulation of transcription by RNA polymerase II / negative regulation of apoptotic process / positive regulation of DNA-templated transcription / positive regulation of transcription by RNA polymerase II / nucleus Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.49 Å | ||||||
Authors | Krojer, T. / Talon, R. / Collins, P. / Bradley, A. / Cox, O. / Amin, J. / Szykowska, A. / Burgess-Brown, N. / Spencer, J. / Brennan, P. ...Krojer, T. / Talon, R. / Collins, P. / Bradley, A. / Cox, O. / Amin, J. / Szykowska, A. / Burgess-Brown, N. / Spencer, J. / Brennan, P. / Bountra, C. / Arrowsmith, C.H. / Edwards, A. / von Delft, F. / Structural Genomics Consortium (SGC) | ||||||
Citation | Journal: Chem Sci / Year: 2016 Title: A poised fragment library enables rapid synthetic expansion yielding the first reported inhibitors of PHIP(2), an atypical bromodomain. Authors: Cox, O.B. / Krojer, T. / Collins, P. / Monteiro, O. / Talon, R. / Bradley, A. / Fedorov, O. / Amin, J. / Marsden, B.D. / Spencer, J. / von Delft, F. / Brennan, P.E. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5ene.cif.gz | 69.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5ene.ent.gz | 50.3 KB | Display | PDB format |
PDBx/mmJSON format | 5ene.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5ene_validation.pdf.gz | 437.9 KB | Display | wwPDB validaton report |
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Full document | 5ene_full_validation.pdf.gz | 437.8 KB | Display | |
Data in XML | 5ene_validation.xml.gz | 8.8 KB | Display | |
Data in CIF | 5ene_validation.cif.gz | 12.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/en/5ene ftp://data.pdbj.org/pub/pdb/validation_reports/en/5ene | HTTPS FTP |
-Related structure data
Related structure data | 5enbC 5encC 5enfC 5enhC 5eniC 5enjC 3mb3S 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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Unit cell |
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-Components
#1: Protein | Mass: 15594.661 Da / Num. of mol.: 1 / Fragment: Bromodomain, UNP residues 1315-1440 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: PHIP, WDR11 / Plasmid: pNIC28-Bsa4 / Production host: Escherichia coli (E. coli) / References: UniProt: Q8WWQ0 |
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#2: Chemical | ChemComp-5Q8 / |
#3: 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: 2.15 Å3/Da / Density % sol: 42.77 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, sitting drop / pH: 7.5 Details: 0.1M HEPES pH 7.5 , 0.15M magnesium chloride , 32% PEG3350 |
-Data collection
Diffraction | Mean temperature: 100 K | |||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I04-1 / Wavelength: 0.92 Å | |||||||||||||||||||||||||||
Detector | Type: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Jul 21, 2014 | |||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.92 Å / Relative weight: 1 | |||||||||||||||||||||||||||
Reflection | Resolution: 1.49→28.76 Å / Num. obs: 22778 / % possible obs: 99.4 % / Redundancy: 6.4 % / CC1/2: 0.999 / Rmerge(I) obs: 0.036 / Rpim(I) all: 0.016 / Net I/σ(I): 23.3 / Num. measured all: 146167 | |||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1 / Rejects: _
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-Phasing
Phasing | Method: molecular replacement |
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3mb3 Resolution: 1.49→28.76 Å / Cor.coef. Fo:Fc: 0.964 / Cor.coef. Fo:Fc free: 0.948 / SU B: 3.601 / SU ML: 0.067 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.082 / ESU R Free: 0.085 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS 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: 79.74 Å2 / Biso mean: 30.205 Å2 / Biso min: 16.72 Å2
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Refinement step | Cycle: final / Resolution: 1.49→28.76 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.488→1.526 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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