[English] 日本語
Yorodumi- PDB-5pbf: PanDDA analysis group deposition -- Crystal Structure of BAZ2B in... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5pbf | ||||||
---|---|---|---|---|---|---|---|
Title | PanDDA analysis group deposition -- Crystal Structure of BAZ2B in complex with N09645a | ||||||
Components | Bromodomain adjacent to zinc finger domain protein 2B | ||||||
Keywords | DNA BINDING PROTEIN / PanDDA / SGC - Diamond I04-1 fragment screening / bromodomain / epigenetics | ||||||
Function / homology | Function and homology information chromatin remodeling / regulation of transcription by RNA polymerase II / DNA binding / metal ion binding / nucleus Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / molecular replacement / Resolution: 1.801 Å | ||||||
Authors | Pearce, N.M. / Krojer, T. / Talon, R. / Bradley, A.R. / Fairhead, M. / Sethi, R. / Wright, N. / MacLean, E. / Collins, P. / Brandao-Neto, J. ...Pearce, N.M. / Krojer, T. / Talon, R. / Bradley, A.R. / Fairhead, M. / Sethi, R. / Wright, N. / MacLean, E. / Collins, P. / Brandao-Neto, J. / Douangamath, A. / Renjie, Z. / Dias, A. / Vollmar, M. / Ng, J. / Brennan, P.E. / Cox, O. / Bountra, C. / Arrowsmith, C.H. / Edwards, A. / von Delft, F. | ||||||
Citation | Journal: Nat Commun / Year: 2017 Title: A multi-crystal method for extracting obscured crystallographic states from conventionally uninterpretable electron density. Authors: Pearce, N.M. / Krojer, T. / Bradley, A.R. / Collins, P. / Nowak, R.P. / Talon, R. / Marsden, B.D. / Kelm, S. / Shi, J. / Deane, C.M. / von Delft, F. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 5pbf.cif.gz | 44.6 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb5pbf.ent.gz | 30.6 KB | Display | PDB format |
PDBx/mmJSON format | 5pbf.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/pb/5pbf ftp://data.pdbj.org/pub/pdb/validation_reports/pb/5pbf | HTTPS FTP |
---|
-Group deposition
ID | G_1002018 (9 entries) |
---|---|
Title | PanDDA analysis group deposition of models with modelled events (e.g. bound ligands) |
Type | changed state |
Description | bromodomain of human BAZ2B screened against the ZENOBIA Fragment Library by X-ray Crystallography at the XChem facility of Diamond Light Source beamline I04-1. Check out the PanDDA event maps at https://zenodo.org/record/290199/files/0_index.html |
-Related structure data
Related structure data | 3g0lS S: Starting model for refinement |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
|
-Components
#1: Protein | Mass: 16090.326 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: BAZ2B, KIAA1476 / Production host: escherichia coli (E. coli) / References: UniProt: Q9UIF8 | ||||||
---|---|---|---|---|---|---|---|
#2: Chemical | #3: Chemical | ChemComp-8HJ / | #4: Water | ChemComp-HOH / | Nonpolymer details | yes C1Cc2ccc(cc2NC1=O)O None 15.85 40.89 40.89 C1Cc2ccc(cc2NC1=O)O 4 - High Confidence None 0.94 ... | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 3.54 Å3/Da / Density % sol: 65.26 % / Mosaicity: 0.14 ° |
---|---|
Crystal grow | Temperature: 277 K / Method: vapor diffusion, sitting drop / pH: 7 / Details: 30% PEG600 -- 0.1M MES pH 6.0 |
-Data collection
Diffraction | Mean temperature: 100 K | ||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I04-1 / Wavelength: 0.92 Å | ||||||||||||||||||||||||||||||
Detector | Type: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Mar 10, 2013 | ||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Scattering type: x-ray | ||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.92 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||
Reflection | Resolution: 1.8→28.98 Å / Num. obs: 21028 / % possible obs: 97.7 % / Redundancy: 6.5 % / Biso Wilson estimate: 27.41 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.077 / Rpim(I) all: 0.033 / Rrim(I) all: 0.084 / Net I/σ(I): 14.7 / Num. measured all: 136847 / Scaling rejects: 7 | ||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
|
-Phasing
Phasing | Method: molecular replacement |
---|
-Processing
Software |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: FOURIER SYNTHESIS Starting model: 3G0L Resolution: 1.801→28.98 Å / SU ML: 0.2 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 22.28 / Stereochemistry target values: ML
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 87.31 Å2 / Biso mean: 31.8667 Å2 / Biso min: 15.86 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 1.801→28.98 Å
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 8
|