[English] 日本語
Yorodumi- PDB-5c4q: Crystal Structure Analysis of bromodomain from Leishmania donovan... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5c4q | ||||||
---|---|---|---|---|---|---|---|
Title | Crystal Structure Analysis of bromodomain from Leishmania donovani complexed with bromosporine | ||||||
Components | Bromodomain | ||||||
Keywords | TRANSCRIPTION / Structural Genomics Consortium / SGC / Bromodomain / Bromosporine / Leishmania donovani | ||||||
Function / homology | Function and homology information Bromodomain-like / Histone Acetyltransferase; Chain A / Bromodomain profile. / bromo domain / Bromodomain / Bromodomain-like superfamily / Bromodomain / Up-down Bundle / Mainly Alpha Similarity search - Domain/homology | ||||||
Biological species | Leishmania donovani (eukaryote) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.932 Å | ||||||
Authors | Jiang, D.Q. / Tempel, W. / Loppnau, P. / Graslund, S. / Arrowsmith, C.H. / Edwards, A.M. / Bountra, C. / Hui, R. / Amani, M. / Hou, C.F.D. / Structural Genomics Consortium (SGC) | ||||||
Citation | Journal: to be published Title: Crystal Structure Analysis of bromodomain from Leishmania donovani complexed with bromosporine Authors: Jiang, D.Q. / Tempel, W. / Loppnau, P. / Graslund, S. / Arrowsmith, C.H. / Edwards, A.M. / Bountra, C. / Hui, R. / Amani, M. / Hou, C.F.D. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 5c4q.cif.gz | 64.5 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb5c4q.ent.gz | 46.6 KB | Display | PDB format |
PDBx/mmJSON format | 5c4q.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5c4q_validation.pdf.gz | 1.2 MB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 5c4q_full_validation.pdf.gz | 1.2 MB | Display | |
Data in XML | 5c4q_validation.xml.gz | 13.1 KB | Display | |
Data in CIF | 5c4q_validation.cif.gz | 17.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/c4/5c4q ftp://data.pdbj.org/pub/pdb/validation_reports/c4/5c4q | HTTPS FTP |
-Related structure data
Related structure data | 4hbwS S: Starting model for refinement |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
2 |
| ||||||||
3 |
| ||||||||
Unit cell |
| ||||||||
Details | The biological assembly of the protein indicated by Mass spectrometry and Gel filtration is monomer. |
-Components
#1: Protein | Mass: 14440.311 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Leishmania donovani (strain BPK282A1) (eukaryote) Strain: BPK282A1 / Gene: LDBPK_363130 / Plasmid: V3R pRARE2 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: E9BU22 #2: Chemical | #3: Chemical | ChemComp-UNX / #4: Water | ChemComp-HOH / | |
---|
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 2.03 Å3/Da / Density % sol: 39.36 % |
---|---|
Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7 / Details: 2.4 M sodium malonate |
-Data collection
Diffraction | Mean temperature: 100 K | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Diffraction source | Source: ROTATING ANODE / Type: RIGAKU FR-E+ SUPERBRIGHT / Wavelength: 1.5418 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Jun 9, 2015 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 1.93→20 Å / Num. obs: 16741 / % possible obs: 94.9 % / Redundancy: 3.7 % / Biso Wilson estimate: 23.97 Å2 / Rmerge(I) obs: 0.094 / Rpim(I) all: 0.055 / Rrim(I) all: 0.109 / Χ2: 1.524 / Net I/av σ(I): 14.418 / Net I/σ(I): 7.2 / Num. measured all: 61331 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1 / Rejects: _
|
-Processing
Software |
| |||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4HBW Resolution: 1.932→19.16 Å / SU ML: 0.27 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 25.06 / Stereochemistry target values: ML Details: Bromosporine restraints generated by PHENIX.ELBOW were modified to restrain coordinates of the lactamate moiety in a single plane, prompted by a MOGUL query of related structures in the ...Details: Bromosporine restraints generated by PHENIX.ELBOW were modified to restrain coordinates of the lactamate moiety in a single plane, prompted by a MOGUL query of related structures in the Cambridge Structural Database.
| |||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 75.05 Å2 / Biso mean: 23.9427 Å2 / Biso min: 10.67 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 1.932→19.16 Å
| |||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| |||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 6
|