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- PDB-5c4q: Crystal Structure Analysis of bromodomain from Leishmania donovan... -
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Open data
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Basic information
Entry | Database: PDB / ID: 5c4q | ||||||
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Title | Crystal Structure Analysis of bromodomain from Leishmania donovani complexed with bromosporine | ||||||
![]() | Bromodomain | ||||||
![]() | TRANSCRIPTION / Structural Genomics Consortium / SGC / Bromodomain / Bromosporine / Leishmania donovani | ||||||
Function / homology | ![]() 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 | ![]() | ||||||
Method | ![]() ![]() | ||||||
![]() | 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) | ||||||
![]() | ![]() 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 |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 64.5 KB | Display | ![]() |
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PDB format | ![]() | 46.6 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 4hbwS S: Starting model for refinement |
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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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3 |
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Unit cell |
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Details | The biological assembly of the protein indicated by Mass spectrometry and Gel filtration is monomer. |
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Components
#1: Protein | Mass: 14440.311 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() Strain: BPK282A1 / Gene: LDBPK_363130 / Plasmid: V3R pRARE2 / Production host: ![]() ![]() #2: Chemical | #3: Chemical | ChemComp-UNX / #4: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.03 Å3/Da / Density % sol: 39.36 % |
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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 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: ![]() | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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: _
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Processing
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Refinement | Method to determine structure: ![]() 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.
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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
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 6
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