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- PDB-5u9n: Second Bromodomain of cdg4_1340 from Cryptosporidium parvum, comp... -
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Open data
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Basic information
Entry | Database: PDB / ID: 5u9n | ||||||
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Title | Second Bromodomain of cdg4_1340 from Cryptosporidium parvum, complexed with bromosporine | ||||||
![]() | Bromo domain containing protein | ||||||
![]() | SIGNALING PROTEIN / Bromodomain / Ligand / Structural Genomics Consortium (SGC) | ||||||
Function / homology | ![]() Bromodomain-like / Histone Acetyltransferase; Chain A / Bromodomain, conserved site / Bromodomain signature. / Bromodomain / Bromodomain profile. / bromo domain / Bromodomain / Bromodomain-like superfamily / Up-down Bundle / Mainly Alpha Similarity search - Domain/homology | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() ![]() | ||||||
Model details | In subunit B the protein appears to be significantly disordered, and while some residues in the ...In subunit B the protein appears to be significantly disordered, and while some residues in the range 413-420 have been placed into the density, there is a possibility that the docking is incorrect. The user should use caution in interpreting these results. | ||||||
![]() | Hou, C.F.D. / Lin, Y.H. / Loppnau, P. / Hutchinson, A. / Dong, A. / Bountra, C. / Edwards, A.M. / Arrowsmith, C.H. / Hui, R. / Walker, J.R. / Structural Genomics Consortium (SGC) | ||||||
![]() | ![]() Title: Second Bromodomain of cdg4_1340 from Cryptosporidium parvum, complexed with bromosporine Authors: Hou, C.F.D. / Lin, Y.H. / Loppnau, P. / Hutchinson, A. / Dong, A. / Bountra, C. / Edwards, A.M. / Arrowsmith, C.H. / Hui, R. / Walker, J.R. / Structural Genomics Consortium (SGC) | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 120.9 KB | Display | ![]() |
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PDB format | ![]() | 92.9 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1 MB | Display | ![]() |
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Full document | ![]() | 1 MB | Display | |
Data in XML | ![]() | 11.8 KB | Display | |
Data in CIF | ![]() | 15.4 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 4py6S 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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Unit cell |
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Components
#1: Protein | Mass: 17863.914 Da / Num. of mol.: 2 / Fragment: Second bromodomain (UNP residues 300-450) Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() Strain: Iowa II / Gene: cgd4_1340 / Plasmid: PET15-MHL / Production host: ![]() ![]() #2: Chemical | #3: Chemical | ChemComp-SO4 / | #4: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 3.95 Å3/Da / Density % sol: 68.84 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7 Details: The protein was crystallized at 293 K in 2.5M ammonium sulfate, 0.1 M bis-tris propane pH 7.0. Bromosporine (ethyl (3-methyl-6-{4-methyl-3-[(methylsulfonyl)amino]phenyl}[1,2,4]triazolo[4,3- ...Details: The protein was crystallized at 293 K in 2.5M ammonium sulfate, 0.1 M bis-tris propane pH 7.0. Bromosporine (ethyl (3-methyl-6-{4-methyl-3-[(methylsulfonyl)amino]phenyl}[1,2,4]triazolo[4,3- b]pyridazin-8-yl)carbamate) was added (final concentration of 1 mM)directly to the concentrated protein immediately prior to setting up the crystallization plate |
-Data collection
Diffraction | Mean temperature: 100 K | ||||||||||||||||||
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Diffraction source | Source: ![]() ![]() ![]() | ||||||||||||||||||
Detector | Type: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Nov 25, 2016 | ||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||
Radiation wavelength | Wavelength: 0.976 Å / Relative weight: 1 | ||||||||||||||||||
Reflection | Resolution: 2.4→33.67 Å / Num. obs: 22425 / % possible obs: 99.8 % / Redundancy: 7.1 % / Biso Wilson estimate: 57.95 Å2 / CC1/2: 0.996 / Rmerge(I) obs: 0.1 / Rpim(I) all: 0.041 / Rrim(I) all: 0.108 / Net I/σ(I): 18 / Num. measured all: 159515 / Scaling rejects: 1179 | ||||||||||||||||||
Reflection shell |
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-Phasing
Phasing | Method: ![]() |
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Processing
Software |
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Refinement | Method to determine structure: ![]() Starting model: 4PY6 Resolution: 2.4→32.54 Å / Cor.coef. Fo:Fc: 0.913 / Cor.coef. Fo:Fc free: 0.884 / SU R Cruickshank DPI: 0.304 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.209 / SU Rfree Blow DPI: 0.187 / SU Rfree Cruickshank DPI: 0.188 Details: In subunit B the protein appears to be significantly disordered, and while some residues in the range 413-420 have been placed into the density, there is a possibility that the docking is ...Details: In subunit B the protein appears to be significantly disordered, and while some residues in the range 413-420 have been placed into the density, there is a possibility that the docking is incorrect. The user should use caution in interpreting these results.
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Displacement parameters | Biso max: 159.17 Å2 / Biso mean: 67.55 Å2 / Biso min: 26.63 Å2
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Refine analyze | Luzzati coordinate error obs: 0.38 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 2.4→32.54 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.4→2.52 Å / Rfactor Rfree error: 0 / Total num. of bins used: 11
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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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