+Open data
-Basic information
Entry | Database: PDB / ID: 6mf9 | ||||||
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Title | Crystal structure of CGD4-650 with compound BI2536 | ||||||
Components | ZnKn (C2HC)+Athook+bromo domain protein, Taf250, transcription initiation factor IID | ||||||
Keywords | BIOSYNTHETIC PROTEIN / CGD4_650 / BI2536 / Structural Genomics / Structural Genomics Consortium / SGC | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Cryptosporidium parvum (eukaryote) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.037 Å | ||||||
Authors | Dong, A. / Lin, Y.L. / Hou, D. / Bountra, C. / Arrowsmith, C.H. / Edwards, A.M. / Vedadi, M. / Hui, R. / Structural Genomics Consortium (SGC) | ||||||
Citation | Journal: to be published Title: Crystal structure of CGD4-650 with compound BI2536 Authors: Dong, A. / Lin, Y.L. / Hou, D. / Bountra, C. / Arrowsmith, C.H. / Edwards, A.M. / Vedadi, M. / Hui, R. / Structural Genomics Consortium (SGC) | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6mf9.cif.gz | 72.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6mf9.ent.gz | 51.8 KB | Display | PDB format |
PDBx/mmJSON format | 6mf9.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6mf9_validation.pdf.gz | 922 KB | Display | wwPDB validaton report |
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Full document | 6mf9_full_validation.pdf.gz | 925.5 KB | Display | |
Data in XML | 6mf9_validation.xml.gz | 13.1 KB | Display | |
Data in CIF | 6mf9_validation.cif.gz | 17.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/mf/6mf9 ftp://data.pdbj.org/pub/pdb/validation_reports/mf/6mf9 | HTTPS FTP |
-Related structure data
Related structure data | 1eqfS S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 18948.520 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Cryptosporidium parvum (strain Iowa II) (eukaryote) Strain: Iowa II / Gene: cgd4_650 / Plasmid: pET15-MHL / Production host: Escherichia coli (E. coli) / Strain (production host): BL21-CodonPlus-RIL / References: UniProt: Q5CQH9 #2: Chemical | #3: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.37 Å3/Da / Density % sol: 48.08 % / Mosaicity: 0.524 ° |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8.5 / Details: 25% PEG 8K, 0.1M Tris 8.5 and 2mM BI2536 |
-Data collection
Diffraction | Mean temperature: 100 K | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 24-ID-E / Wavelength: 0.9789 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Apr 8, 2018 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.9789 Å / Relative weight: 1 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 2.03→50 Å / Num. obs: 23656 / % possible obs: 99.7 % / Redundancy: 4.9 % / Rmerge(I) obs: 0.09 / Rpim(I) all: 0.045 / Rrim(I) all: 0.101 / Χ2: 1.076 / Net I/σ(I): 6.9 / Num. measured all: 116351 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1EQF Resolution: 2.037→47.86 Å / Cor.coef. Fo:Fc: 0.963 / Cor.coef. Fo:Fc free: 0.945 / SU B: 4.091 / SU ML: 0.107 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.152 / ESU R Free: 0.146 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
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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: 89.64 Å2 / Biso mean: 37.473 Å2 / Biso min: 23.6 Å2
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Refinement step | Cycle: final / Resolution: 2.037→47.86 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.037→2.09 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
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