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Open data
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Basic information
Entry | Database: PDB / ID: 3mxx | ||||||
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Title | Crystal structure of WDR5 mutant (S62A) | ||||||
![]() | WD repeat-containing protein 5 | ||||||
![]() | ![]() ![]() ![]() ![]() ![]() ![]() | ||||||
Function / homology | ![]() MLL3/4 complex / Set1C/COMPASS complex / MLL1/2 complex / ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() | ||||||
![]() | Wu, Y.-D. / Wu, X.-H. / Gao, Y. / Chen, R.-C. | ||||||
![]() | ![]() Title: The Effect of Asp-His-Ser/Thr-Trp Tetrad on the Thermostability of WD40-Repeat Proteins Authors: Wu, X.-H. / Chen, R.-C. / Gao, Y. / Wu, Y.-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 | ![]() | 73.3 KB | Display | ![]() |
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PDB format | ![]() | 53.2 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 3n0dC ![]() 3n0eC ![]() 2h14S C: citing same article ( 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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Unit cell |
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Components
#1: Protein | Mass: 34612.234 Da / Num. of mol.: 1 / Fragment: RESIDUES 31-334 / Mutation: S62A Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() ![]() |
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#2: Water | ChemComp-HOH / ![]() |
Compound details | WDR5 CAN BIND A SERIES OF PROTEINS INVOLVED IN HISTONE H3K4 METHYLATION. THE BINDING CANDIDATES OF ...WDR5 CAN BIND A SERIES OF PROTEINS INVOLVED IN HISTONE H3K4 METHYLATIO |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.24 Å3/Da / Density % sol: 45.13 % |
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Crystal grow![]() | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: 18% PEG 3350, 0.1M Hepes, 18mM (NH4)2SO4, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() |
Detector | Type: RIGAKU SATURN 944+ / Detector: CCD / Date: Feb 3, 2010 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength![]() |
Reflection | Resolution: 2.05→42.67 Å / Num. obs: 19198 / % possible obs: 99.8 % / Redundancy: 3.49 % / Rmerge(I) obs: 0.064 / Num. measured all: 66969 |
Reflection shell | Resolution: 2.05→2.12 Å / Redundancy: 2.84 % / Rmerge(I) obs: 0.142 / % possible all: 98.9 |
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Processing
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Refinement | Method to determine structure![]() ![]() Starting model: PDB ENTRY 2H14 Resolution: 2.05→42.67 Å / Cor.coef. Fo:Fc: 0.942 / Cor.coef. Fo:Fc free: 0.905 / SU B: 4.203 / SU ML: 0.116 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R Free: 0.184 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 15.973 Å2
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Refinement step | Cycle: LAST / Resolution: 2.05→42.67 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.05→2.103 Å / Total num. of bins used: 20
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