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Open data
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Basic information
Entry | Database: PDB / ID: 3mew | ||||||
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Title | Crystal structure of Novel Tudor domain-containing protein SGF29 | ||||||
![]() | SAGA-associated factor 29 homolog | ||||||
![]() | TRANSCRIPTION / Structural Genomics Consortium / SGC / Nucleus / Transcription regulation / Chromosomal protein / DNA-binding / Nucleosome core | ||||||
Function / homology | ![]() SAGA-type complex / establishment of protein localization to chromatin / ATAC complex / SAGA complex / regulation of tubulin deacetylation / Formation of WDR5-containing histone-modifying complexes / regulation of cell division / regulation of RNA splicing / regulation of embryonic development / regulation of DNA repair ...SAGA-type complex / establishment of protein localization to chromatin / ATAC complex / SAGA complex / regulation of tubulin deacetylation / Formation of WDR5-containing histone-modifying complexes / regulation of cell division / regulation of RNA splicing / regulation of embryonic development / regulation of DNA repair / methylated histone binding / transcription initiation-coupled chromatin remodeling / response to endoplasmic reticulum stress / mitotic spindle / HATs acetylate histones / regulation of cell cycle / regulation of transcription by RNA polymerase II / positive regulation of DNA-templated transcription / regulation of DNA-templated transcription / negative regulation of transcription by RNA polymerase II / nucleoplasm Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() | ||||||
![]() | Xu, C. / Bian, C.B. / Lam, R. / Bountra, C. / Arrowsmith, C.H. / Weigelt, J. / Edwards, A.M. / Bochkarev, A. / Min, J. / Structural Genomics Consortium (SGC) | ||||||
![]() | ![]() Title: Sgf29 binds histone H3K4me2/3 and is required for SAGA complex recruitment and histone H3 acetylation. Authors: Bian, C. / Xu, C. / Ruan, J. / Lee, K.K. / Burke, T.L. / Tempel, W. / Barsyte, D. / Li, J. / Wu, M. / Zhou, B.O. / Fleharty, B.E. / Paulson, A. / Allali-Hassani, A. / Zhou, J.Q. / Mer, G. / ...Authors: Bian, C. / Xu, C. / Ruan, J. / Lee, K.K. / Burke, T.L. / Tempel, W. / Barsyte, D. / Li, J. / Wu, M. / Zhou, B.O. / Fleharty, B.E. / Paulson, A. / Allali-Hassani, A. / Zhou, J.Q. / Mer, G. / Grant, P.A. / Workman, J.L. / Zang, J. / Min, J. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 46.4 KB | Display | ![]() |
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PDB format | ![]() | 32 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 418.5 KB | Display | ![]() |
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Full document | ![]() | 419.4 KB | Display | |
Data in XML | ![]() | 8.9 KB | Display | |
Data in CIF | ![]() | 11.9 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 3lx7C ![]() 3me9SC ![]() 3meaC ![]() 3metC ![]() 3meuC ![]() 3mevC ![]() 3mp1C ![]() 3mp6C ![]() 3mp8C S: Starting model for refinement C: citing same article ( |
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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: 17813.990 Da / Num. of mol.: 1 / Fragment: UNP Residues 115-287 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() |
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#2: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.4 Å3/Da / Density % sol: 48.84 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, sitting drop / pH: 5.5 Details: 20-28% PEG3350, 0.1M Bis-Tris pH 5.5, vapor diffusion, Sitting drop, temperature 291K, VAPOR DIFFUSION, SITTING DROP |
-Data collection
Diffraction source | Source: ![]() |
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Detector | Type: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Nov 4, 2009 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 1.92→44.65 Å / Num. all: 13104 / Num. obs: 12062 / % possible obs: 92.2 % / Redundancy: 3.8 % / Rmerge(I) obs: 0.0381 / Net I/σ(I): 37.9 |
Reflection shell | Resolution: 1.92→1.95 Å / Redundancy: 3.8 % / Rmerge(I) obs: 0.119 / Mean I/σ(I) obs: 15.4 / % possible all: 88.8 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 3ME9 Resolution: 1.92→44.65 Å / Cor.coef. Fo:Fc: 0.948 / Cor.coef. Fo:Fc free: 0.933 / Occupancy max: 1 / Occupancy min: 1 / SU B: 3.551 / SU ML: 0.105 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.185 / ESU R Free: 0.16 / 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: 1.4 Å / Solvent model: MASK | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 66.14 Å2 / Biso mean: 31.39 Å2 / Biso min: 16.79 Å2
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Refinement step | Cycle: LAST / Resolution: 1.92→44.65 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.92→1.971 Å / Total num. of bins used: 20
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