[English] 日本語
Yorodumi- PDB-6cps: Crystal structure of the bromodomain of human ATAD2 with a disulf... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6cps | ||||||
---|---|---|---|---|---|---|---|
Title | Crystal structure of the bromodomain of human ATAD2 with a disulfide bridge | ||||||
Components | ATPase family AAA domain-containing protein 2 | ||||||
Keywords | PROTEIN BINDING / disulfide bridge / bromodomain / epigenetics / chromatin reader domain | ||||||
Function / homology | Function and homology information Hydrolases; Acting on acid anhydrides; In phosphorus-containing anhydrides / TFAP2 (AP-2) family regulates transcription of growth factors and their receptors / histone binding / chromatin binding / positive regulation of DNA-templated transcription / ATP hydrolysis activity / positive regulation of transcription by RNA polymerase II / extracellular exosome / nucleoplasm / ATP binding / nucleus Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.93 Å | ||||||
Authors | Glass, K.C. / Eckenroth, B.E. / Carlson, S. | ||||||
Funding support | United States, 1items
| ||||||
Citation | Journal: Proteins / Year: 2019 Title: Disulfide bridge formation influences ligand recognition by the ATAD2 bromodomain. Authors: Gay, J.C. / Eckenroth, B.E. / Evans, C.M. / Langini, C. / Carlson, S. / Lloyd, J.T. / Caflisch, A. / Glass, K.C. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 6cps.cif.gz | 80 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb6cps.ent.gz | 55.1 KB | Display | PDB format |
PDBx/mmJSON format | 6cps.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/cp/6cps ftp://data.pdbj.org/pub/pdb/validation_reports/cp/6cps | HTTPS FTP |
---|
-Related structure data
Related structure data | 3daiS S: Starting model for refinement |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||||||
Unit cell |
|
-Components
#1: Protein | Mass: 15502.567 Da / Num. of mol.: 1 / Fragment: bromodomain (UNP residues 981-1108) Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: ATAD2, L16, PRO2000 / Plasmid: pDEST15 Details (production host): N-terminal GST (glutathione transferase) tag followed by a PreScission Protease site (GE Healthcare) Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): RosettaTM 2 (DE3) pLysS / References: UniProt: Q6PL18 | ||||
---|---|---|---|---|---|
#2: Chemical | #3: Chemical | ChemComp-EPE / | #4: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 4.07 Å3/Da / Density % sol: 69.81 % |
---|---|
Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 7.5 / Details: 0.1 M HEPES sodium, pH 7.5, 1.6 M lithium sulfate |
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: ROTATING ANODE / Type: BRUKER D8 QUEST / Wavelength: 1.5418 Å |
Detector | Type: Bruker PHOTON II / Detector: CMOS / Date: Apr 21, 2014 / Details: Helios MX |
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→39.68 Å / Num. obs: 36485 / % possible obs: 99.37 % / Redundancy: 16.4 % / Biso Wilson estimate: 20.11 Å2 / CC1/2: 0.999 / Rpim(I) all: 0.02663 / Rrim(I) all: 0.1109 / Net I/σ(I): 20 |
Reflection shell | Resolution: 1.93→1.999 Å / Redundancy: 6.9 % / Mean I/σ(I) obs: 1.32 / CC1/2: 0.545 / Rpim(I) all: 0.5868 / Rrim(I) all: 1.627 / % possible all: 97 |
-Processing
Software |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB entry 3DAI Resolution: 1.93→39.68 Å / SU ML: 0.2112 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 20.0837
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 27.81 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.93→39.68 Å
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell |
|