+
Open data
-
Basic information
Entry | Database: PDB / ID: 9ozv | |||||||||
---|---|---|---|---|---|---|---|---|---|---|
Title | Structure of the self-association domain of LDB2 | |||||||||
![]() | LIM domain-binding protein 2 | |||||||||
![]() | STRUCTURAL PROTEIN / lim domain binding / transcriptional factors | |||||||||
Function / homology | ![]() positive regulation of cellular component biogenesis / regulation of kinase activity / epithelial structure maintenance / LIM domain binding / cell leading edge / somatic stem cell population maintenance / hair follicle development / regulation of cell migration / transcription regulator complex / nucleolus ...positive regulation of cellular component biogenesis / regulation of kinase activity / epithelial structure maintenance / LIM domain binding / cell leading edge / somatic stem cell population maintenance / hair follicle development / regulation of cell migration / transcription regulator complex / nucleolus / enzyme binding / positive regulation of transcription by RNA polymerase II / nucleoplasm / nucleus / plasma membrane Similarity search - Function | |||||||||
Biological species | ![]() ![]() | |||||||||
Method | ![]() ![]() ![]() | |||||||||
![]() | Vu, T.H. / Patel, K. / Smith, N.C. / Matthews, J.M. | |||||||||
Funding support | ![]()
| |||||||||
![]() | ![]() Title: Structure of the self-association domain of LDB2 Authors: Vu, T.H. / Patel, K. / Smith, N.C. / Matthews, J.M. | |||||||||
History |
|
-
Structure visualization
Structure viewer | Molecule: ![]() ![]() |
---|
-
Downloads & links
-
Download
PDBx/mmCIF format | ![]() | 273.9 KB | Display | ![]() |
---|---|---|---|---|
PDB format | ![]() | 191.3 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 435.2 KB | Display | ![]() |
---|---|---|---|---|
Full document | ![]() | 441 KB | Display | |
Data in XML | ![]() | 17 KB | Display | |
Data in CIF | ![]() | 21.2 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 9bpoC C: citing same article ( |
---|---|
Similar structure data | Similarity search - Function & homology ![]() |
-
Links
-
Assembly
Deposited unit | ![]()
| ||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||||||||||||
Unit cell |
| ||||||||||||||||||
Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments: Component-ID: 1 / Ens-ID: ens_1 / Beg auth comp-ID: GLN / Beg label comp-ID: GLN / End auth comp-ID: LEU / End label comp-ID: LEU / Auth seq-ID: 27 - 204 / Label seq-ID: 6 - 183
NCS oper: (Code: givenMatrix: (-0.998539171787, -0.0132953054593, 0.0523713400513), (0.0230757231977, -0.981349418886, 0.190842419424), (0.0488572758648, 0.19177213798, 0.980222634757)Vector: 19. ...NCS oper: (Code: given Matrix: (-0.998539171787, -0.0132953054593, 0.0523713400513), Vector: |
-
Components
#1: Protein | Mass: 21825.814 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Details: LDB2 self-association domain, residues 22-205 / Source: (gene. exp.) ![]() ![]() ![]() ![]() Has protein modification | N | |
---|
-Experimental details
-Experiment
Experiment | Method: ![]() |
---|
-
Sample preparation
Crystal | Density Matthews: 2.08 Å3/Da / Density % sol: 41.17 % |
---|---|
Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / Details: Ammonium sulfate, HEPES, PEG 8000, MPD |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
---|---|
Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Dec 8, 2023 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.95373 Å / Relative weight: 1 |
Reflection | Resolution: 2.59→47.94 Å / Num. obs: 10574 / % possible obs: 99.1 % / Redundancy: 1.9 % / Biso Wilson estimate: 70.55 Å2 / CC1/2: 0.998 / Net I/σ(I): 6.4 |
Reflection shell | Resolution: 2.59→2.7 Å / Num. unique obs: 10574 / CC1/2: 0.999 |
-
Processing
Software |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: ![]() Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 111.32 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.59→46.72 Å
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints NCS | Type: Torsion NCS / Rms dev position: 1.41571371034 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement TLS group | Refine-ID: X-RAY DIFFRACTION
|