+Open data
-Basic information
Entry | Database: PDB / ID: 5xqh | ||||||
---|---|---|---|---|---|---|---|
Title | Crystal structure of truncated human Rogdi | ||||||
Components | Protein rogdi homolog | ||||||
Keywords | CELL CYCLE / Rogdi / Kohlschutter-Tonz syndrome | ||||||
Function / homology | Function and homology information RAVE complex / odontogenesis of dentin-containing tooth / hemopoiesis / hippocampal mossy fiber to CA3 synapse / neurogenesis / brain development / synaptic vesicle / nuclear envelope / perikaryon / axon ...RAVE complex / odontogenesis of dentin-containing tooth / hemopoiesis / hippocampal mossy fiber to CA3 synapse / neurogenesis / brain development / synaptic vesicle / nuclear envelope / perikaryon / axon / dendrite / positive regulation of cell population proliferation Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.04 Å | ||||||
Authors | Lee, H. / Lee, C. | ||||||
Citation | Journal: Sci Rep / Year: 2017 Title: The crystal structure of human Rogdi provides insight into the causes of Kohlschutter-Tonz Syndrome Authors: Lee, H. / Jeong, H. / Choe, J. / Jun, Y. / Lim, C. / Lee, C. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 5xqh.cif.gz | 58 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb5xqh.ent.gz | 44.4 KB | Display | PDB format |
PDBx/mmJSON format | 5xqh.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/xq/5xqh ftp://data.pdbj.org/pub/pdb/validation_reports/xq/5xqh | HTTPS FTP |
---|
-Related structure data
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
|
-Components
#1: Protein | Mass: 30328.027 Da / Num. of mol.: 1 / Fragment: UNP residues 11-276 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: ROGDI / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q9GZN7 |
---|---|
#2: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 2.66 Å3/Da / Density % sol: 53.77 % |
---|---|
Crystal grow | Temperature: 277.15 K / Method: vapor diffusion, hanging drop / Details: 11% PEG 4000, 100mM MES pH 6.5, 5mM DTT |
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: PAL/PLS / Beamline: 5C (4A) / Wavelength: 0.9794 Å |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Jul 8, 2014 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9794 Å / Relative weight: 1 |
Reflection | Resolution: 2.04→50 Å / Num. obs: 39509 / % possible obs: 99.9 % / Redundancy: 9.4 % / Rmerge(I) obs: 0.082 / Net I/σ(I): 49.8 |
Reflection shell | Highest resolution: 2.04 Å / Redundancy: 9.3 % / Rmerge(I) obs: 0.469 / Mean I/σ(I) obs: 5.9 / % possible all: 99.9 |
-Processing
Software |
| ||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: SAD / Resolution: 2.04→34.57 Å / Cross valid method: FREE R-VALUE Details: THE STRUCTURE FACTOR FILE CONTAINS FRIEDEL PAIRS IN I_PLUS/MINUS COLUMNS
| ||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.04→34.57 Å
|