+Open data
-Basic information
Entry | Database: PDB / ID: 5xqi | ||||||
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Title | Crystal structure of full-length 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 / MOLECULAR REPLACEMENT / Resolution: 2.8 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 |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5xqi.cif.gz | 221.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5xqi.ent.gz | 179 KB | Display | PDB format |
PDBx/mmJSON format | 5xqi.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/xq/5xqi ftp://data.pdbj.org/pub/pdb/validation_reports/xq/5xqi | HTTPS FTP |
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-Related structure data
Related structure data | 5xqhSC S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 32434.248 Da / Num. of mol.: 4 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 / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 4.71 Å3/Da / Density % sol: 73.88 % |
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Crystal grow | Temperature: 277.15 K / Method: vapor diffusion, hanging drop Details: 2M sodium chloride, 130mM magnesium chloride, 100mM TRIS pH 7.0 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: PAL/PLS / Beamline: 5C (4A) / Wavelength: 1 Å |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Jul 8, 2014 |
Radiation | Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.8→50 Å / Num. obs: 57790 / % possible obs: 99.8 % / Redundancy: 9.1 % / Rmerge(I) obs: 0.067 / Net I/σ(I): 44.6 |
Reflection shell | Highest resolution: 2.8 Å / Redundancy: 9.2 % / Rmerge(I) obs: 0.551 / Mean I/σ(I) obs: 5.7 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 5XQH Resolution: 2.8→36.17 Å / Cross valid method: FREE R-VALUE / Details: THE STRUCTURE FACTOR FILE CONTAINS FRIEDEL PAIRS
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Refinement step | Cycle: LAST / Resolution: 2.8→36.17 Å
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