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Yorodumi- PDB-1kdk: THE STRUCTURE OF THE N-TERMINAL LG DOMAIN OF SHBG IN CRYSTALS SOA... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1kdk | ||||||
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Title | THE STRUCTURE OF THE N-TERMINAL LG DOMAIN OF SHBG IN CRYSTALS SOAKED WITH EDTA | ||||||
Components | Sex Hormone-Binding Globulin | ||||||
Keywords | TRANSPORT PROTEIN / SHBG / DHT | ||||||
Function / homology | Function and homology information androgen binding / steroid binding / extracellular exosome / extracellular region Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 1.7 Å | ||||||
Authors | Grishkovskaya, I. / Avvakumov, G.V. / Hammond, G.L. / Muller, Y.A. | ||||||
Citation | Journal: J.Mol.Biol. / Year: 2002 Title: Resolution of a disordered region at the entrance of the human sex hormone-binding globulin steroid-binding site. Authors: Grishkovskaya, I. / Avvakumov, G.V. / Hammond, G.L. / Muller, Y.A. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1kdk.cif.gz | 51.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1kdk.ent.gz | 35.8 KB | Display | PDB format |
PDBx/mmJSON format | 1kdk.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1kdk_validation.pdf.gz | 712.6 KB | Display | wwPDB validaton report |
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Full document | 1kdk_full_validation.pdf.gz | 721.4 KB | Display | |
Data in XML | 1kdk_validation.xml.gz | 11 KB | Display | |
Data in CIF | 1kdk_validation.cif.gz | 14.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/kd/1kdk ftp://data.pdbj.org/pub/pdb/validation_reports/kd/1kdk | HTTPS FTP |
-Related structure data
Related structure data | 1kdmC 1d2sS 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: 19655.336 Da / Num. of mol.: 1 / Fragment: N-terminal LG-domain Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Plasmid: pGEX-2T / Production host: Escherichia coli (E. coli) / Strain (production host): JM109 / References: UniProt: P04278 |
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#2: Chemical | ChemComp-DHT / |
#3: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.26 Å3/Da / Density % sol: 45.5 % | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: PEG400, Isopropanol, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Details: Grishkovskaya, I., (1999) Acta Crystallog. D55, 2053. | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: BM14 / Wavelength: 0.93 Å |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE |
Radiation | Monochromator: diamond(111), Ge(220) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.93 Å / Relative weight: 1 |
Reflection | Resolution: 1.7→40 Å / Num. all: 19262 / Num. obs: 19262 / % possible obs: 98.1 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.7 % / Biso Wilson estimate: 33.1 Å2 / Rmerge(I) obs: 0.064 |
Reflection shell | Resolution: 1.7→1.8 Å / Rmerge(I) obs: 0.37 / % possible all: 99.2 |
Reflection | *PLUS Highest resolution: 1.7 Å / Lowest resolution: 40 Å / Num. measured all: 90466 / Rmerge(I) obs: 0.062 |
Reflection shell | *PLUS Highest resolution: 1.7 Å / Lowest resolution: 1.8 Å / % possible obs: 99.2 % |
-Processing
Software |
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Refinement | Method to determine structure: FOURIER SYNTHESIS Starting model: 1D2S Resolution: 1.7→20 Å / Cross valid method: THROUGHOUT / σ(F): 0
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Displacement parameters | Biso mean: 36.2 Å2 | ||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.7→20 Å
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Refine LS restraints |
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LS refinement shell | Highest resolution: 1.7 Å
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Refinement | *PLUS Highest resolution: 1.7 Å / Lowest resolution: 20 Å / Rfactor obs: 0.194 | ||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||
Displacement parameters | *PLUS |