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Yorodumi- PDB-1d2s: CRYSTAL STRUCTURE OF THE N-TERMINAL LAMININ G-LIKE DOMAIN OF SHBG... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1d2s | ||||||
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Title | CRYSTAL STRUCTURE OF THE N-TERMINAL LAMININ G-LIKE DOMAIN OF SHBG IN COMPLEX WITH DIHYDROTESTOSTERONE | ||||||
Components | SEX HORMONE-BINDING GLOBULIN | ||||||
Keywords | TRANSPORT PROTEIN / STEROID TRANSPORT / LAMININ G-LIKE DOMAIN / JELLYROLL / ANDROGEN BINDING PROTEIN (ABP) / SEX STEROID BINDING PROTEIN (SBP) | ||||||
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 / Resolution: 1.55 Å | ||||||
Authors | Grishkovskaya, I. / Avvakumov, G.V. / Sklenar, G. / Dales, D. / Hammond, G.L. / Muller, Y.A. | ||||||
Citation | Journal: EMBO J. / Year: 2000 Title: Crystal structure of human sex hormone-binding globulin: steroid transport by a laminin G-like domain. Authors: Grishkovskaya, I. / Avvakumov, G.V. / Sklenar, G. / Dales, D. / 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 | 1d2s.cif.gz | 47.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1d2s.ent.gz | 36.8 KB | Display | PDB format |
PDBx/mmJSON format | 1d2s.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/d2/1d2s ftp://data.pdbj.org/pub/pdb/validation_reports/d2/1d2s | HTTPS FTP |
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-Related structure data
Similar structure data |
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-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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Components on special symmetry positions |
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-Components
#1: Protein | Mass: 18855.418 Da / Num. of mol.: 1 / Fragment: RESIDUES 1 TO 205 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Plasmid: PGEX-2T / Production host: Escherichia coli (E. coli) / References: UniProt: P04278 | ||||
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#2: Chemical | #3: Chemical | ChemComp-DHT / | #4: 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: 2.33 Å3/Da / Density % sol: 47.25 % | ||||||||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: PEG400, HEPES, CALCIUM CHLORIDE, DIHYDROTESTOSTERONE, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 20K | ||||||||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Details: drop consists of equal volume of protein and reservoir solutions | ||||||||||||||||||||||||||||||||||||||||||||||||
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: EMBL/DESY, Hamburg / Beamline: X11 / Wavelength: 0.9116 |
Detector | Type: MARRESEARCH / Detector: AREA DETECTOR / Date: Apr 1, 1999 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9116 Å / Relative weight: 1 |
Reflection | Resolution: 1.55→40 Å / Num. all: 24678 / Num. obs: 24678 / % possible obs: 96.4 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.4 % / Biso Wilson estimate: 29.3 Å2 / Rmerge(I) obs: 0.042 / Net I/σ(I): 16.5 |
Reflection shell | Resolution: 1.55→1.75 Å / Redundancy: 2.3 % / Rmerge(I) obs: 0.234 / % possible all: 95 |
Reflection shell | *PLUS % possible obs: 95 % / Mean I/σ(I) obs: 3.35 |
-Processing
Software |
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Refinement | Resolution: 1.55→40 Å / σ(F): 0 / σ(I): 0 / Stereochemistry target values: ENGH & HUBER
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Displacement parameters | Biso mean: 29.19 Å2
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Refinement step | Cycle: LAST / Resolution: 1.55→40 Å
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Refine LS restraints |
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