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- PDB-4bb2: Crystal structure of cleaved corticosteroid-binding globulin in c... -
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Open data
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Basic information
Entry | Database: PDB / ID: 4bb2 | ||||||
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Title | Crystal structure of cleaved corticosteroid-binding globulin in complex with progesterone | ||||||
![]() | (CORTICOSTEROID-BINDING ...) x 2 | ||||||
![]() | TRANSPORT PROTEIN / SERPINS / STEROID BINDING | ||||||
Function / homology | ![]() Glucocorticoid biosynthesis / glucocorticoid metabolic process / Prednisone ADME / steroid binding / serine-type endopeptidase inhibitor activity / extracellular space / extracellular exosome / extracellular region Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Gardill, B.R. / Vogl, M.R. / Lin, H. / Hammond, G.L. / Muller, Y.A. | ||||||
![]() | ![]() Title: Corticosteroid-Binding Globulin: Structure-Function Implications from Species Differences Authors: Gardill, B.R. / Vogl, M.R. / Lin, H. / Hammond, G.L. / Muller, Y.A. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 161.5 KB | Display | ![]() |
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PDB format | ![]() | 127.5 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 735 KB | Display | ![]() |
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Full document | ![]() | 738.2 KB | Display | |
Data in XML | ![]() | 16.6 KB | Display | |
Data in CIF | ![]() | 22.7 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 2vdyS S: Starting model for refinement |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Components
-CORTICOSTEROID-BINDING ... , 2 types, 2 molecules AB
#1: Protein | Mass: 37502.410 Da / Num. of mol.: 1 / Fragment: RESIDUES 33-371 / Mutation: YES Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() |
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#2: Protein/peptide | Mass: 4083.906 Da / Num. of mol.: 1 / Fragment: RESIDUES 373-405 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() |
-Non-polymers , 4 types, 118 molecules ![](data/chem/img/EDO.gif)
![](data/chem/img/CYS.gif)
![](data/chem/img/STR.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/CYS.gif)
![](data/chem/img/STR.gif)
![](data/chem/img/HOH.gif)
#3: Chemical | ChemComp-EDO / #4: Chemical | ChemComp-CYS / | #5: Chemical | ChemComp-STR / | #6: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.68 Å3/Da / Density % sol: 54.07 % Description: DIFFRACTION PATTERN IMPROVED AFTER A 2 SEC AND A 4 SEC CRYSTAL ANNEALING STEP. |
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Crystal grow | pH: 7.5 / Details: 0.1 M HEPES 7.5, 2 % PEG 400, 2 M AMMONIUM SULFATE |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: MARRESEARCH / Detector: CCD / Date: Feb 12, 2010 / Details: MIRRORS |
Radiation | Monochromator: SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9184 Å / Relative weight: 1 |
Reflection | Resolution: 2.48→35 Å / Num. obs: 16184 / % possible obs: 99.6 % / Observed criterion σ(I): 2 / Redundancy: 7.2 % / Rmerge(I) obs: 0.12 / Net I/σ(I): 12.9 |
Reflection shell | Resolution: 2.48→2.63 Å / Redundancy: 7 % / Rmerge(I) obs: 0.6 / Mean I/σ(I) obs: 3.2 / % possible all: 97.6 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 2VDY Resolution: 2.48→34.07 Å / Cor.coef. Fo:Fc: 0.952 / Cor.coef. Fo:Fc free: 0.921 / SU B: 16.864 / SU ML: 0.188 / Cross valid method: THROUGHOUT / ESU R: 0.509 / ESU R Free: 0.275 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 36.83 Å2
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Refinement step | Cycle: LAST / Resolution: 2.48→34.07 Å
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Refine LS restraints |
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