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Yorodumi- PDB-2vdy: Crystal structure of the reactive loop cleaved Corticosteroid Bin... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2vdy | ||||||
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Title | Crystal structure of the reactive loop cleaved Corticosteroid Binding Globulin complexed with Cortisol | ||||||
Components | CORTICOSTEROID-BINDING GLOBULIN | ||||||
Keywords | TRANSPORT PROTEIN / GLYCOPROTEIN / LIPID-BINDING / STEROID-BINDING / DISEASE MUTATION / CORTICOSTEROID BINDING GLOBULIN / CBG / SERPIN / CLEAVED / SECRETED / CORTISOL / TRANSPORT | ||||||
Function / homology | Function and homology information 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 | HOMO SAPIENS (human) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.3 Å | ||||||
Authors | Zhou, A. / Wei, Z. / Read, R.J. | ||||||
Citation | Journal: J.Mol.Biol. / Year: 2008 Title: The S-to-R Transition of Corticosteroid-Binding Globulin and the Mechanism of Hormone Release. Authors: Zhou, A. / Wei, Z. / Stanley, P.L. / Read, R.J. / Stein, P.E. / Carrell, R.W. | ||||||
History |
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Remark 700 | SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN ... SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN THE SHEET RECORDS BELOW, TWO SHEETS ARE DEFINED. |
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2vdy.cif.gz | 152.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2vdy.ent.gz | 119.7 KB | Display | PDB format |
PDBx/mmJSON format | 2vdy.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2vdy_validation.pdf.gz | 961.1 KB | Display | wwPDB validaton report |
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Full document | 2vdy_full_validation.pdf.gz | 964.3 KB | Display | |
Data in XML | 2vdy_validation.xml.gz | 26.9 KB | Display | |
Data in CIF | 2vdy_validation.cif.gz | 37.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/vd/2vdy ftp://data.pdbj.org/pub/pdb/validation_reports/vd/2vdy | HTTPS FTP |
-Related structure data
Related structure data | 2vdxC 1qmnS C: citing same article (ref.) S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 41685.590 Da / Num. of mol.: 2 / Fragment: RESIDUES 33-405 / Mutation: YES Source method: isolated from a genetically manipulated source Details: COMPLEXED WITH CORTISOL / Source: (gene. exp.) HOMO SAPIENS (human) / Plasmid: PSUMO3-CBG / Production host: Escherichia coli BL21(DE3) COLI, / References: UniProt: P08185 #2: Chemical | #3: Water | ChemComp-HOH / | Compound details | THE REACTIVE LOOP OF THE PROTEIN FOR BOTH CHAINS A AND B (CORRESPONDING TO UNIPROT RESIDUES 358-371) ...THE REACTIVE LOOP OF THE PROTEIN FOR BOTH CHAINS A AND B (CORRESPOND | Nonpolymer details | (8S,9S,10R,11S,13S,14S,17R)-11, 17-DIHYDROXY-17-(2-HYDROXYACETYL)-10,13-DIMETHYL-2,6,7,8,9, ...(8S,9S,10R,11S,13S,14S,17R)-11, 17-DIHYDROXY-17-(2-HYDROXYACE | Sequence details | RESIDUES 336-349 OF HUMAN CBG MUTATED TO TEAAGAMFLEAIPR. THIS PROTEIN WAS CLEAVED BY THROMBIN AT ...RESIDUES 336-349 OF HUMAN CBG MUTATED TO TEAAGAMFLE | |
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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: 1.93 Å3/Da / Density % sol: 34 % / Description: NONE |
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Crystal grow | pH: 7.4 / Details: 10-20% PEG3350, 0.2M NACL, pH 7.4 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU RUH3R / Wavelength: 1.5419 |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE / Date: Jun 10, 2007 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5419 Å / Relative weight: 1 |
Reflection | Resolution: 2.3→19.4 Å / Num. obs: 22575 / % possible obs: 93.5 % / Observed criterion σ(I): 2 / Redundancy: 2.2 % / Rmerge(I) obs: 0.08 / Net I/σ(I): 11 |
Reflection shell | Resolution: 2.3→2.42 Å / Redundancy: 2.2 % / Rmerge(I) obs: 0.46 / Mean I/σ(I) obs: 2.5 / % possible all: 91.1 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1QMN Resolution: 2.3→19.43 Å / Cor.coef. Fo:Fc: 0.935 / Cor.coef. Fo:Fc free: 0.895 / SU B: 19.362 / SU ML: 0.237 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 1.431 / ESU R Free: 0.32 / 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: 28.75 Å2
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Refinement step | Cycle: LAST / Resolution: 2.3→19.43 Å
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Refine LS restraints |
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