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- PDB-6hgk: Crystal structure of Alpha1-antichymotrypsin variant NewBG-III: a... -
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Open data
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Basic information
Entry | Database: PDB / ID: 6hgk | ||||||
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Title | Crystal structure of Alpha1-antichymotrypsin variant NewBG-III: a new binding globulin in complex with progesterone | ||||||
![]() | (Alpha-1-antichymotrypsin) x 2 | ||||||
![]() | TRANSPORT PROTEIN / Serpin / alpha1-Antichymotrypsin / computational protein design | ||||||
Function / homology | ![]() maintenance of gastrointestinal epithelium / regulation of lipid metabolic process / platelet alpha granule lumen / acute-phase response / serine-type endopeptidase inhibitor activity / azurophil granule lumen / Platelet degranulation / secretory granule lumen / collagen-containing extracellular matrix / blood microparticle ...maintenance of gastrointestinal epithelium / regulation of lipid metabolic process / platelet alpha granule lumen / acute-phase response / serine-type endopeptidase inhibitor activity / azurophil granule lumen / Platelet degranulation / secretory granule lumen / collagen-containing extracellular matrix / blood microparticle / inflammatory response / Neutrophil degranulation / DNA binding / extracellular space / extracellular exosome / extracellular region / nucleus Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Schmidt, K. / Muller, Y.A. | ||||||
Funding support | ![]()
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![]() | ![]() Title: NewBG: A surrogate corticosteroid-binding globulin with an unprecedentedly high ligand release efficacy. Authors: Gardill, B.R. / Schmidt, K. / 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 | ![]() | 97.4 KB | Display | ![]() |
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PDB format | ![]() | 71.8 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1.2 MB | Display | ![]() |
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Full document | ![]() | 1.2 MB | Display | |
Data in XML | ![]() | 17.8 KB | Display | |
Data in CIF | ![]() | 25.1 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 6hgdC ![]() 6hgeC ![]() 6hgfC ![]() 6hggSC ![]() 6hghC ![]() 6hgiC ![]() 6hgjC ![]() 6hglC ![]() 6hgmC ![]() 6hgnC S: Starting model for refinement C: citing same article ( |
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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
#1: Protein | Mass: 41897.488 Da / Num. of mol.: 1 Mutation: L24R, L55V, E242Q, K244N, A251V, L252F, L269S, P270R, K274A, R277G Source method: isolated from a genetically manipulated source Details: - all N-terminal residues that are present in the sample sequence but not in the PDB file could not be modelled due to missing electron density - residues following the sequence ..KITLL are ...Details: - all N-terminal residues that are present in the sample sequence but not in the PDB file could not be modelled due to missing electron density - residues following the sequence ..KITLL are part of chain B, as the protein is a family member of serine proteinase inhibitors (serpins) and proteolytically cleaved between KITLL-SALVE Source: (gene. exp.) ![]() ![]() ![]() | ||
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#2: Protein/peptide | Mass: 4748.613 Da / Num. of mol.: 1 / Mutation: P382D, T383H, D384F, Q386W, N387S Source method: isolated from a genetically manipulated source Details: the residues SALVET that are present in the sample sequence but not in the PDB file could not be modelled due to missing electron density Source: (gene. exp.) ![]() ![]() ![]() | ||
#3: Chemical | ChemComp-STR / | ||
#4: Chemical | #5: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.29 Å3/Da / Density % sol: 46.25 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop Details: 2 % Tacsimate pH 6.0, 0.1 M BIS-Tris pH 6.5, 20 % w/v PEG 3350 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Sep 30, 2013 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97731 Å / Relative weight: 1 |
Reflection | Resolution: 1.855→43.326 Å / Num. obs: 36786 / % possible obs: 99.6 % / Redundancy: 12.9 % / CC1/2: 0.999 / Rrim(I) all: 0.105 / Net I/σ(I): 17.31 |
Reflection shell | Resolution: 1.855→1.97 Å / Mean I/σ(I) obs: 1.9 / CC1/2: 0.808 / Rrim(I) all: 1.245 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 6HGG Resolution: 1.855→38.85 Å / SU ML: 0.23 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 24.29
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.855→38.85 Å
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Refine LS restraints |
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LS refinement shell |
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