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- PDB-6hgm: Crystal structure of Alpha1-antichymotrypsin variant NewBG-III-al... -
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Open data
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Basic information
Entry | Database: PDB / ID: 6hgm | ||||||
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Title | Crystal structure of Alpha1-antichymotrypsin variant NewBG-III-allo: an allosterically controlled new binding globulin with an unprecedentedly high ligand release efficacy | ||||||
![]() | (Alpha-1-antichymotrypsin) x 2 | ||||||
![]() | TRANSPORT PROTEIN / Serpin / alpha1-Antichymotrypsin / computational protein design / allosteric coupling | ||||||
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 | ![]() | 170.9 KB | Display | ![]() |
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PDB format | ![]() | 134.6 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 452.2 KB | Display | ![]() |
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Full document | ![]() | 455.6 KB | Display | |
Data in XML | ![]() | 20 KB | Display | |
Data in CIF | ![]() | 30.3 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 6hgdC ![]() 6hgeC ![]() 6hgfC ![]() 6hggSC ![]() 6hghC ![]() 6hgiC ![]() 6hgjC ![]() 6hgkC ![]() 6hglC ![]() 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
-Protein / Protein/peptide , 2 types, 2 molecules AB
#1: Protein | Mass: 41983.605 Da / Num. of mol.: 1 Mutation: L24R, L55V, E242Q, K244N, A251V, L252F, L269S, P270R, K274A, R277G, A349R Source method: isolated from a genetically manipulated source Details: - all 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 ...Details: - all 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: all residues 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.) ![]() ![]() ![]() |
-Non-polymers , 4 types, 421 molecules ![](data/chem/img/CL.gif)
![](data/chem/img/CA.gif)
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![](data/chem/img/HOH.gif)
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#3: Chemical | #4: Chemical | #5: Chemical | #6: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.34 Å3/Da / Density % sol: 47.44 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop Details: 0.3 M calcium chloride dihydrate, 20 % w/v PEG 3350 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Sep 17, 2016 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9184 Å / Relative weight: 1 |
Reflection | Resolution: 1.369→38.671 Å / Num. obs: 91858 / % possible obs: 98.9 % / Redundancy: 4.44 % / CC1/2: 0.998 / Rrim(I) all: 0.067 / Net I/σ(I): 12.7 |
Reflection shell | Resolution: 1.37→1.45 Å / Mean I/σ(I) obs: 2.15 / CC1/2: 0.757 / Rrim(I) all: 0.702 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 6HGG Resolution: 1.369→38.67 Å / SU ML: 0.13 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 18.77
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.369→38.67 Å
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Refine LS restraints |
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LS refinement shell |
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