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Yorodumi- PDB-6hge: Crystal structure of Alpha1-antichymotrypsin variant NewBG-I in t... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6hge | ||||||
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Title | Crystal structure of Alpha1-antichymotrypsin variant NewBG-I in the uncleaved S-conformation | ||||||
Components | (Alpha-1-antichymotrypsin) x 4 | ||||||
Keywords | TRANSPORT PROTEIN / Serpin / alpha1-Antichymotrypsin / computational protein design | ||||||
Function / homology | Function and homology information 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 | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.8 Å | ||||||
Authors | Gardill, B.R. / Schmidt, K. / Muller, Y.A. | ||||||
Citation | Journal: J.Struct.Biol. / Year: 2019 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: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6hge.cif.gz | 300.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6hge.ent.gz | 241.7 KB | Display | PDB format |
PDBx/mmJSON format | 6hge.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6hge_validation.pdf.gz | 485 KB | Display | wwPDB validaton report |
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Full document | 6hge_full_validation.pdf.gz | 514.4 KB | Display | |
Data in XML | 6hge_validation.xml.gz | 53.8 KB | Display | |
Data in CIF | 6hge_validation.cif.gz | 71.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/hg/6hge ftp://data.pdbj.org/pub/pdb/validation_reports/hg/6hge | HTTPS FTP |
-Related structure data
Related structure data | 6hgdC 6hgfC 6hggC 6hghC 6hgiC 6hgjC 6hgkC 6hglC 6hgmC 6hgnC 1yxaS S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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Unit cell |
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-Components
#1: Protein | Mass: 46893.504 Da / Num. of mol.: 1 Mutation: L24R, E242Q, K244N, L269S, P270R, K274N, R277G, 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 - dimethyl-lysines (MLY) have been modelled instead 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 - dimethyl-lysines (MLY) have been modelled instead of lysines (LYS) when the electron density confirmed the success of the reductive methylation process of surface lysines Source: (gene. exp.) Homo sapiens (human) / Gene: SERPINA3, AACT, GIG24, GIG25 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): Star / References: UniProt: P01011 |
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#2: Protein | Mass: 46947.594 Da / Num. of mol.: 1 Mutation: L24R, E242Q, K244N, L269S, P270R, K274N, R277G, 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.) Homo sapiens (human) / Gene: SERPINA3, AACT, GIG24, GIG25 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): Star / References: UniProt: P01011 |
#3: Protein | Mass: 46893.504 Da / Num. of mol.: 1 Mutation: L24R, E242Q, K244N, L269S, P270R, K274N, R277G, 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.) Homo sapiens (human) / Gene: SERPINA3, AACT, GIG24, GIG25 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): Star / References: UniProt: P01011 |
#4: Protein | Mass: 46974.641 Da / Num. of mol.: 1 Mutation: L24R, E242Q, K244N, L269S, P270R, K274N, R277G, 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.) Homo sapiens (human) / Gene: SERPINA3, AACT, GIG24, GIG25 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): Star / References: UniProt: P01011 |
#5: 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: 2.46 Å3/Da / Density % sol: 49.92 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop Details: 0.2 M NaCl, 0.1 M Tris-HCl, pH 8.5, 25 % PEG 3350 supplemented with 10 % of a 0.5 M NaF solution, and additional 0.1 ul of a silver bullets bio reagent mixture consisting of thymidine, ...Details: 0.2 M NaCl, 0.1 M Tris-HCl, pH 8.5, 25 % PEG 3350 supplemented with 10 % of a 0.5 M NaF solution, and additional 0.1 ul of a silver bullets bio reagent mixture consisting of thymidine, adenosine 3,5-cyclic monophosphate sodium salt monohydrate, sarcosine, 4-aminobenzoic acid, acarbose, inosine, 0.02 M HEPES sodium pH 6.8 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 0.91841 Å |
Detector | Type: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Sep 16, 2011 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.91841 Å / Relative weight: 1 |
Reflection | Resolution: 2.8→34.538 Å / Num. obs: 43876 / % possible obs: 98.1 % / Redundancy: 3.86 % / Rrim(I) all: 0.091 / Net I/σ(I): 15.31 |
Reflection shell | Resolution: 2.8→2.97 Å / Mean I/σ(I) obs: 2.62 / Rrim(I) all: 0.581 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1YXA Resolution: 2.8→34.538 Å / SU ML: 0.4 / Cross valid method: FREE R-VALUE / σ(F): 1.99 / Phase error: 27.33
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.8→34.538 Å
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Refine LS restraints |
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LS refinement shell |
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