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Yorodumi- PDB-8gqq: The three-dimensional structure of Cystatin A2, a cysteine protea... -
+Open data
-Basic information
Entry | Database: PDB / ID: 8gqq | ||||||
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Title | The three-dimensional structure of Cystatin A2, a cysteine protease inhibitor from Dictyostelium discoideum | ||||||
Components | Cystatin-A2 | ||||||
Keywords | STRUCTURAL PROTEIN / cystatin A2 / cysteine protease inhibitor / inhibition activity | ||||||
Function / homology | Function and homology information negative regulation of peptidase activity / Neutrophil degranulation / regulation of protein metabolic process / cysteine-type endopeptidase inhibitor activity / cytosol Similarity search - Function | ||||||
Biological species | Dictyostelium discoideum AX3 (eukaryote) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.069 Å | ||||||
Authors | Dinh, T.T. / Dao, O. / Lee, K.H. | ||||||
Funding support | Korea, Republic Of, 1items
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Citation | Journal: To Be Published Title: The three-dimensional structure of Cystatin A2, a cysteine protease inhibitor from Dictyostelium discoideum Authors: Dinh, T.T. / Dao, O. / Lee, K.H. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8gqq.cif.gz | 57.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8gqq.ent.gz | 40.3 KB | Display | PDB format |
PDBx/mmJSON format | 8gqq.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/gq/8gqq ftp://data.pdbj.org/pub/pdb/validation_reports/gq/8gqq | HTTPS FTP |
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-Related structure data
Related structure data | 3kfqS S: Starting model for refinement |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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Components on special symmetry positions |
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-Components
#1: Protein | Mass: 10852.265 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Dictyostelium discoideum AX3 (eukaryote) Gene: cpiB, DDB_G0280439 Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria) References: UniProt: Q65YR7 |
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#2: 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: 2.15 Å3/Da / Density % sol: 42.85 % |
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Crystal grow | Temperature: 291.15 K / Method: vapor diffusion, hanging drop Details: 22% (w/v) PEG 2K, 100 mM MES pH 6.5, 60 mM sodium acetate, 10 mM TCEP |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: PAL/PLS / Beamline: 7A (6B, 6C1) / Wavelength: 0.97934 Å |
Detector | Type: ADSC QUANTUM 270 / Detector: CCD / Date: Feb 21, 2022 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97934 Å / Relative weight: 1 |
Reflection | Resolution: 1.069→24.911 Å / Num. obs: 42018 / % possible obs: 99.05 % / Redundancy: 13.5 % / Biso Wilson estimate: 9.34 Å2 / Rmerge(I) obs: 0.128 / Net I/σ(I): 10.8 |
Reflection shell | Resolution: 1.069→1.107 Å / Rmerge(I) obs: 0.39 / Num. unique obs: 4113 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3KFQ Resolution: 1.069→24.911 Å / SU ML: 0.09 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 17.93 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 45.58 Å2 / Biso mean: 14.9737 Å2 / Biso min: 5.57 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 1.069→24.911 Å
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0
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Refinement TLS params. | Method: refined / Origin x: 2.1566 Å / Origin y: 16.2658 Å / Origin z: 4.6508 Å
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Refinement TLS group |
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