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Yorodumi- PDB-7yoa: High-resolution crystal structure of the mouse alpha-defensin cry... -
+Open data
-Basic information
Entry | Database: PDB / ID: 7yoa | ||||||
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Title | High-resolution crystal structure of the mouse alpha-defensin cryptdin 14 | ||||||
Components | Alpha-defensin 14Alpha defensin | ||||||
Keywords | ANTIBIOTIC / defensin / antimicrobial peptide / dimer | ||||||
Function / homology | Function and homology information disruption of plasma membrane integrity in another organism / innate immune response in mucosa / secretory granule / antimicrobial humoral immune response mediated by antimicrobial peptide / midbody / antibacterial humoral response / cellular response to lipopolysaccharide / defense response to Gram-negative bacterium / defense response to Gram-positive bacterium / intracellular membrane-bounded organelle ...disruption of plasma membrane integrity in another organism / innate immune response in mucosa / secretory granule / antimicrobial humoral immune response mediated by antimicrobial peptide / midbody / antibacterial humoral response / cellular response to lipopolysaccharide / defense response to Gram-negative bacterium / defense response to Gram-positive bacterium / intracellular membrane-bounded organelle / protein homodimerization activity / extracellular space Similarity search - Function | ||||||
Biological species | Mus musculus (house mouse) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.67 Å | ||||||
Authors | Yang, Y. / Lu, W. | ||||||
Funding support | China, 1items
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Citation | Journal: Infect.Immun. / Year: 2023 Title: Mouse alpha-Defensins: Structural and Functional Analysis of the 17 Cryptdin Isoforms Identified from a Single Jejunal Crypt. Authors: Wang, Q. / Yang, Y. / Luo, G. / Zhou, Y. / Tolbert, W.D. / Pazgier, M. / Liao, C. / Lu, W. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7yoa.cif.gz | 42.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7yoa.ent.gz | 28.9 KB | Display | PDB format |
PDBx/mmJSON format | 7yoa.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/yo/7yoa ftp://data.pdbj.org/pub/pdb/validation_reports/yo/7yoa | HTTPS FTP |
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-Related structure data
Related structure data | 2gw9S 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
#1: Protein/peptide | Mass: 4239.174 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) Mus musculus (house mouse) / References: UniProt: P50712 #2: Chemical | ChemComp-SO4 / #3: Water | ChemComp-HOH / | Has ligand of interest | N | |
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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: 2.69 Å3/Da / Density % sol: 54.19 % |
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Crystal grow | Temperature: 300 K / Method: vapor diffusion, sitting drop / pH: 5.6 Details: 0.1 M Sodium acetate trihydrate;1.5 M ammonium sulfate |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.97853 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Jan 10, 2022 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.97853 Å / Relative weight: 1 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 1.67→50 Å / Num. obs: 17321 / % possible obs: 98.7 % / Redundancy: 35.4 % / Biso Wilson estimate: 11.66 Å2 / Rmerge(I) obs: 0.053 / Rrim(I) all: 0.054 / Χ2: 0.95 / Net I/σ(I): 9.5 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 2GW9 Resolution: 1.67→27.22 Å / SU ML: 0.17 / Cross valid method: THROUGHOUT / σ(F): 0.34 / Phase error: 27.15 / 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: 80.31 Å2 / Biso mean: 28.7786 Å2 / Biso min: 9.72 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 1.67→27.22 Å
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 6
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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