+Open data
-Basic information
Entry | Database: PDB / ID: 5ki9 | ||||||
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Title | Crystal structure of human beta-defensin 4 (HBD4) | ||||||
Components | Beta-defensin 104 | ||||||
Keywords | ANTIMICROBIAL PROTEIN / DEFENSIN / ANTIMICROBIAL / CHEMOTACTIC / DIMERIZATION | ||||||
Function / homology | Function and homology information Beta defensins / Defensins / cellular response to phorbol 13-acetate 12-myristate / positive chemotaxis / chemoattractant activity / monocyte chemotaxis / defense response to Gram-negative bacterium / defense response to Gram-positive bacterium / innate immune response / extracellular region Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.6 Å | ||||||
Authors | Jacek, L. / Adam, P. / Marzenam, P. | ||||||
Citation | Journal: To Be Published Title: Human beta-Defensin 4: defensin without the "twist" Authors: Adam, P. / Marzenam, P. / Jerry, A. / Jacek, L. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5ki9.cif.gz | 30.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5ki9.ent.gz | 22.8 KB | Display | PDB format |
PDBx/mmJSON format | 5ki9.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ki/5ki9 ftp://data.pdbj.org/pub/pdb/validation_reports/ki/5ki9 | HTTPS FTP |
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-Related structure data
Related structure data | |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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Details | author states the biological assembly is unknown |
-Components
#1: Protein/peptide | Mass: 5257.094 Da / Num. of mol.: 1 / Fragment: UNP residues 23-65 Source method: isolated from a genetically manipulated source Details: LYSINE RESIDUES ARE DI-METHYLATED / Source: (gene. exp.) Homo sapiens (human) / Gene: DEFB104A, DEFB104, DEFB4, DEFB104B / Production host: Escherichia coli (E. coli) / References: UniProt: Q8WTQ1 | ||||
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#2: Chemical | #3: Chemical | ChemComp-TFA / | #4: 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: 2.19 Å3/Da / Density % sol: 43.82 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 4.5 Details: 25.5% PEG 8,000, 0.085 M sodium acetate buffer pH 4.5, 0.17 M Lithium Sulfate, 15% Glycerol |
-Data collection
Diffraction | Mean temperature: 100 K | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Oct 10, 2010 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 1.55→50 Å / Num. obs: 6994 / % possible obs: 95.6 % / Redundancy: 16.6 % / Rmerge(I) obs: 0.059 / Rpim(I) all: 0.014 / Rrim(I) all: 0.06 / Χ2: 1.697 / Net I/av σ(I): 90.17 / Net I/σ(I): 16.7 / Num. measured all: 116371 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell |
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-Phasing
Phasing | Method: MAD |
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-Processing
Software |
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Refinement | Method to determine structure: MAD / Resolution: 1.6→15 Å / Cor.coef. Fo:Fc: 0.956 / Cor.coef. Fo:Fc free: 0.931 / SU B: 5.658 / SU ML: 0.087 / SU R Cruickshank DPI: 0.1588 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.159 / ESU R Free: 0.115 Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 170.24 Å2 / Biso mean: 51.173 Å2 / Biso min: 30.09 Å2
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Refinement step | Cycle: final / Resolution: 1.6→15 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.6→1.641 Å / Total num. of bins used: 20
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