+Open data
-Basic information
Entry | Database: PDB / ID: 2nlc | ||||||
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Title | Human beta-defensin-1 (mutant Ser8Ala) | ||||||
Components | Beta-defensin 1 | ||||||
Keywords | ANTIMICROBIAL PROTEIN / antimicrobial / chemotactic / defensin / mutant | ||||||
Function / homology | Function and homology information positive regulation of flagellated sperm motility involved in capacitation / microvesicle / CCR6 chemokine receptor binding / Beta defensins / Defensins / : / sperm midpiece / cAMP-mediated signaling / innate immune response in mucosa / response to bacterium ...positive regulation of flagellated sperm motility involved in capacitation / microvesicle / CCR6 chemokine receptor binding / Beta defensins / Defensins / : / sperm midpiece / cAMP-mediated signaling / innate immune response in mucosa / response to bacterium / Golgi lumen / antimicrobial humoral immune response mediated by antimicrobial peptide / chemotaxis / antibacterial humoral response / defense response to Gram-negative bacterium / defense response to Gram-positive bacterium / defense response to bacterium / immune response / G protein-coupled receptor signaling pathway / innate immune response / extracellular space / extracellular exosome / extracellular region / identical protein binding / membrane Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.65 Å | ||||||
Authors | Lubkowski, J. / Pazgier, M. | ||||||
Citation | Journal: J.Biol.Chem. / Year: 2007 Title: Studies of the Biological Properties of Human beta-Defensin 1. Authors: Pazgier, M. / Prahl, A. / Hoover, D.M. / Lubkowski, J. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2nlc.cif.gz | 47.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2nlc.ent.gz | 33.7 KB | Display | PDB format |
PDBx/mmJSON format | 2nlc.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2nlc_validation.pdf.gz | 454.8 KB | Display | wwPDB validaton report |
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Full document | 2nlc_full_validation.pdf.gz | 455.4 KB | Display | |
Data in XML | 2nlc_validation.xml.gz | 10.5 KB | Display | |
Data in CIF | 2nlc_validation.cif.gz | 15.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/nl/2nlc ftp://data.pdbj.org/pub/pdb/validation_reports/nl/2nlc | HTTPS FTP |
-Related structure data
Related structure data | 2nlbC 2nldC 2nleC 2nlfC 2nlgC 2nlhC 2nlpC 2nlqC 2nlsC 1ijvS 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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Details | Biological assembly is a monomer |
-Components
#1: Protein/peptide | Mass: 3924.598 Da / Num. of mol.: 4 / Fragment: HUMAN BETA-DEFENSIN 1, residues 33-68 / Mutation: S8A Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: DEFB1, BD1, HBD1 / Plasmid: pAED4 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)pLysE / References: UniProt: P60022 #2: Chemical | ChemComp-SO4 / #3: Chemical | ChemComp-ACT / | #4: Water | ChemComp-HOH / | |
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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: 2.18 Å3/Da / Density % sol: 43.54 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion / pH: 7 Details: PEG 8000, LITHIUM SULFATE, pH 7.0, vapor diffusion, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.54178 Å |
Detector | Type: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Aug 10, 2005 / Details: Osmic mirrors |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.54178 Å / Relative weight: 1 |
Reflection | Resolution: 1.65→30 Å / Num. all: 14783 / Num. obs: 14783 / % possible obs: 92.6 % / Observed criterion σ(I): -3 / Redundancy: 6.4 % / Rmerge(I) obs: 0.051 / Χ2: 0.958 / Net I/σ(I): 29 |
Reflection shell | Resolution: 1.65→1.71 Å / Redundancy: 5 % / Rmerge(I) obs: 0.207 / Mean I/σ(I) obs: 6.4 / Num. unique all: 1367 / Χ2: 1.046 / % possible all: 85.8 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB entry 1IJV Resolution: 1.65→30 Å / Cor.coef. Fo:Fc: 0.965 / Cor.coef. Fo:Fc free: 0.951 / SU B: 2.086 / SU ML: 0.068 / SU R Cruickshank DPI: 0.113 / Cross valid method: THROUGHOUT / ESU R Free: 0.108 / Stereochemistry target values: Engh & Huber
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 17.276 Å2
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Refinement step | Cycle: LAST / Resolution: 1.65→30 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.649→1.692 Å / Total num. of bins used: 20
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