+Open data
-Basic information
Entry | Database: PDB / ID: 2pm4 | ||||||
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Title | Human alpha-defensin 1 (multiple Arg->Lys mutant) | ||||||
Components | Neutrophil defensin 1 (HNP-1) (HP-1) (HP1) (Defensin, alpha 1) | ||||||
Keywords | ANTIMICROBIAL PROTEIN / antimicrobial / defensin / mutant | ||||||
Function / homology | Function and homology information pore-forming activity / Defensins / disruption of plasma membrane integrity in another organism / killing by host of symbiont cells / T cell chemotaxis / Alpha-defensins / defense response to protozoan / intracellular estrogen receptor signaling pathway / defense response to fungus / innate immune response in mucosa ...pore-forming activity / Defensins / disruption of plasma membrane integrity in another organism / killing by host of symbiont cells / T cell chemotaxis / Alpha-defensins / defense response to protozoan / intracellular estrogen receptor signaling pathway / defense response to fungus / innate immune response in mucosa / Golgi lumen / chemotaxis / azurophil granule lumen / antimicrobial humoral immune response mediated by antimicrobial peptide / antibacterial humoral response / collagen-containing extracellular matrix / defense response to virus / killing of cells of another organism / cellular response to lipopolysaccharide / defense response to Gram-negative bacterium / defense response to Gram-positive bacterium / immune response / Neutrophil degranulation / protein homodimerization activity / extracellular space / extracellular exosome / extracellular region Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.95 Å | ||||||
Authors | Lubkowski, J. / Pazgier, M. / Lu, W. | ||||||
Citation | Journal: J.Biol.Chem. / Year: 2007 Title: Toward understanding the cationicity of defensins. Arg and Lys versus their noncoded analogs. Authors: Zou, G. / de Leeuw, E. / Li, C. / Pazgier, M. / Li, C. / Zeng, P. / Lu, W.Y. / Lubkowski, J. / Lu, W. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2pm4.cif.gz | 25.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2pm4.ent.gz | 16.8 KB | Display | PDB format |
PDBx/mmJSON format | 2pm4.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/pm/2pm4 ftp://data.pdbj.org/pub/pdb/validation_reports/pm/2pm4 | HTTPS FTP |
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-Related structure data
Related structure data | 2plzC 1dfnS 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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1 |
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2 |
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Unit cell |
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Components on special symmetry positions |
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Details | biological dimer is formed by chain B and its symmetry related by operator -x,-y,z |
-Components
#1: Protein/peptide | Mass: 3412.079 Da / Num. of mol.: 2 / Mutation: Arg14->Lys, Arg15->Lys, Arg24->Lys Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: DEFA1, DEF1, DEFA2 / Production host: Escherichia coli (E. coli) / References: UniProt: P59665, UniProt: P59666*PLUS #2: 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: 3.05 Å3/Da / Density % sol: 59.63 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop Details: 0.4 M ammonium phosphate monobasic, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418 |
Detector | Type: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Mar 2, 2007 / Details: mirrors |
Radiation | Monochromator: Si crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 1.95→30 Å / Num. all: 6505 / Num. obs: 6505 / % possible obs: 97 % / Observed criterion σ(I): -3 / Redundancy: 3.4 % / Rmerge(I) obs: 0.048 / Rsym value: 0.048 / Net I/σ(I): 21 |
Reflection shell | Resolution: 1.95→2.02 Å / Redundancy: 3.5 % / Rmerge(I) obs: 0.412 / Mean I/σ(I) obs: 3.1 / Num. unique all: 610 / Rsym value: 0.412 / % possible all: 95.5 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1DFN Resolution: 1.95→20 Å / Cor.coef. Fo:Fc: 0.96 / Cor.coef. Fo:Fc free: 0.938 / SU B: 6.802 / SU ML: 0.1 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.145 / ESU R Free: 0.15 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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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: BABINET MODEL WITH MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 49.312 Å2
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Refine analyze | Luzzati coordinate error obs: 0.3333 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.95→20 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.949→1.999 Å / Total num. of bins used: 20
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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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