[English] 日本語
Yorodumi- PDB-5i7j: Crystal Structure of Human SPLUNC1 Disulfide Mutant M3 (I76C, V214C) -
+Open data
-Basic information
Entry | Database: PDB / ID: 5i7j | ||||||
---|---|---|---|---|---|---|---|
Title | Crystal Structure of Human SPLUNC1 Disulfide Mutant M3 (I76C, V214C) | ||||||
Components | BPI fold-containing family A member 1 | ||||||
Keywords | ANTIMICROBIAL PROTEIN / Innate pulmonary defense protein | ||||||
Function / homology | Function and homology information immune response in nasopharyngeal-associated lymphoid tissue / regulation of sodium ion transmembrane transport / negative regulation of single-species biofilm formation in or on host organism / multicellular organismal-level water homeostasis / surfactant homeostasis / Antimicrobial peptides / antimicrobial humoral immune response mediated by antimicrobial peptide / antibacterial humoral response / defense response to virus / innate immune response ...immune response in nasopharyngeal-associated lymphoid tissue / regulation of sodium ion transmembrane transport / negative regulation of single-species biofilm formation in or on host organism / multicellular organismal-level water homeostasis / surfactant homeostasis / Antimicrobial peptides / antimicrobial humoral immune response mediated by antimicrobial peptide / antibacterial humoral response / defense response to virus / innate immune response / lipid binding / extracellular space / extracellular region Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.544 Å | ||||||
Authors | Walton, W.G. / Redinbo, M.R. | ||||||
Funding support | United States, 1items
| ||||||
Citation | Journal: Biochemistry / Year: 2016 Title: Structural Features Essential to the Antimicrobial Functions of Human SPLUNC1. Authors: Walton, W.G. / Ahmad, S. / Little, M.S. / Kim, C.S. / Tyrrell, J. / Lin, Q. / Di, Y.P. / Tarran, R. / Redinbo, M.R. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 5i7j.cif.gz | 88 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb5i7j.ent.gz | 65.1 KB | Display | PDB format |
PDBx/mmJSON format | 5i7j.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5i7j_validation.pdf.gz | 437.2 KB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 5i7j_full_validation.pdf.gz | 444.5 KB | Display | |
Data in XML | 5i7j_validation.xml.gz | 16 KB | Display | |
Data in CIF | 5i7j_validation.cif.gz | 21.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/i7/5i7j ftp://data.pdbj.org/pub/pdb/validation_reports/i7/5i7j | HTTPS FTP |
-Related structure data
Related structure data | 5i7kC 5i7lC 4kghS C: citing same article (ref.) S: Starting model for refinement |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
2 |
| ||||||||
Unit cell |
|
-Components
#1: Protein | Mass: 24953.320 Da / Num. of mol.: 2 / Mutation: I76C, V214C Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) Gene: BPIFA1, LUNX, NASG, PLUNC, SPLUNC1, SPURT, UNQ787/PRO1606 Production host: Escherichia coli (E. coli) / References: UniProt: Q9NP55 #2: Water | ChemComp-HOH / | |
---|
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 2.9 Å3/Da / Density % sol: 57.62 % |
---|---|
Crystal grow | Temperature: 310 K / Method: vapor diffusion, hanging drop / pH: 8.5 / Details: 6M Ammonium Nitrate, 0.1M Tris-HCL, pH 8.5 |
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 23-BM-B / Wavelength: 1.0332 Å |
Detector | Type: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Apr 23, 2015 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.0332 Å / Relative weight: 1 |
Reflection | Resolution: 2.544→28.283 Å / Num. obs: 19395 / % possible obs: 98.74 % / Redundancy: 3.5 % / Biso Wilson estimate: 58.95 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.05465 / Net I/σ(I): 14.54 |
Reflection shell | Resolution: 2.544→2.634 Å / Redundancy: 3.4 % / Rmerge(I) obs: 0.7058 / % possible all: 94.45 |
-Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4KGH Resolution: 2.544→28.283 Å / SU ML: 0.36 / Cross valid method: FREE R-VALUE / σ(F): 0 / Phase error: 32.38
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.544→28.283 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell |
|