+Open data
-Basic information
Entry | Database: PDB / ID: 5i7l | ||||||
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Title | Crystal Structure of SPLUNC1 Disulfide Mutant M2 (A48C, V253C) | ||||||
Components | BPI fold-containing family A member 1 | ||||||
Keywords | ANTIMICROBIAL PROTEIN / Surfactant / Antimicrobial / Airway | ||||||
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: 2.598 Å | ||||||
Authors | Walton, W.G. / Redinbo, M.R. | ||||||
Funding support | United States, 1items
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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 |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5i7l.cif.gz | 88 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5i7l.ent.gz | 65.4 KB | Display | PDB format |
PDBx/mmJSON format | 5i7l.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5i7l_validation.pdf.gz | 436.3 KB | Display | wwPDB validaton report |
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Full document | 5i7l_full_validation.pdf.gz | 447.3 KB | Display | |
Data in XML | 5i7l_validation.xml.gz | 16.5 KB | Display | |
Data in CIF | 5i7l_validation.cif.gz | 21.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/i7/5i7l ftp://data.pdbj.org/pub/pdb/validation_reports/i7/5i7l | HTTPS FTP |
-Related structure data
Related structure data | 5i7jC 5i7kC 4kghS C: citing same article (ref.) S: Starting model for refinement |
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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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3 |
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Unit cell |
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-Components
#1: Protein | Mass: 24995.402 Da / Num. of mol.: 2 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 / | |
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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: 2.88 Å3/Da / Density % sol: 57.31 % |
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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 |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 23-ID-B / Wavelength: 1.03319 Å |
Detector | Type: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Oct 17, 2014 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.03319 Å / Relative weight: 1 |
Reflection | Resolution: 2.598→38.842 Å / Num. obs: 18284 / % possible obs: 99.63 % / Redundancy: 5.1 % / Biso Wilson estimate: 57.56 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.06155 / Net I/σ(I): 21.33 |
Reflection shell | Resolution: 2.598→2.691 Å / Rmerge(I) obs: 0.5798 / Mean I/σ(I) obs: 4.34 / % possible all: 96.67 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4KGH Resolution: 2.598→38.842 Å / SU ML: 0.34 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 31.81
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.598→38.842 Å
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Refine LS restraints |
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LS refinement shell |
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