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- PDB-5i7k: Crystal Structure of Human SPLUNC1 Dolphin Mutant D1 (G58A, S61A,... -
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Open data
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Basic information
Entry | Database: PDB / ID: 5i7k | ||||||
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Title | Crystal Structure of Human SPLUNC1 Dolphin Mutant D1 (G58A, S61A, G62E, G63D, G66D, I67T) | ||||||
![]() | BPI fold-containing family A member 1 | ||||||
![]() | ANTIMICROBIAL PROTEIN / Surfactant / Antimicrobial / Airway | ||||||
Function / homology | ![]() 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 | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Walton, W.G. / Redinbo, M.R. | ||||||
Funding support | ![]()
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![]() | ![]() 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: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 89.2 KB | Display | ![]() |
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PDB format | ![]() | 66.9 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 435.6 KB | Display | ![]() |
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Full document | ![]() | 441.8 KB | Display | |
Data in XML | ![]() | 16.4 KB | Display | |
Data in CIF | ![]() | 22.1 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 5i7jC ![]() 5i7lC ![]() 4kghS C: citing same article ( S: Starting model for refinement |
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Similar structure data |
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Links
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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: 25133.432 Da / Num. of mol.: 2 / Mutation: G58A, S61A, G62E, G63D, G66D, I67T Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() Gene: BPIFA1, LUNX, NASG, PLUNC, SPLUNC1, SPURT, UNQ787/PRO1606 Production host: ![]() ![]() #2: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.9 Å3/Da / Density % sol: 57.64 % |
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Crystal grow | Temperature: 310 K / Method: vapor diffusion, hanging drop / pH: 8.5 / Details: 6M Ammonium Nitrate, and 0.1M Tris HCL pH 8.5 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
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: 2.552→29.6 Å / Num. obs: 19300 / % possible obs: 98.65 % / Redundancy: 3.5 % / Biso Wilson estimate: 54.92 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.05676 / Rsym value: 0.045 / Net I/σ(I): 13.8 |
Reflection shell | Resolution: 2.552→2.644 Å / Redundancy: 3.2 % / Rmerge(I) obs: 0.6574 / Mean I/σ(I) obs: 2.11 / % possible all: 89.42 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 4KGH Resolution: 2.552→29.6 Å / SU ML: 0.37 / Cross valid method: FREE R-VALUE / σ(F): 0 / Phase error: 31.97
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.552→29.6 Å
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Refine LS restraints |
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LS refinement shell |
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