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- PDB-5i7k: Crystal Structure of Human SPLUNC1 Dolphin Mutant D1 (G58A, S61A,... -

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Basic information

Entry
Database: PDB / ID: 5i7k
TitleCrystal Structure of Human SPLUNC1 Dolphin Mutant D1 (G58A, S61A, G62E, G63D, G66D, I67T)
ComponentsBPI fold-containing family A member 1
KeywordsANTIMICROBIAL PROTEIN / Surfactant / Antimicrobial / Airway
Function / homology
Function and homology information


immune response in nasopharyngeal-associated lymphoid tissue / negative regulation of single-species biofilm formation in or on host organism / regulation of sodium ion transmembrane transport / 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 / negative regulation of single-species biofilm formation in or on host organism / regulation of sodium ion transmembrane transport / 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
: / Bactericidal permeability-increasing protein; domain 1 / Lipid-binding serum glycoprotein, N-terminal / Bactericidal permeability-increasing protein, alpha/beta domain superfamily / LBP / BPI / CETP family, N-terminal domain / Bactericidal permeability-increasing protein; domain 1 / Super Roll / Alpha Beta
Similarity search - Domain/homology
BPI fold-containing family A member 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.552 Å
AuthorsWalton, W.G. / Redinbo, M.R.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Heart, Lung, and Blood Institute (NIH/NHLBI)R01 HL108927 United States
CitationJournal: 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
DepositionFeb 17, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 18, 2016Provider: repository / Type: Initial release
Revision 1.1Jun 8, 2016Group: Database references
Revision 1.2Sep 20, 2017Group: Author supporting evidence / Database references / Derived calculations
Category: citation / pdbx_audit_support / pdbx_struct_oper_list
Item: _citation.journal_id_CSD / _pdbx_audit_support.funding_organization / _pdbx_struct_oper_list.symmetry_operation
Revision 1.3Dec 4, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.4Sep 27, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.5Nov 13, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: BPI fold-containing family A member 1
B: BPI fold-containing family A member 1


Theoretical massNumber of molelcules
Total (without water)50,2672
Polymers50,2672
Non-polymers00
Water59433
1
A: BPI fold-containing family A member 1


Theoretical massNumber of molelcules
Total (without water)25,1331
Polymers25,1331
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: BPI fold-containing family A member 1


Theoretical massNumber of molelcules
Total (without water)25,1331
Polymers25,1331
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2550 Å2
ΔGint-30 kcal/mol
Surface area20520 Å2
MethodPISA
Unit cell
Length a, b, c (Å)48.027, 204.927, 118.652
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221

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Components

#1: Protein BPI fold-containing family A member 1 / Lung-specific protein X / Nasopharyngeal carcinoma-related protein / Palate lung and nasal ...Lung-specific protein X / Nasopharyngeal carcinoma-related protein / Palate lung and nasal epithelium clone protein / Secretory protein in upper respiratory tracts / Short PLUNC1 / SPLUNC1 / Tracheal epithelium-enriched protein / Von Ebner protein Hl


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.) 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 / water


Mass: 18.015 Da / Num. of mol.: 33 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.9 Å3/Da / Density % sol: 57.64 %
Crystal growTemperature: 310 K / Method: vapor diffusion, hanging drop / pH: 8.5 / Details: 6M Ammonium Nitrate, and 0.1M Tris HCL pH 8.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-B / Wavelength: 1.0332 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Apr 23, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0332 Å / Relative weight: 1
ReflectionResolution: 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 shellResolution: 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

Software
NameVersionClassification
PHENIX1.9_1692refinement
XDSdata reduction
XSCALEdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4KGH

4kgh


Resolution: 2.552→29.6 Å / SU ML: 0.37 / Cross valid method: FREE R-VALUE / σ(F): 0 / Phase error: 31.97
RfactorNum. reflection% reflection
Rfree0.2744 1820 10.01 %
Rwork0.2122 --
obs0.2184 18174 92.9 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.552→29.6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3005 0 0 33 3038
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0093040
X-RAY DIFFRACTIONf_angle_d1.5044147
X-RAY DIFFRACTIONf_dihedral_angle_d15.8971130
X-RAY DIFFRACTIONf_chiral_restr0.052554
X-RAY DIFFRACTIONf_plane_restr0.007520
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.5524-2.62140.4023990.3294926X-RAY DIFFRACTION70
2.6214-2.69840.40421240.30171123X-RAY DIFFRACTION83
2.6984-2.78550.33551300.28671138X-RAY DIFFRACTION86
2.7855-2.8850.38381350.27761165X-RAY DIFFRACTION89
2.885-3.00040.34991370.28791251X-RAY DIFFRACTION93
3.0004-3.13680.33451370.27561284X-RAY DIFFRACTION96
3.1368-3.30190.30961470.26081298X-RAY DIFFRACTION97
3.3019-3.50850.29761490.22761320X-RAY DIFFRACTION98
3.5085-3.77890.29921480.22721330X-RAY DIFFRACTION99
3.7789-4.15830.27131480.1931341X-RAY DIFFRACTION99
4.1583-4.75780.20371520.16061362X-RAY DIFFRACTION99
4.7578-5.98620.26941540.20071379X-RAY DIFFRACTION99
5.9862-29.60170.22771600.17591437X-RAY DIFFRACTION99

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