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- PDB-4kgh: Crystal Structure of human splunc1 lacking the secretion signal s... -

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Basic information

Entry
Database: PDB / ID: 4kgh
TitleCrystal Structure of human splunc1 lacking the secretion signal sequence
ComponentsBPI fold-containing family A member 1
KeywordsIMMUNE SYSTEM / beta barrel / BPI-like fold
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
AMMONIUM ION / NITRATE ION / BPI fold-containing family A member 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.806 Å
AuthorsBetts, L. / Walton, W.G.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2013
Title: Molecular basis for pH-dependent mucosal dehydration in cystic fibrosis airways.
Authors: Garland, A.L. / Walton, W.G. / Coakley, R.D. / Tan, C.D. / Gilmore, R.C. / Hobbs, C.A. / Tripathy, A. / Clunes, L.A. / Bencharit, S. / Stutts, M.J. / Betts, L. / Redinbo, M.R. / Tarran, R.
History
DepositionApr 29, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 25, 2013Provider: repository / Type: Initial release
Revision 1.1Oct 9, 2013Group: Database references
Revision 1.2Nov 15, 2017Group: Refinement description / Category: software
Item: _software.classification / _software.contact_author ..._software.classification / _software.contact_author / _software.contact_author_email / _software.date / _software.language / _software.location / _software.name / _software.type / _software.version
Revision 1.3Nov 20, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_entry_details.has_protein_modification / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)50,0866
Polymers49,8912
Non-polymers1954
Water1448
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2120 Å2
ΔGint-21 kcal/mol
Surface area19510 Å2
MethodPISA
2
B: BPI fold-containing family A member 1
hetero molecules

A: BPI fold-containing family A member 1


Theoretical massNumber of molelcules
Total (without water)50,0866
Polymers49,8912
Non-polymers1954
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_455x-1/2,y+1/2,z1
Buried area1930 Å2
ΔGint-25 kcal/mol
Surface area19700 Å2
MethodPISA
Unit cell
Length a, b, c (Å)47.475, 203.727, 118.612
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221

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Components

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Protein , 1 types, 2 molecules BA

#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 / Tracheal epithelium-enriched protein / Von Ebner protein Hl


Mass: 24945.297 Da / Num. of mol.: 2 / Fragment: UNP residues 19-256
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: BPIFA1, LUNX, NASG, PLUNC, SPURT, UNQ787/PRO1606 / Plasmid: pMCSG7 / Production host: Escherichia coli (E. coli) / Strain (production host): Bl21(DE3)codon plus RIPL / References: UniProt: Q9NP55

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Non-polymers , 5 types, 12 molecules

#2: Chemical ChemComp-NO3 / NITRATE ION


Mass: 62.005 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: NO3
#3: Chemical ChemComp-NH4 / AMMONIUM ION


Mass: 18.038 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: H4N
#4: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#5: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 8 / Source method: isolated from a natural source / Formula: H2O

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Details

Has protein modificationY
Sequence detailsRESIDUE 105 IS AN ACCIDENTAL MUTATION

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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: 2.87 Å3/Da / Density % sol: 57.21 %
Crystal growTemperature: 298 K / Method: vapor diffusion / pH: 8.5
Details: 8% PEG 400, .2 M tri-sodium citrate, .1 M Tris-HCl pH 8.5, vapor diffusion, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-D / Wavelength: 1 Å
DetectorType: MAR scanner 300 mm plate / Detector: IMAGE PLATE / Date: Feb 20, 2012
RadiationProtocol: SINGLE WAVELENGTH / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.8→100 Å / Num. obs: 13819 / % possible obs: 95.8 % / Redundancy: 6.5 % / Rmerge(I) obs: 0.092 / Χ2: 2.757 / Net I/σ(I): 12
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
2.8-2.854.40.3794991.25172.5
2.85-2.94.70.3345501.353177.5
2.9-2.965.10.3446031.443183.8
2.96-3.025.50.3286351.465193.5
3.02-3.085.80.3126891.472196.6
3.08-3.156.30.2877181.444197.4
3.15-3.236.60.2336921.656199.6
3.23-3.326.70.2116991.9541100
3.32-3.426.90.1887202.081199
3.42-3.536.90.1696992.3671100
3.53-3.6570.1697302.6511100
3.65-3.87.10.1426972.814199.7
3.8-3.9770.1257344.051199.6
3.97-4.187.20.1087023.623199.6
4.18-4.4470.097163.887199.3
4.44-4.796.80.0767263.944198.8
4.79-5.277.10.0767283.415199.2
5.27-6.037.10.087333.398199.9
6.03-7.67.20.0687463.473199.9
7.6-1006.30.0538034.003198.9

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
PHASERphasing
RESOLVEphasing
PHENIX1.8.1_1168refinement
PDB_EXTRACT3.11data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.806→38.639 Å / Occupancy max: 1 / Occupancy min: 0.43 / FOM work R set: 0.6818 / SU ML: 0.43 / σ(F): 1.34 / Phase error: 36.33 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2952 1374 9.99 %
Rwork0.2458 --
obs0.2507 13752 94.44 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 147.47 Å2 / Biso mean: 74.7266 Å2 / Biso min: 32.87 Å2
Refinement stepCycle: LAST / Resolution: 2.806→38.639 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2754 0 12 8 2774
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0042801
X-RAY DIFFRACTIONf_angle_d0.8543827
X-RAY DIFFRACTIONf_chiral_restr0.041512
X-RAY DIFFRACTIONf_plane_restr0.005485
X-RAY DIFFRACTIONf_dihedral_angle_d17.677983
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 10

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.8064-2.90670.3942910.30782491564
2.9067-3.0230.43061260.31151122124887
3.023-3.16050.36851380.30651260139897
3.1605-3.32710.32021390.27821260139999
3.3271-3.53540.35341430.26021288143199
3.5354-3.80820.29711430.253112931436100
3.8082-4.1910.29871450.22561294143999
4.191-4.79650.25741450.19881314145999
4.7965-6.03930.29711480.244213241472100
6.0393-38.64230.25511560.248313991555100
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
14.0394-0.03131.16092.4644-1.44362.10020.2653-0.0776-0.4625-1.6211-0.07370.58130.60910.8965-0.15460.55560.01270.11470.5295-0.01330.264615.18231.4875-15.3097
2-0.4582-0.2488-0.662.0486.7964.51840.61412.67690.0638-1.87430.6469-0.2229-0.62190.0983-0.6541.1880.0325-0.04210.82940.31250.999712.82657.2546-18.4756
31.6579-0.39762.08192.4597-0.15692.4512-0.5481-0.1058-0.8136-0.39010.95660.002-0.5402-0.53890.08351.1310.07820.05421.07170.38241.032315.18574.0293-20.4369
41.25923.0887-2.06095.3507-4.40433.22420.17380.12571.1608-0.13140.80960.6823-0.28931.0396-0.53720.882-0.07220.15120.66740.01060.864321.907562.4711-17.0286
50.2320.0573-0.60715.16521.12242.0727-0.070.08740.3786-0.51580.11250.1220.08240.1247-0.0810.36780.0586-0.06870.38440.02050.451212.232242.9389-9.0132
63.5198-0.2657-2.16880.20580.28652.16130.3470.1439-0.933-0.460.10030.22021.2855-0.4277-0.3460.98970.0065-0.20990.45260.1340.6361-1.037332.5489-18.7048
72.85450.31860.95994.85891.20913.0919-0.089-0.19290.6463-0.5431-0.28870.2855-0.08570.01480.32210.4127-0.01040.040.43090.00650.444712.15152.2999-8.2036
86.29880.1471-0.77055.10520.26665.6773-0.29730.3261-0.4401-1.24920.01410.70250.569-0.54660.48040.7496-0.043-0.19940.4063-0.02040.73112.446420.3565-14.2139
93.5995-1.68040.40224.4309-0.26910.682-0.20310.24170.65440.0301-0.0464-0.95670.00870.17870.08720.46640.0344-0.0620.5678-0.02910.498224.38851.4007-11.9571
100.4951-0.7503-0.55661.22320.370.32150.23170.28551.05971.8881-0.0064-0.08640.72910.63590.0021.44350.3486-0.07630.90810.0070.937743.369-27.4112-8.6997
115.9296-3.0942-0.38864.5354-0.23.23821.00911.0620.2574-1.8919-0.9560.07480.3284-0.05780.07560.8628-0.0366-0.44130.3309-0.08480.396119.7112-1.038-17.5599
122.6291-1.3289-0.06415.3045-0.4563.44380.25110.614-0.1802-0.5432-0.0075-0.17510.14540.3942-0.14570.43570.056-0.11140.4754-0.11460.435324.5522-7.1318-16.8706
130.34230.3424-1.19320.1072-0.42514.356-1.37760.74680.04360.96260.77751.5398-1.6568-2.1878-0.35010.85670.44990.20860.82080.03630.73112.90335.06991.6672
142.1654-1.8781-0.04162.8489-0.59020.87030.10550.2591-0.4473-0.629-0.23620.33210.2793-0.0932-0.02050.78890.1132-0.10940.53110.00090.588217.7386-4.1973-13.774
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'B' and (resid 43 through 69 )B0
2X-RAY DIFFRACTION2chain 'B' and (resid 70 through 89 )B0
3X-RAY DIFFRACTION3chain 'B' and (resid 90 through 99 )B0
4X-RAY DIFFRACTION4chain 'B' and (resid 100 through 111 )B0
5X-RAY DIFFRACTION5chain 'B' and (resid 112 through 165 )B0
6X-RAY DIFFRACTION6chain 'B' and (resid 166 through 182 )B0
7X-RAY DIFFRACTION7chain 'B' and (resid 183 through 231 )B0
8X-RAY DIFFRACTION8chain 'B' and (resid 232 through 254 )B0
9X-RAY DIFFRACTION9chain 'A' and (resid 43 through 91 )A0
10X-RAY DIFFRACTION10chain 'A' and (resid 92 through 106 )A0
11X-RAY DIFFRACTION11chain 'A' and (resid 107 through 127 )A0
12X-RAY DIFFRACTION12chain 'A' and (resid 128 through 167 )A0
13X-RAY DIFFRACTION13chain 'A' and (resid 168 through 176 )A0
14X-RAY DIFFRACTION14chain 'A' and (resid 177 through 254 )A0

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