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- PDB-4keg: Crystal Structure of MBP Fused Human SPLUNC1 -

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Basic information

Entry
Database: PDB / ID: 4keg
TitleCrystal Structure of MBP Fused Human SPLUNC1
ComponentsMaltose-binding periplasmic/Palate lung and nasal epithelium clone fusion protein
KeywordsLIPID BINDING PROTEIN / BPI fold / lipid binding / Secreted
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 / detection of maltose stimulus / maltose transport complex / carbohydrate transport / carbohydrate transmembrane transporter activity ...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 / detection of maltose stimulus / maltose transport complex / carbohydrate transport / carbohydrate transmembrane transporter activity / maltose binding / maltose transport / maltodextrin transmembrane transport / ATP-binding cassette (ABC) transporter complex, substrate-binding subunit-containing / ATP-binding cassette (ABC) transporter complex / cell chemotaxis / antimicrobial humoral immune response mediated by antimicrobial peptide / antibacterial humoral response / outer membrane-bounded periplasmic space / defense response to virus / periplasmic space / innate immune response / lipid binding / DNA damage response / extracellular space / extracellular region / membrane
Similarity search - Function
Lipid-binding serum glycoprotein, N-terminal / Bactericidal permeability-increasing protein, alpha/beta domain superfamily / LBP / BPI / CETP family, N-terminal domain / Maltose/Cyclodextrin ABC transporter, substrate-binding protein / Solute-binding family 1, conserved site / Bacterial extracellular solute-binding proteins, family 1 signature. / Bacterial extracellular solute-binding protein / Bacterial extracellular solute-binding protein
Similarity search - Domain/homology
Maltose/maltodextrin-binding periplasmic protein / BPI fold-containing family A member 1
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.5 Å
AuthorsNing, F. / Wang, C. / Niu, L. / Chu, H.W. / Zhang, G.
CitationJournal: To be Published
Title: The Lipid Ligands of the SPLUNC1 Protein
Authors: Ning, F. / Wang, C. / Berry, K.Z. / Kandasamy, P. / Liu, H. / Murphy, R.C. / Voelker, D. / Nho, C.W. / Pan, C.H. / Dai, S. / Niu, L. / Chu, H.W. / Zhang, G.
History
DepositionApr 25, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 30, 2014Provider: repository / Type: Initial release
Revision 1.1Aug 2, 2017Group: Advisory / Data collection ...Advisory / Data collection / Refinement description / Source and taxonomy
Category: diffrn_detector / entity_src_gen ...diffrn_detector / entity_src_gen / pdbx_unobs_or_zero_occ_atoms / software
Item: _diffrn_detector.detector
Revision 1.2Jul 29, 2020Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / struct_ref_seq_dif / struct_site / struct_site_gen
Item: _chem_comp.mon_nstd_flag / _chem_comp.name ..._chem_comp.mon_nstd_flag / _chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_entity_nonpoly.name / _struct_ref_seq_dif.details
Description: Carbohydrate remediation / Provider: repository / Type: Remediation

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Maltose-binding periplasmic/Palate lung and nasal epithelium clone fusion protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)63,0683
Polymers62,7511
Non-polymers3172
Water2,378132
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: Maltose-binding periplasmic/Palate lung and nasal epithelium clone fusion protein
hetero molecules

A: Maltose-binding periplasmic/Palate lung and nasal epithelium clone fusion protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)126,1356
Polymers125,5022
Non-polymers6334
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_554x-y,-y,-z-2/31
Buried area4730 Å2
ΔGint-36 kcal/mol
Surface area43750 Å2
MethodPISA
Unit cell
Length a, b, c (Å)118.768, 118.768, 98.223
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221
Components on special symmetry positions
IDModelComponents
11A-1459-

HOH

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Components

#1: Protein Maltose-binding periplasmic/Palate lung and nasal epithelium clone fusion protein


Mass: 62750.879 Da / Num. of mol.: 1
Fragment: UNP P0AEX9 residues 27-387, UNP Q9NP55 residues 43-256
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli), (gene. exp.) Homo sapiens (human)
Gene: PLUNC / Plasmid: pMAL-c2X / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta2(DE3) / References: UniProt: P0AEX9, UniProt: Q9NP55
#2: Sugar ChemComp-BOG / octyl beta-D-glucopyranoside


Type: D-saccharide / Mass: 292.369 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Formula: C14H28O6 / Comment: detergent*YM
IdentifierTypeProgram
b-octylglucosideIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 132 / Source method: isolated from a natural source / Formula: H2O

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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: 3.19 Å3/Da / Density % sol: 61.4 %
Crystal growTemperature: 292 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 25% PEG 550 MME, 0.05M HEPES, 0.02M magnesium chloride, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 292K

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Data collection

DiffractionMean temperature: 200 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.2.2 / Wavelength: 0.979 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Dec 23, 2010
RadiationMonochromator: Double Crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2.5→45.461 Å / Num. obs: 28083

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Processing

Software
NameVersionClassification
HKL-2000data collection
SOLVEphasing
PHENIX(phenix.refine: 1.7.1_743)refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: SAD / Resolution: 2.5→45.461 Å / SU ML: 0.64 / σ(F): 1.34 / Phase error: 25.85 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2586 1408 5.02 %
Rwork0.2052 --
obs0.2077 28047 99.84 %
all-28083 -
Solvent computationShrinkage radii: 0.72 Å / VDW probe radii: 1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 49.925 Å2 / ksol: 0.332 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-2.619 Å20 Å2-0 Å2
2--2.619 Å20 Å2
3----5.2381 Å2
Refinement stepCycle: LAST / Resolution: 2.5→45.461 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4005 0 21 132 4158
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0084107
X-RAY DIFFRACTIONf_angle_d1.1165598
X-RAY DIFFRACTIONf_dihedral_angle_d15.5241458
X-RAY DIFFRACTIONf_chiral_restr0.079663
X-RAY DIFFRACTIONf_plane_restr0.006716
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.4996-2.5890.32231470.25912627X-RAY DIFFRACTION100
2.589-2.69260.29851380.23252617X-RAY DIFFRACTION100
2.6926-2.81510.33551610.2562601X-RAY DIFFRACTION100
2.8151-2.96350.31161510.24692648X-RAY DIFFRACTION100
2.9635-3.14920.29021300.23542634X-RAY DIFFRACTION100
3.1492-3.39220.27581290.22782678X-RAY DIFFRACTION100
3.3922-3.73350.25911400.19162640X-RAY DIFFRACTION100
3.7335-4.27340.19881390.17972682X-RAY DIFFRACTION100
4.2734-5.38260.19791290.16162706X-RAY DIFFRACTION100
5.3826-45.56830.27771440.21262806X-RAY DIFFRACTION100

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