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- PDB-7mbk: N-terminal domain of mouse surfactant protein B, 6W mutant -

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Basic information

Entry
Database: PDB / ID: 7mbk
TitleN-terminal domain of mouse surfactant protein B, 6W mutant
ComponentsPulmonary surfactant-associated protein B
KeywordsSURFACTANT PROTEIN
Function / homology
Function and homology information


Surfactant metabolism / alveolar lamellar body / sphingolipid metabolic process / respiratory gaseous exchange by respiratory system / multivesicular body / collagen-containing extracellular matrix / lysosome / extracellular space / cytoplasm
Similarity search - Function
Saposin A-type domain / Saposin / Saposin A-type domain / Saposin A-type domain profile. / Saposin/surfactant protein-B A-type DOMAIN / Saposin-like type B, region 1 / Saposin-like type B, region 1 / Saposin B type, region 2 / Saposin-like type B, region 2 / Saposin (B) Domains ...Saposin A-type domain / Saposin / Saposin A-type domain / Saposin A-type domain profile. / Saposin/surfactant protein-B A-type DOMAIN / Saposin-like type B, region 1 / Saposin-like type B, region 1 / Saposin B type, region 2 / Saposin-like type B, region 2 / Saposin (B) Domains / Saposin B type domain / Saposin-like / Saposin B type domain profile.
Similarity search - Domain/homology
Pulmonary surfactant-associated protein B
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.17 Å
AuthorsMilicic, G. / Rapoport, T.A.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS) United States
CitationJournal: Mol.Cell / Year: 2021
Title: Mechanism of Lamellar Body Formation by Lung Surfactant Protein B.
Authors: Sever, N. / Milicic, G. / Bodnar, N.O. / Wu, X. / Rapoport, T.A.
History
DepositionMar 31, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 14, 2021Provider: repository / Type: Initial release
Revision 1.1Oct 18, 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
B: Pulmonary surfactant-associated protein B
A: Pulmonary surfactant-associated protein B


Theoretical massNumber of molelcules
Total (without water)20,8602
Polymers20,8602
Non-polymers00
Water21612
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3460 Å2
ΔGint-42 kcal/mol
Surface area9220 Å2
MethodPISA
Unit cell
Length a, b, c (Å)38.482, 60.251, 76.995
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x,y+1/2,-z+1/2
#4: -x+1/2,-y,z+1/2

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Components

#1: Protein Pulmonary surfactant-associated protein B / SP-B / Pulmonary surfactant-associated proteolipid SPL(Phe)


Mass: 10429.968 Da / Num. of mol.: 2 / Fragment: N-terminal domain, UNP residues 61-146 / Mutation: L35W, L44W, V48W, V62W, I75W, V79W
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Sftpb, Sftp3 / Production host: Escherichia coli (E. coli) / References: UniProt: P50405
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 12 / 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: 2.16 Å3/Da / Density % sol: 42.99 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, hanging drop / pH: 5.5
Details: 0.1 M ammonium sulfate, 0.05 M magnesium sulfate, 0.1 M sodium citrate, 16.5 % PEG smear medium

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 1.2827 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Jun 13, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.2827 Å / Relative weight: 1
ReflectionResolution: 2.17→47.45 Å / Num. obs: 9974 / % possible obs: 96.6 % / Redundancy: 20 % / Biso Wilson estimate: 50.16 Å2 / Rrim(I) all: 0.147 / Net I/σ(I): 23.1
Reflection shellResolution: 2.17→2.29 Å / Num. unique obs: 375 / Rrim(I) all: 0.148

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Processing

Software
NameVersionClassification
Coot1.19.1_4122model building
PHENIX1.19.1_4122refinement
SDMSdata collection
XDSdata reduction
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6vyn

6vyn


Resolution: 2.17→47.45 Å / SU ML: 0.2981 / Cross valid method: FREE R-VALUE / σ(F): 0 / Phase error: 28.3877
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2389 956 9.95 %
Rwork0.2196 8648 -
obs0.2215 9604 96.6 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 60.79 Å2
Refinement stepCycle: LAST / Resolution: 2.17→47.45 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1361 0 0 12 1373
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0151406
X-RAY DIFFRACTIONf_angle_d1.86871915
X-RAY DIFFRACTIONf_chiral_restr0.0959196
X-RAY DIFFRACTIONf_plane_restr0.0126240
X-RAY DIFFRACTIONf_dihedral_angle_d15.5152511
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.17-2.280.3241200.28641101X-RAY DIFFRACTION88.48
2.28-2.430.26491310.26761178X-RAY DIFFRACTION93.84
2.43-2.610.2851340.27311217X-RAY DIFFRACTION96.98
2.62-2.880.28441350.24821240X-RAY DIFFRACTION97.66
2.88-3.290.28291390.23661259X-RAY DIFFRACTION99.36
3.3-4.150.21131430.19261285X-RAY DIFFRACTION99.86
4.15-47.450.21931540.20691368X-RAY DIFFRACTION99.67

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