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- PDB-6vz0: C-terminal domain of mouse surfactant protein B crystallized at h... -

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Basic information

Entry
Database: PDB / ID: 6vz0
TitleC-terminal domain of mouse surfactant protein B crystallized at high pH
ComponentsPulmonary surfactant-associated protein B
KeywordsSURFACTANT PROTEIN / Lipid-binding / Lipid transfer / Saposin-like
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 / AB INITIO PHASING / Resolution: 1.75 Å
AuthorsRapoport, T.A. / Bodnar, N.O.
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS) United States
Howard Hughes Medical Institute (HHMI) 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
DepositionFeb 27, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 25, 2020Provider: repository / Type: Initial release
Revision 1.1Dec 2, 2020Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.title / _citation.year
Revision 1.2Dec 9, 2020Group: Database references / Category: citation / Item: _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.3Jan 20, 2021Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.year

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)17,5713
Polymers17,5062
Non-polymers651
Water1,802100
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2870 Å2
ΔGint-52 kcal/mol
Surface area8970 Å2
MethodPISA
Unit cell
Length a, b, c (Å)38.396, 58.360, 64.673
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: 8752.949 Da / Num. of mol.: 2 / Fragment: C-terminal residues 292-367
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Sftpb, Sftp3 / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta-gami 2 / References: UniProt: P50405
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 100 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 2.11 Å3/Da / Density % sol: 41.7 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 100 mM Tris pH 8.5, 200 mM lithium sulfate, 1260 mM ammonium sulfate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.979 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Aug 15, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 1.75→43.33 Å / Num. obs: 14990 / % possible obs: 98.91 % / Redundancy: 6.4 % / Biso Wilson estimate: 30.31 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.09072 / Rpim(I) all: 0.03881 / Rrim(I) all: 0.09891 / Net I/σ(I): 16.52
Reflection shellResolution: 1.75→1.817 Å / Num. unique obs: 1392 / CC1/2: 0.495 / % possible all: 95.21

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Processing

Software
NameVersionClassification
PHENIX1.17.1_3660refinement
Cootmodel building
XDSdata scaling
Arcimboldophasing
XDSdata reduction
RefinementMethod to determine structure: AB INITIO PHASING / Resolution: 1.75→43.33 Å / SU ML: 0.2551 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 26.8755
RfactorNum. reflection% reflection
Rfree0.2122 703 4.71 %
Rwork0.1773 --
obs0.179 14923 98.91 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 43.84 Å2
Refinement stepCycle: LAST / Resolution: 1.75→43.33 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1191 0 1 100 1292
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0131225
X-RAY DIFFRACTIONf_angle_d1.04171662
X-RAY DIFFRACTIONf_chiral_restr0.0664179
X-RAY DIFFRACTIONf_plane_restr0.0084221
X-RAY DIFFRACTIONf_dihedral_angle_d20.7482452
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.75-1.890.33341430.29632717X-RAY DIFFRACTION97.41
1.89-2.080.25851240.20692831X-RAY DIFFRACTION99.39
2.08-2.380.24111270.16772838X-RAY DIFFRACTION99.46
2.38-30.21711620.17052860X-RAY DIFFRACTION99.77
3-43.330.1861470.16682974X-RAY DIFFRACTION98.52
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)
1-0.00715398410996-0.0173418487468-0.01356163040910.002820350488550.02608488953720.0187630093789-0.117002063465-0.40701161994-0.204853434289-0.09056237657340.01163500576880.345678284422-0.2337963971470.193650418821.02798946626E-60.212542946336-0.01597066674820.01119808068730.201300156165-0.05122286286160.1209806586395.7135511231154.468941814241.1048055126
20.0416601904199-0.01569519676230.01219261318970.0327306802072-0.05712636990980.0285627076915-0.055066849858-0.266440288224-0.192502079705-0.05332584654930.304893257130.0839791686891-0.1416880831510.1468627186295.66177386339E-70.231774733567-0.01205330188430.009992380784430.2375337832690.02706993294880.229013969788-0.2319151881330.070417282438.2759698755
3-0.04457698585540.015085451230.0330668799375-0.00905063295543-0.02095676742820.0124354569989-0.259008748213-0.300954721973-0.8264297191880.121328979982-0.6079674205880.492155772215-0.135117258371-0.1573373035871.18094623599E-60.281094329828-0.127060006856-0.0256623859716-0.7221576675061.40336849609-0.5831128004861.2402894298420.00010031244.7029484282
4-0.01210381635430.03045196390540.007506262727070.005189159997150.01089717179980.06933058233070.200357211947-0.243039340086-0.2620583857370.2406220912050.0802249322757-0.118136763744-0.1687273214450.06087259321611.46206910318E-60.281693545097-0.0265972803829-0.06483921210910.2610610846260.1083782415440.25682230843410.288103590532.115603175742.0296777532
50.0234047492267-0.01274938149480.007000558000310.02027511081610.01695697944740.01069278479870.0904946320744-0.0776994026181-0.215622876782-0.02760513476850.0165233695494-0.132437825857-0.09475195239730.05384279496782.9436672434E-70.190632591881-0.007276018302110.01466177112710.2345945046140.007526133974440.17098511959514.564556777753.39409476140.2869159893
60.05456564081510.004703492192290.02046434182240.02751832074470.03780446250350.0517749658393-0.04109080972950.08336377851290.133539400227-0.03726805507660.1718917975710.05817984572940.1302093766180.0340533910156-1.35754165676E-60.2132352132140.005757065310870.0007678975072930.2221601175170.02556520443570.15810309288610.127737540655.31127333726.1597135496
70.0456228681017-0.017467218601-0.01538135093580.01757194853460.0163923161730.02385791826720.0409353133427-0.0120863060619-0.426715151948-0.1845400836450.07810269150520.0275933549639-0.24228879072-0.0446650091263-3.18852313338E-70.1324454668250.00462475801139-0.02987313951740.1942574381930.06592703834150.3432198907812.256098144429.092361039335.1817850659
80.01092895059530.01819854006240.02305730225720.0214287554190.004796450038820.0615809245291-0.1442780698620.0543259357459-0.369759738409-0.1590882804980.262859007546-0.202675262985-0.138447066468-0.00364201667666-1.14713075614E-80.1930021268820.03036739147860.0003330413777330.168368935411-0.03686112155490.3871527434346.6176604517922.19567141730.9826864828
90.007093190610050.01224160583340.01845638400450.01244552350970.01058550217470.0168947606458-0.07457432354660.1373145082290.00182067151653-0.1665704568680.0605194549692-0.04505565587360.1083430977440.05648685544651.63019675596E-60.218383076089-0.00428482147265-0.01788107926720.216404684683-0.008575311862250.1816278320082.2161213122549.023622405327.7859103552
10-0.00360907899731-0.006059458779110.00318706161622-0.000519263323353-0.001958266205660.002043519752890.04761878972690.2449979343940.1538437268980.3706967016830.2182153938790.101171080181-0.14211201852-0.1204283455956.31707976532E-60.2402346335450.01922583633650.0267942529720.297074032590.1041610636480.3924105179272.1277078782658.677398770926.02803343
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 2 through 16 )
2X-RAY DIFFRACTION2chain 'A' and (resid 17 through 34 )
3X-RAY DIFFRACTION3chain 'A' and (resid 35 through 47 )
4X-RAY DIFFRACTION4chain 'A' and (resid 48 through 58 )
5X-RAY DIFFRACTION5chain 'A' and (resid 59 through 75 )
6X-RAY DIFFRACTION6chain 'B' and (resid 1 through 13 )
7X-RAY DIFFRACTION7chain 'B' and (resid 14 through 35 )
8X-RAY DIFFRACTION8chain 'B' and (resid 36 through 55 )
9X-RAY DIFFRACTION9chain 'B' and (resid 56 through 68 )
10X-RAY DIFFRACTION10chain 'B' and (resid 69 through 76 )

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