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- PDB-6vzd: N-terminal domain of mouse surfactant protein B (K46E/R51E mutant... -

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Basic information

Entry
Database: PDB / ID: 6vzd
TitleN-terminal domain of mouse surfactant protein B (K46E/R51E mutant) with bound lipid
ComponentsPulmonary surfactant-associated protein B
KeywordsSURFACTANT PROTEIN / Lipid-binding / Lipid transfer / Saposin-like
Function / homology
Function and homology information


Surfactant metabolism / sphingolipid metabolic process / respiratory gaseous exchange by respiratory system / : / lysosome / extracellular region / membrane / cytoplasm
Similarity search - Function
Saposin-like / NK-Lysin / 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-like / NK-Lysin / 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. / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Chem-RXY / Pulmonary surfactant-associated protein B
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.88 Å
AuthorsRapoport, T.A. / Bodnar, N.O.
Funding support United States, 1items
OrganizationGrant numberCountry
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 28, 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
Revision 1.4Oct 11, 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 1.5Oct 23, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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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
E: Pulmonary surfactant-associated protein B
B: Pulmonary surfactant-associated protein B
C: Pulmonary surfactant-associated protein B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,98210
Polymers39,6864
Non-polymers4,2966
Water5,729318
1
A: Pulmonary surfactant-associated protein B
E: Pulmonary surfactant-associated protein B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,9915
Polymers19,8432
Non-polymers2,1483
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4430 Å2
ΔGint-36 kcal/mol
Surface area9020 Å2
MethodPISA
2
B: Pulmonary surfactant-associated protein B
C: Pulmonary surfactant-associated protein B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,9915
Polymers19,8432
Non-polymers2,1483
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3410 Å2
ΔGint-35 kcal/mol
Surface area8730 Å2
MethodPISA
Unit cell
Length a, b, c (Å)49.793, 66.124, 59.620
Angle α, β, γ (deg.)90.000, 97.370, 90.000
Int Tables number4
Space group name H-MP1211
Space group name HallP2yb
Symmetry operation#1: x,y,z
#2: -x,y+1/2,-z

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Components

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


Mass: 9921.431 Da / Num. of mol.: 4 / Mutation: K46E, R51E
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-RXY / (7Z,19R,22R)-25-amino-22-hydroxy-16,22-dioxo-17,21,23-trioxa-22lambda~5~-phosphapentacos-7-en-19-yl (9Z)-octadec-9-enoate


Mass: 715.981 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C39H74NO8P
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 318 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
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: 2.45 Å3/Da / Density % sol: 49.85 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, hanging drop / pH: 5.4
Details: 100 mM citrate buffer pH 5.4, 23-25% PEG 4000, 14-15% 2-propanol

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-E / Wavelength: 0.979 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Dec 10, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 1.88→59.13 Å / Num. obs: 31237 / % possible obs: 92.19 % / Redundancy: 53.8 % / Biso Wilson estimate: 18.78 Å2 / CC1/2: 1 / Rmerge(I) obs: 0.1001 / Net I/σ(I): 40.86
Reflection shellResolution: 1.88→1.947 Å / Rmerge(I) obs: 1.511 / Mean I/σ(I) obs: 2.41 / Num. unique obs: 2186 / CC1/2: 0.897

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Processing

Software
NameVersionClassification
PHENIX1.17.1_3660refinement
Cootmodel building
XDSdata scaling
PHENIXphasing
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6VYN (lipid removed)

6vyn


Resolution: 1.88→59.13 Å / SU ML: 0.2362 / Cross valid method: FREE R-VALUE / σ(F): 0 / Phase error: 23.6668
RfactorNum. reflection% reflection
Rfree0.2175 1841 6.37 %
Rwork0.1697 --
obs0.1727 28915 91.84 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 35.02 Å2
Refinement stepCycle: LAST / Resolution: 1.88→59.13 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2571 0 294 318 3183
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00613042
X-RAY DIFFRACTIONf_angle_d0.73574043
X-RAY DIFFRACTIONf_chiral_restr0.0437434
X-RAY DIFFRACTIONf_plane_restr0.0054509
X-RAY DIFFRACTIONf_dihedral_angle_d30.74081294
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.88-1.930.39091030.32331514X-RAY DIFFRACTION66.68
1.93-1.980.24881110.25261694X-RAY DIFFRACTION75.65
1.98-2.050.27381320.22031864X-RAY DIFFRACTION83.06
2.05-2.120.21941420.18541997X-RAY DIFFRACTION88.06
2.12-2.210.2221380.16522064X-RAY DIFFRACTION91.83
2.21-2.310.23581420.15842150X-RAY DIFFRACTION95.74
2.31-2.430.23271450.162201X-RAY DIFFRACTION97.06
2.43-2.580.18291530.16082226X-RAY DIFFRACTION98.18
2.58-2.780.20591520.16062259X-RAY DIFFRACTION98.85
2.78-3.060.24691530.16212237X-RAY DIFFRACTION99.05
3.06-3.50.18441550.152264X-RAY DIFFRACTION99.75
3.5-4.410.17981570.13852284X-RAY DIFFRACTION100
4.41-59.130.23071580.18692320X-RAY DIFFRACTION99.64
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)
12.63775591188-0.159069466943-1.264679355175.19007850595-0.4567693765466.9887142201-0.2253328936620.4878109881270.134762819825-0.3641389324220.12950098888-0.08993272763270.0272557064272-0.0366305193634-0.01438495194140.122051320794-0.027094699281-0.01429017985250.1190200025340.02636708423560.0800507537352-22.699760579.50393040363-18.4373114391
25.905994874053.371340918354.769407426612.431472771342.961492958524.582374439110.220842456429-0.353516654333-0.1463990068570.249481783569-0.09429588322130.07055140972520.227420513433-0.450348471203-0.1869551052370.118301405112-0.06000488972050.04700291659260.1593900351640.002404922291970.158482768591-25.72365122274.120055131631.56124011326
35.00422738951-2.127172849023.676829854341.3420244167-1.847120970325.03019670037-0.134179348737-0.426316185990.08165747695840.1151690261260.153818457743-0.0763504705597-0.146886931464-0.408907076441-0.01903072221160.128153945319-0.02707655465820.009212568802730.101018156956-0.02454842307860.13714429047-23.111082682513.40376208342.5900631861
47.90479608119-2.007930413180.6641732133934.600641136571.258040221642.36321711313-0.07362260814470.2699978910.634552929594-0.306966244491-0.0201646548583-0.297651404433-0.6040066071090.1347655459320.02171513871690.293971433601-0.0541411892541-0.08582152440930.153500391790.06425122332810.228521259942-22.244649879219.7148068241-18.641892743
54.695948771790.270233400193-0.3272636980484.33862147588-0.5062683293014.36543443895-0.1777166589780.362631800812-0.324121504154-0.3112971961210.123335551046-0.1553581013020.3609859540720.09761187734630.003601781043020.180410735491-0.003880654079690.04588277444260.104865124665-0.02618838942090.0968922368441-19.37573018321.30058662161-14.9274238248
63.66190478358-1.44546873574-1.517048116014.584424215333.403672580035.88519503269-0.0009407807554350.3730956585430.388439949239-0.3238900103970.194311544756-0.645554275807-0.6607221524590.459132271323-0.2859089730740.165605509195-0.061121606860.01418245280050.2095721957130.06169152271970.291069958218-9.188645052519.596789652-11.5030107989
73.85557941571-0.947347088124-0.2257400570075.881201363730.1205967693683.44772647223-0.01575717660190.0132027786020.232583226574-0.172154963820.0232074606805-0.323007195626-0.1652638651060.114682375602-0.04853528574050.139528759593-0.001283961260351.28449610091E-50.07802607739630.01338942892440.16743687884-9.4060495653315.9424395872-2.59085449088
88.12578685564-1.71712910169-6.752199909413.423232705721.1378530426.072702142340.428100989083-0.5855465632710.4264209051430.05973671256670.18377177839-0.500264731409-0.05299622020180.532193534882-0.6040531589720.2041513240040.002202308478710.006592935702040.150235105536-0.05011463725230.186320212363-13.7152068785-3.08054576556-7.66149198993
94.721826694731.164700504962.314700482382.147764056344.074342347527.735644864990.02865337848120.233256196584-0.551270743862-0.2094643459090.158660212427-0.1881381760440.720606658701-0.159428251942-0.1689532533730.236338844865-0.05403566102180.01567627520310.1574440856940.01134041608050.250403154329-23.2808601013-6.58587750472-6.71067671767
105.20319649669-2.71808740155-2.637418248755.044529296050.7722185550218.38430102454-0.0192043070552-0.318392135679-0.2065909772020.170295992271-0.09119747389890.07534386080920.1366291941780.05217767833040.1498311357020.207792546808-0.0800480815608-0.05474553249880.200149606950.09076567452150.157649920822-31.47865823898.94963337874-26.2776464207
115.30075046149-1.272271615713.572961760084.55972429429-2.001728450445.63949422864-0.23765243350.8844967975390.209240816689-0.222701394514-0.0483800174545-0.437763365786-0.1933195198541.206282220260.2236494902890.194632814957-0.0167270856870.04286071580480.353618017990.06255902213350.253348196757-28.050977910711.3403112071-46.2249935891
124.320521954360.1222295174270.1169883125737.581887938945.246025144443.76924050636-0.2680136419460.382903230210.621351466166-0.499012008514-0.220006439542-0.21770333649-0.4063527972310.476365295920.3674442681070.2267077229950.0058924745117-0.02855051672280.1768567135160.04452237526320.249022718564-42.163099212815.2988397415-51.918275982
130.169205903850.093987878141-0.1579884650380.487128366165-0.4809901136730.795128270239-0.04036225863960.070864710050.0340511631456-0.134517751799-0.0193240611084-0.05462289367570.007316568744970.03296452740860.005688429614310.340007493576-0.206347257447-0.04937085368410.174579791330.3014911231230.198654013858-31.065121725720.3631368676-42.2184396145
146.380581482892.96899492766-0.1583959456786.920393968440.8210164277025.87647569956-0.0907117510351-0.08055469607860.02682414720750.233723937403-0.240568730780.100094432651-0.273224383888-0.4518952949770.2598585816180.187741825166-0.03149758573-0.06934926653930.1934717437190.04766758671090.144526709823-35.620684178917.2785414802-23.5814141468
154.70174768116-1.78572649441-2.690536598736.9151603212-0.4462417531755.35668388314-0.202957971311-0.57018525993-1.031994254670.0363958316023-0.198428423418-0.2192686603661.000076782360.2181633026240.3747739180150.458633698975-0.0466355933387-0.08043515171820.2443604313920.1273085807080.31586969338-33.46605985841.10789443983-31.5750486227
165.66977294579-2.141121092160.1443976630589.1287762099-5.828683693827.928393953530.12293143897-0.519520914729-0.2893148958440.4419271889120.02337266642690.905561429795-0.12381039489-0.938184679399-0.2057365492730.207557890029-0.08352021488310.005537508108830.520203816276-0.07029277837180.244884511562-48.757753094614.2203281266-30.7058738333
177.96736257741.717736223510.902477627882.89500333617-1.114770888497.336349510430.0927873894448-0.1517773283670.2274893833990.0113538057026-0.1540016978230.46261481332-0.20961144811-0.4390068733030.0563236643850.182272551981-0.00477349518114-0.0462584711180.249323550141-0.05969407128660.147922205514-47.637802677114.1545716742-40.5521485965
182.49817438981.75643779-2.906550255355.68885781476-6.62280394918.25084160149-0.6833805995360.675407021864-3.017695357930.5103294818110.4415583457080.4951020170012.43379764163-0.2546877028590.2125724180830.887078443711-0.0491181176624-0.1041943842650.511498599642-0.09777017507121.25735217029-41.9528563714-5.00296873857-37.266355111
196.017171727373.78650074325-2.294279885833.74289820685-3.695197330484.60423189560.0468147584907-0.478706993873-1.69591387214-0.181251099864-0.219146413708-0.8697636239221.644351962420.8458466588180.2109998253870.5243301271440.0679461320972-0.08270970967350.3186739708110.05750419039440.509438733101-29.9833560069-0.153545644095-42.1111962549
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 6 through 24 )
2X-RAY DIFFRACTION2chain 'A' and (resid 25 through 41 )
3X-RAY DIFFRACTION3chain 'A' and (resid 42 through 68 )
4X-RAY DIFFRACTION4chain 'A' and (resid 69 through 84 )
5X-RAY DIFFRACTION5chain 'E' and (resid 3 through 24 )
6X-RAY DIFFRACTION6chain 'E' and (resid 25 through 41 )
7X-RAY DIFFRACTION7chain 'E' and (resid 42 through 69 )
8X-RAY DIFFRACTION8chain 'E' and (resid 70 through 79 )
9X-RAY DIFFRACTION9chain 'E' and (resid 80 through 87 )
10X-RAY DIFFRACTION10chain 'B' and (resid 7 through 24 )
11X-RAY DIFFRACTION11chain 'B' and (resid 25 through 41 )
12X-RAY DIFFRACTION12chain 'B' and (resid 42 through 51 )
13X-RAY DIFFRACTION13chain 'B' and (resid 52 through 67 )
14X-RAY DIFFRACTION14chain 'B' and (resid 68 through 84 )
15X-RAY DIFFRACTION15chain 'C' and (resid 7 through 24 )
16X-RAY DIFFRACTION16chain 'C' and (resid 25 through 41 )
17X-RAY DIFFRACTION17chain 'C' and (resid 42 through 67 )
18X-RAY DIFFRACTION18chain 'C' and (resid 68 through 72 )
19X-RAY DIFFRACTION19chain 'C' and (resid 73 through 84 )

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