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- PDB-11if: Crystal Structure of an exported phospholipid binding protein fro... -

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Basic information

Entry
Database: PDB / ID: 11if
TitleCrystal Structure of an exported phospholipid binding protein from Bordetella pertussis in complex with Di-palmitoyl-3-sn-phosphatidylethanolamine (DPPE), P43 form 2
ComponentsExported protein
KeywordsTRANSPORT PROTEIN / SSGCID / STRUCTURAL GENOMICS / SEATTLE STRUCTURAL GENOMICS CENTER FOR INFECTIOUS DISEASE / phospholipid binding / Bordetella pertussis
Function / homologyToluene tolerance Ttg2/phospholipid-binding protein MlaC / MlaC protein / DI-PALMITOYL-3-SN-PHOSPHATIDYLETHANOLAMINE / Exported protein
Function and homology information
Biological speciesBordetella pertussis Tohama I (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.51 Å
AuthorsSeattle Structural Genomics Center for Infectious Disease (SSGCID)
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)75N93022C00036 United States
National Institutes of Health/Office of the DirectorS10OD030394 United States
CitationJournal: To be published
Title: Crystal Structure of an exported phospholipid binding protein from Bordetella pertussis in complex with Di-palmitoyl-3-sn-phosphatidylethanolamine (DPPE), P43 form 2
Authors: Lovell, S. / Liu, L. / Seibold, S. / Battaile, K.P.
History
DepositionFeb 25, 2026Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 11, 2026Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Exported protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,0913
Polymers21,3591
Non-polymers7322
Water1,928107
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration, monomeric
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)51.144, 51.144, 71.918
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number78
Space group name H-MP43

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Components

#1: Protein Exported protein


Mass: 21358.996 Da / Num. of mol.: 1 / Fragment: A27-Q207
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bordetella pertussis Tohama I (bacteria)
Gene: BP3761 / Plasmid: BopeA.18500.a.B2 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q7VSZ6
#2: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#3: Chemical ChemComp-PEF / DI-PALMITOYL-3-SN-PHOSPHATIDYLETHANOLAMINE / 3-[AMINOETHYLPHOSPHORYL]-[1,2-DI-PALMITOYL]-SN-GLYCEROL


Mass: 691.959 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C37H74NO8P / Feature type: SUBJECT OF INVESTIGATION / Comment: phospholipid*YM
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 107 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationN

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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: 2.2 Å3/Da / Density % sol: 44.14 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: Morpheus A4: 12.5%(v/v) MPD, 12.5%(v/v) PEG 1000, 12.5%(w/v) PEG 3350, 100 mM Imidazole/MES, pH 6.5, 30 mM MgCl2 and 30 mM CaCl2. BopeA.18500.a.B2.PW39485 at 22.8 mg/mL. Large mass of ...Details: Morpheus A4: 12.5%(v/v) MPD, 12.5%(v/v) PEG 1000, 12.5%(w/v) PEG 3350, 100 mM Imidazole/MES, pH 6.5, 30 mM MgCl2 and 30 mM CaCl2. BopeA.18500.a.B2.PW39485 at 22.8 mg/mL. Large mass of electron density observed in the core was modeled as a DPPE phospholipid that was acquired from the E. coli expression host. plate 20557 A1 drop 1, Puck: PSL-1503, Cryo: direct

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: NSLS-II / Beamline: 19-ID / Wavelength: 0.9786 Å
DetectorType: DECTRIS EIGER2 XE 9M / Detector: PIXEL / Date: Jan 31, 2026
RadiationMonochromator: Double Crystal Si 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9786 Å / Relative weight: 1
ReflectionResolution: 1.51→41.68 Å / Num. obs: 28912 / % possible obs: 99.4 % / Redundancy: 12.4 % / CC1/2: 1 / Rmerge(I) obs: 0.042 / Rpim(I) all: 0.012 / Rrim(I) all: 0.044 / Χ2: 1.02 / Net I/σ(I): 25.7 / Num. measured all: 359048
Reflection shellResolution: 1.51→1.54 Å / % possible obs: 90.8 % / Redundancy: 6 % / Rmerge(I) obs: 1.12 / Num. measured all: 7928 / Num. unique obs: 1313 / CC1/2: 0.566 / Rpim(I) all: 0.489 / Rrim(I) all: 1.229 / Χ2: 1.06 / Net I/σ(I) obs: 1.5

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Processing

Software
NameVersionClassification
PHENIX2.0_5936refinement
Aimlessdata scaling
XDSdata reduction
PHASERphasing
PDB_EXTRACTdata extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.51→41.68 Å / SU ML: 0.16 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 27.41 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2097 1438 4.98 %
Rwork0.1798 --
obs0.1812 28870 99.35 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.51→41.68 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1400 0 45 107 1552
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0071525
X-RAY DIFFRACTIONf_angle_d0.832079
X-RAY DIFFRACTIONf_dihedral_angle_d19.301603
X-RAY DIFFRACTIONf_chiral_restr0.052231
X-RAY DIFFRACTIONf_plane_restr0.008273
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.51-1.560.27931260.27432578X-RAY DIFFRACTION94
1.56-1.630.29741580.26092732X-RAY DIFFRACTION100
1.63-1.70.29981290.25072784X-RAY DIFFRACTION100
1.7-1.790.23281390.20282736X-RAY DIFFRACTION100
1.79-1.90.21671470.20772777X-RAY DIFFRACTION100
1.9-2.050.22481500.18192746X-RAY DIFFRACTION100
2.05-2.260.21981620.19682723X-RAY DIFFRACTION100
2.26-2.580.20641710.18112736X-RAY DIFFRACTION100
2.58-3.250.19341170.18452793X-RAY DIFFRACTION100
3.25-41.680.1961390.15452827X-RAY DIFFRACTION100
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)
12.99180.3249-0.76992.1612-0.82523.0438-0.10650.33130.1289-0.1160.13310.30390.1589-0.4310.00010.2332-0.03-0.00490.2420.03680.24377.9648-13.8143-11.5324
27.04811.2329-2.24455.9987-0.93719.7856-0.06891.4419-0.416-0.75220.4821.1611-0.3011-0.9179-0.41650.3558-0.0740.11520.4348-0.03940.5955-9.0659-22.4989-3.8925
36.44850.2582-1.77781.10370.84432.1715-0.3660.5423-0.57160.0409-0.0060.42120.2007-0.38730.27860.2333-0.0540.02390.2833-0.02450.33733.7208-26.2778-7.176
42.62791.2183-0.05543.2180.54620.7213-0.11990.006-0.51920.48640.3098-0.41940.8061.0438-0.12360.37980.1795-0.0110.348-0.01590.270820.9076-33.38161.6447
54.4744-2.36230.03513.46-0.74522.6482-0.05930.0505-0.2696-0.17640.0690.26840.3734-0.0343-0.01050.2786-0.03030.04810.2041-0.00740.2587.2396-30.59791.3567
68.59812.3349-1.96553.3583-0.35531.37280.56950.64840.81050.2722-0.198-0.0168-0.2256-0.1759-0.33640.28920.02360.09760.29770.02770.34740.8299-8.2001-3.647
73.5082-4.1154-1.77244.84411.74693.3128-0.2804-0.37731.9707-0.94230.5478-0.8149-0.56371.2005-0.40990.4321-0.0532-0.00990.3028-0.10320.857323.5167-9.2496-6.4153
85.5582-1.2443-2.20151.05260.62462.25640.11540.00630.46950.1778-0.06640.0102-0.2513-0.1647-0.00750.28560.00930.03860.247-0.03120.30437.7936-8.3251.6298
92.53760.30630.48893.4622-1.77782.71960.0096-0.14180.2112-0.0064-0.0497-0.0361-0.19660.0731-0.00520.1732-0.0144-0.02490.1733-0.00340.184916.1679-17.3173-2.3036
102.87640.924-1.09794.9449-0.11061.0594-0.1315-0.7864-0.55310.8223-0.0446-0.34811.10430.41320.15320.66020.03730.03750.32120.11510.283614.1977-34.088610.4042
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 27 through 51 )
2X-RAY DIFFRACTION2chain 'A' and (resid 52 through 59 )
3X-RAY DIFFRACTION3chain 'A' and (resid 60 through 76 )
4X-RAY DIFFRACTION4chain 'A' and (resid 77 through 93 )
5X-RAY DIFFRACTION5chain 'A' and (resid 94 through 118 )
6X-RAY DIFFRACTION6chain 'A' and (resid 119 through 127 )
7X-RAY DIFFRACTION7chain 'A' and (resid 128 through 137 )
8X-RAY DIFFRACTION8chain 'A' and (resid 138 through 152 )
9X-RAY DIFFRACTION9chain 'A' and (resid 153 through 177 )
10X-RAY DIFFRACTION10chain 'A' and (resid 178 through 205 )

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