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

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Basic information

Entry
Database: PDB / ID: 11hy
TitleCrystal Structure of an exported phospholipid binding protein from Bordetella pertussis in complex with Di-palmitoyl-3-sn-phosphatidylethanolamine (DPPE), P43 Form 1
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: 1.8 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 1
Authors: Seibold, S. / Lovell, 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)22,1794
Polymers21,3591
Non-polymers8203
Water90150
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)50.794, 50.794, 74.422
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-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#4: 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
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 50 / 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: 2.25 Å3/Da / Density % sol: 45.27 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: Berkeley C9: 25% PEG 3350, 100 mM Bis-Tris pH 6.5, 100 mM sodium acetate. BopeA.18500.a.B2.PW39485 at 22.8 mg/mL. Large mass of electron density observed in the core was modeled as a DPPE ...Details: Berkeley C9: 25% PEG 3350, 100 mM Bis-Tris pH 6.5, 100 mM sodium acetate. 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 20555 C9 drop 1, Puck: PSL-1511, Cryo: 80% crystallant + 20% glycerol

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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: 1.8→41.95 Å / Num. obs: 17541 / % possible obs: 99.9 % / Redundancy: 13.9 % / CC1/2: 1 / Rmerge(I) obs: 0.045 / Rpim(I) all: 0.013 / Rrim(I) all: 0.047 / Χ2: 0.99 / Net I/σ(I): 25.6 / Num. measured all: 243697
Reflection shellResolution: 1.8→1.84 Å / % possible obs: 99.5 % / Redundancy: 14.5 % / Rmerge(I) obs: 1.777 / Num. measured all: 14861 / Num. unique obs: 1028 / CC1/2: 0.713 / Rpim(I) all: 0.479 / Rrim(I) all: 1.841 / Χ2: 0.98 / 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: 1.8→41.95 Å / SU ML: 0.22 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 37.32 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2504 844 4.82 %
Rwork0.2088 --
obs0.2108 17517 99.86 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.8→41.95 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1407 0 51 50 1508
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0041490
X-RAY DIFFRACTIONf_angle_d0.5562017
X-RAY DIFFRACTIONf_dihedral_angle_d18.072575
X-RAY DIFFRACTIONf_chiral_restr0.043223
X-RAY DIFFRACTIONf_plane_restr0.005263
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.8-1.910.3561540.3162738X-RAY DIFFRACTION100
1.91-2.060.29481310.21852785X-RAY DIFFRACTION100
2.06-2.270.31911240.28622766X-RAY DIFFRACTION100
2.27-2.60.31171620.2582761X-RAY DIFFRACTION100
2.6-3.270.24541310.2322798X-RAY DIFFRACTION100
3.27-41.950.22021420.17192825X-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)
13.59741.2111-2.69734.0891-0.32453.65-0.1311-0.4823-0.1129-0.0817-0.0724-0.55080.04110.5740.13160.22280.0583-0.01130.31950.02050.2745-3.7972-18.95997.2827
24.0513-0.0988-0.16792.5614-0.22037.4305-0.00260.3744-0.2046-0.56640.18980.46990.2744-0.6849-0.13990.355-0.0747-0.00130.3789-0.0380.3693-21.641-33.07-2.6801
33.43711.8758-0.00643.14950.34873.1329-0.1415-0.00110.1687-0.14740.2101-0.03390.02590.1067-0.06660.29780.02630.01690.28070.01290.3402-9.0527-21.5638-0.6208
45.34132.6343-0.4455.114-0.23883.4882-0.01560.10070.2458-0.0404-0.06340.0217-0.1246-0.07630.05460.25780.0308-0.02410.2167-0.0090.2671-13.8944-14.0368-0.7638
53.9311-1.4051-1.52233.74820.68264.55650.14280.7842-0.5212-1.2123-0.11190.27720.90340.0852-0.05770.70020.02040.00960.4747-0.05980.335-13.6637-34.119-11.0665
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 26 through 76 )
2X-RAY DIFFRACTION2chain 'A' and (resid 77 through 93 )
3X-RAY DIFFRACTION3chain 'A' and (resid 94 through 137 )
4X-RAY DIFFRACTION4chain 'A' and (resid 138 through 177 )
5X-RAY DIFFRACTION5chain 'A' and (resid 178 through 207 )

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