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- PDB-9c89: Crystal structure of outer membrane lipoprotein carrier protein (... -

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Basic information

Entry
Database: PDB / ID: 9c89
TitleCrystal structure of outer membrane lipoprotein carrier protein (LolA) from Ehrlichia chaffeensis
ComponentsOuter membrane lipoprotein carrier protein LolA
KeywordsLIPID TRANSPORT / SSGCID / STRUCTURAL GENOMICS / SEATTLE STRUCTURAL GENOMICS CENTER FOR INFECTIOUS DISEASE / LolA
Function / homologyOuter membrane lipoprotein carrier protein LolA / Outer membrane lipoprotein carrier protein LolA-like / Lipoprotein localisation LolA/LolB/LppX / lipoprotein localization to outer membrane / outer membrane-bounded periplasmic space / membrane / Outer membrane lipoprotein carrier protein LolA
Function and homology information
Biological speciesEhrlichia chaffeensis str. Arkansas (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3 Å
AuthorsSeattle Structural Genomics Center for Infectious Disease / Seattle 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 outer membrane lipoprotein carrier protein (LolA) from Ehrlichia chaffeensis
Authors: Lovell, S. / Cooper, A. / Buchko, G.W. / Battaile, K.P.
History
DepositionJun 12, 2024Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 19, 2024Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Outer membrane lipoprotein carrier protein LolA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,5875
Polymers22,1691
Non-polymers4184
Water1086
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)100.956, 100.956, 63.669
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number172
Space group name H-MP64

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Components

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Protein , 1 types, 1 molecules A

#1: Protein Outer membrane lipoprotein carrier protein LolA


Mass: 22168.889 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Ehrlichia chaffeensis str. Arkansas (bacteria)
Gene: ECH_1053 / Plasmid: EhchA.17554.a.VL2 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q2GFE5

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Non-polymers , 5 types, 10 molecules

#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-CL / CHLORIDE ION


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


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#5: Chemical ChemComp-PG4 / TETRAETHYLENE GLYCOL


Mass: 194.226 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H18O5 / Comment: precipitant*YM
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 6 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 4.23 Å3/Da / Density % sol: 70.89 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 7
Details: Index HT C11 + 10% Hampton Additive E5: 1 M ammonium sulfate, 100 mM Hepes pH 7.0, 0.5% (w/v) PEG 8000, 1% (w/v) PEG 3350, EhchA.17554.a.VL2.PK00002 at 3.7 mg/mL. plate 13803 well E5 drop 1. ...Details: Index HT C11 + 10% Hampton Additive E5: 1 M ammonium sulfate, 100 mM Hepes pH 7.0, 0.5% (w/v) PEG 8000, 1% (w/v) PEG 3350, EhchA.17554.a.VL2.PK00002 at 3.7 mg/mL. plate 13803 well E5 drop 1. Puck: PSL-0312, 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: Feb 14, 2024
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: 3→43.72 Å / Num. obs: 7533 / % possible obs: 100 % / Redundancy: 9.7 % / CC1/2: 0.994 / Rmerge(I) obs: 0.192 / Rpim(I) all: 0.066 / Rrim(I) all: 0.204 / Χ2: 1.01 / Net I/σ(I): 8.7 / Num. measured all: 73361
Reflection shellResolution: 3→3.18 Å / % possible obs: 100 % / Redundancy: 10.8 % / Rmerge(I) obs: 1.317 / Num. measured all: 13177 / Num. unique obs: 1218 / CC1/2: 0.702 / Rpim(I) all: 0.419 / Rrim(I) all: 1.383 / Χ2: 0.94 / Net I/σ(I) obs: 2

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Processing

Software
NameVersionClassification
PHENIXdev_5357refinement
Aimlessdata scaling
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3→43.72 Å / SU ML: 0.42 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 30 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2587 394 5.25 %
Rwork0.23 --
obs0.2316 7508 99.85 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 3→43.72 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1342 0 25 6 1373
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0031393
X-RAY DIFFRACTIONf_angle_d0.6231891
X-RAY DIFFRACTIONf_dihedral_angle_d13.017505
X-RAY DIFFRACTIONf_chiral_restr0.049221
X-RAY DIFFRACTIONf_plane_restr0.005235
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3-3.430.35631400.32362339X-RAY DIFFRACTION100
3.43-4.330.30631210.26562369X-RAY DIFFRACTION100
4.33-43.720.2091330.18512406X-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)
15.7711.21971.32984.1299-0.2982.9124-0.2381-0.2133-0.0749-0.12580.10360.02740.0982-0.20710.14590.42850.0150.03050.49910.01050.48334.9029-34.206818.4601
27.0876-0.65260.64244.3392-0.84454.47560.1162-0.81660.02130.42810.09880.4193-0.1082-0.4951-0.19250.4565-0.08430.03920.64960.01030.409337.5899-31.807326.7914
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 21 through 105 )
2X-RAY DIFFRACTION2chain 'A' and (resid 106 through 189 )

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