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- PDB-8t5j: Crystal structure of outer membrane lipoprotein carrier protein (... -

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Basic information

Entry
Database: PDB / ID: 8t5j
TitleCrystal structure of outer membrane lipoprotein carrier protein (LolA) from Francisella philomiragia
ComponentsOuter membrane lipocarrier LolA family protein
KeywordsLIPID TRANSPORT / SSGCID / STRUCTURAL GENOMICS / SEATTLE STRUCTURAL GENOMICS CENTER FOR INFECTIOUS DISEASE / lipoprotein carrier / LolA
Function / homologyOuter membrane lipoprotein carrier protein LolA-like / Outer membrane lipoprotein carrier protein LolA-like / Lipoprotein localisation LolA/LolB/LppX / protein transport / metal ion binding / HEXANE-1,6-DIOL / Outer membrane lipocarrier LolA family protein
Function and homology information
Biological speciesFrancisella philomiragia (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.55 Å
AuthorsSeattle Structural Genomics Center for Infectious Disease (SSGCID)
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)HHSN272201700059C United States
CitationJournal: To be published
Title: Crystal structure of outer membrane lipoprotein carrier protein (LolA) from Francisella philomiragia
Authors: Woodward, E.L. / Lovell, S. / Cooper, A. / Buchko, G.
History
DepositionJun 13, 2023Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 28, 2023Provider: repository / Type: Initial release
Revision 1.1May 22, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Outer membrane lipocarrier LolA family protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,9079
Polymers22,1951
Non-polymers7128
Water2,738152
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)61.850, 61.850, 86.611
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121
Components on special symmetry positions
IDModelComponents
11A-464-

HOH

21A-548-

HOH

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Components

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Protein , 1 types, 1 molecules A

#1: Protein Outer membrane lipocarrier LolA family protein


Mass: 22194.951 Da / Num. of mol.: 1 / Fragment: L32-N205
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Francisella philomiragia (bacteria) / Gene: Fphi_1079 / Plasmid: FrphA.20731.a.VL2 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: B0TX44

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Non-polymers , 5 types, 160 molecules

#2: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#4: Chemical ChemComp-HEZ / HEXANE-1,6-DIOL


Mass: 118.174 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C6H14O2
#5: Chemical ChemComp-1PE / PENTAETHYLENE GLYCOL / PEG400


Mass: 238.278 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H22O6 / Comment: precipitant*YM
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 152 / 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: 2.15 Å3/Da / Density % sol: 42.91 % / Description: hexagonal prisms
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: Berkeley D10: 20% (w/v) PEG 3350, 100 mM Hepes pH 7.5, 100 mM Lithium sulfate, 100 mM Magnesium chloride, 10% (w/v) 1,6-Hexanediol. FrphA.20731.a.VL2.PB00125 at 14.5 mg/mL. plate 13468 well ...Details: Berkeley D10: 20% (w/v) PEG 3350, 100 mM Hepes pH 7.5, 100 mM Lithium sulfate, 100 mM Magnesium chloride, 10% (w/v) 1,6-Hexanediol. FrphA.20731.a.VL2.PB00125 at 14.5 mg/mL. plate 13468 well D10 drop1, Cryo: 80% crystallant+20% PEG200

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SEALED TUBE / Type: BRUKER D8 QUEST / Wavelength: 1.5418 Å
DetectorType: Bruker PHOTON III / Detector: PIXEL / Date: Jun 8, 2023
RadiationMonochromator: HELIOS MULTILAYER / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.55→25.17 Å / Num. obs: 28420 / % possible obs: 100 % / Redundancy: 25.3 % / CC1/2: 1 / Rmerge(I) obs: 0.097 / Rpim(I) all: 0.02 / Rrim(I) all: 0.099 / Χ2: 0.94 / Net I/σ(I): 24.7 / Num. measured all: 718556
Reflection shellResolution: 1.55→1.58 Å / % possible obs: 100 % / Redundancy: 17 % / Rmerge(I) obs: 2.648 / Num. measured all: 23447 / Num. unique obs: 1382 / CC1/2: 0.516 / Rpim(I) all: 0.662 / Rrim(I) all: 2.73 / Χ2: 1.35 / Net I/σ(I) obs: 1.6

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Processing

Software
NameVersionClassification
PHENIX(1.21rc1_4933: ???)refinement
Aimlessdata scaling
SAINTdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.55→21.1 Å / SU ML: 0.15 / Cross valid method: FREE R-VALUE / σ(F): 1.04 / Phase error: 21.84 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2076 1452 5.12 %
Rwork0.1704 --
obs0.1723 28378 99.99 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.55→21.1 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1213 0 44 152 1409
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.011357
X-RAY DIFFRACTIONf_angle_d0.9621845
X-RAY DIFFRACTIONf_dihedral_angle_d17.566540
X-RAY DIFFRACTIONf_chiral_restr0.062222
X-RAY DIFFRACTIONf_plane_restr0.01231
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.55-1.610.25611640.24522615X-RAY DIFFRACTION100
1.61-1.670.30761460.2292666X-RAY DIFFRACTION100
1.67-1.750.261730.20432614X-RAY DIFFRACTION100
1.75-1.840.22311280.18752678X-RAY DIFFRACTION100
1.84-1.950.19781250.17282680X-RAY DIFFRACTION100
1.95-2.10.2051290.14932696X-RAY DIFFRACTION100
2.1-2.310.1861410.17132692X-RAY DIFFRACTION100
2.31-2.650.18321470.17042706X-RAY DIFFRACTION100
2.65-3.330.20081560.17132715X-RAY DIFFRACTION100
3.34-21.10.20371430.15312864X-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)
11.6390.38960.00513.48070.7811.2999-0.007-0.0290.008-0.26470.04220.3201-00.018-0.04730.14480.0291-0.03370.0845-0.01190.1561-20.2533-16.683620.5157
21.19990.81570.36635.0091-0.44322.48220.08530.0247-0.05580.12010.0501-0.2076-0.05330.0897-0.15740.09720.0496-0.00130.0845-0.04040.1303-14.203-12.260121.9906
32.1114-0.37360.04361.96340.65112.57640.25960.20630.0507-0.437-0.0222-0.31450.0340.6107-0.10880.22290.04960.04230.2139-0.05580.1808-8.0503-11.528714.496
43.33370.26291.69351.5772-0.63374.5780.01680.3291-0.2242-0.1035-0.1213-0.25740.22520.45090.03320.27070.11870.05980.2843-0.05890.2041-8.7733-18.42626.7095
51.2318-0.66340.06381.6476-0.01781.31240.03350.10380.2015-0.2338-0.0281-0.1205-0.11440.0785-0.01040.15430.04910.00920.1378-0.01740.1516-22.471-2.96298.7781
61.8848-0.22420.17412.66220.75952.763-0.00220.1093-0.0434-0.2614-0.06550.1645-0.0294-0.17170.07290.15540.0563-0.03790.1102-0.01780.1237-28.9094-6.451510.0742
71.2605-0.04590.84441.76531.08852.61840.08070.0215-0.0541-0.17520.01510.032-0.0965-0.0067-0.08520.14230.0304-0.01160.0909-0.02570.1385-22.2125-7.880319.5823
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 52 through 69 )
2X-RAY DIFFRACTION2chain 'A' and (resid 70 through 78 )
3X-RAY DIFFRACTION3chain 'A' and (resid 79 through 107 )
4X-RAY DIFFRACTION4chain 'A' and (resid 108 through 120 )
5X-RAY DIFFRACTION5chain 'A' and (resid 121 through 152 )
6X-RAY DIFFRACTION6chain 'A' and (resid 153 through 178 )
7X-RAY DIFFRACTION7chain 'A' and (resid 179 through 205 )

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