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- PDB-8t5t: Crystal structure of outer membrane lipoprotein carrier protein (... -

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Basic information

Entry
Database: PDB / ID: 8t5t
TitleCrystal structure of outer membrane lipoprotein carrier protein (LolA) from Borrelia burgdorferi (steric acid bound)
ComponentsOuter membrane lipoprotein carrier protein (LolA)
KeywordsLIPID TRANSPORT / SSGCID / STRUCTURAL GENOMICS / SEATTLE STRUCTURAL GENOMICS CENTER FOR INFECTIOUS DISEASE / Borrelia / LolA / lipoprotein carrier
Function / homologyOuter membrane lipoprotein carrier protein LolA / Lipoprotein localisation LolA/LolB/LppX / Outer membrane lipoprotein carrier protein LolA-like / outer membrane lipoprotein receptor (LolB), chain A / Lipoprotein localisation LolA/LolB/LppX / Clam / Mainly Beta / STEARIC ACID / Export chaperone
Function and homology information
Biological speciesBorreliella burgdorferi B31 (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)HHSN272201700059C 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 Borrelia burgdorferi (steric acid bound)
Authors: Lovell, S. / Cooper, A. / Battaile, K.P. / Zueckert, W.
History
DepositionJun 14, 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 lipoprotein carrier protein (LolA)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,55311
Polymers23,4041
Non-polymers1,14910
Water2,900161
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)122.291, 122.291, 122.291
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number213
Space group name H-MP4132
Components on special symmetry positions
IDModelComponents
11A-304-

SO4

21A-486-

HOH

31A-553-

HOH

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Components

#1: Protein Outer membrane lipoprotein carrier protein (LolA)


Mass: 23403.543 Da / Num. of mol.: 1 / Fragment: Q18-N216
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Borreliella burgdorferi B31 (bacteria) / Gene: BB_0346 / Plasmid: BobuA.17454.a.DH3 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: O51321
#2: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-STE / STEARIC ACID


Mass: 284.477 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C18H36O2 / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 161 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 3.26 Å3/Da / Density % sol: 62.22 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: Berkeley E4: 1500 mM Ammonium sulfate, 100 mM Hepes pH 7.5. BobuA.17454.a.DH3.PK00001 at 10 mg/mL. plate 13170, well E4 drop 3. Puck: PSL-1107, Cryo: 2.5M lithium sulfate, Large mass of ...Details: Berkeley E4: 1500 mM Ammonium sulfate, 100 mM Hepes pH 7.5. BobuA.17454.a.DH3.PK00001 at 10 mg/mL. plate 13170, well E4 drop 3. Puck: PSL-1107, Cryo: 2.5M lithium sulfate, Large mass of electron density in the binding pocket that appeared to be a fatty acid from the expression host. Modelled as steric acid

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: NSLS-II / Beamline: 19-ID / Wavelength: 0.9795 Å
DetectorType: DECTRIS EIGER2 XE 9M / Detector: PIXEL / Date: Mar 5, 2023
RadiationMonochromator: Double Crystal Si 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 1.8→49.93 Å / Num. obs: 29577 / % possible obs: 100 % / Redundancy: 39.1 % / CC1/2: 1 / Rmerge(I) obs: 0.077 / Rpim(I) all: 0.012 / Rrim(I) all: 0.078 / Χ2: 0.96 / Net I/σ(I): 30.1 / Num. measured all: 1157377
Reflection shellResolution: 1.8→1.84 Å / % possible obs: 100 % / Redundancy: 39.4 % / Rmerge(I) obs: 2.755 / Num. measured all: 67350 / Num. unique obs: 1709 / CC1/2: 0.77 / Rpim(I) all: 0.443 / Rrim(I) all: 2.791 / Χ2: 0.9 / Net I/σ(I) obs: 1.7

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Processing

Software
NameVersionClassification
PHENIX(1.21rc1_4933: ???)refinement
Aimlessdata scaling
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.8→28.82 Å / SU ML: 0.23 / Cross valid method: FREE R-VALUE / σ(F): 1.1 / Phase error: 24.67 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2362 1475 5 %
Rwork0.1962 --
obs0.1982 29510 99.97 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.8→28.82 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1507 0 65 161 1733
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0111620
X-RAY DIFFRACTIONf_angle_d1.1512201
X-RAY DIFFRACTIONf_dihedral_angle_d11.196232
X-RAY DIFFRACTIONf_chiral_restr0.065240
X-RAY DIFFRACTIONf_plane_restr0.011277
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.8-1.860.37841330.36932477X-RAY DIFFRACTION100
1.86-1.920.31941150.27682525X-RAY DIFFRACTION100
1.92-20.26781270.2252487X-RAY DIFFRACTION100
2-2.090.22271410.20852501X-RAY DIFFRACTION100
2.09-2.20.2611260.20342518X-RAY DIFFRACTION100
2.2-2.340.25231350.22092523X-RAY DIFFRACTION100
2.34-2.520.21571350.21522518X-RAY DIFFRACTION100
2.52-2.780.28271380.21722547X-RAY DIFFRACTION100
2.78-3.180.24821380.22052562X-RAY DIFFRACTION100
3.18-40.22311320.17412614X-RAY DIFFRACTION100
4-28.820.21391550.16812763X-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)
17.9495-0.1912.21196.52713.75942.8841-0.1192-0.17830.5064-0.3717-0.14660.593-0.6818-0.25090.21020.5031-0.0049-0.03160.2590.01240.388845.668622.500545.2806
23.78030.06940.30335.8947-0.34812.4714-0.17170.19610.0063-0.4170.0541-0.3465-0.24460.07250.15130.3613-0.07520.04980.2884-0.04390.243852.25372.718237.9021
30.94790.43750.14886.66471.65292.7502-0.02780.0207-0.0305-0.2351-0.05930.1452-0.13310.04610.07320.2645-0.0273-0.03020.311-0.04830.233344.5499-4.340440.6491
43.03622.6696-0.9934.2031-0.63163.99440.0626-0.35640.02670.2191-0.2783-0.007-0.45720.23770.19480.3294-0.03480.01040.2387-0.02240.20251.59615.305252.2407
56.22990.3329-1.07756.2201-2.15447.1312-0.10830.35130.1571-0.2651-0.0657-0.195-0.64250.04530.18750.2987-0.0571-0.00050.2385-0.01720.232753.224614.391545.0008
64.19020.0519-0.09915.513-1.36655.13680.0725-0.1475-0.4781-0.29390.09170.10510.06610.3194-0.23120.22-0.03160.05210.21340.01840.278652.9815.985243.3329
76.15070.5261-2.72033.2655-1.56315.1304-0.0703-0.3357-0.09390.2643-0.0932-0.2371-0.1662-0.06180.0710.3363-0.0079-0.06990.2776-0.0920.329540.63-7.087741.3069
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 1 through 18 )
2X-RAY DIFFRACTION2chain 'A' and (resid 19 through 42 )
3X-RAY DIFFRACTION3chain 'A' and (resid 43 through 88 )
4X-RAY DIFFRACTION4chain 'A' and (resid 89 through 133 )
5X-RAY DIFFRACTION5chain 'A' and (resid 134 through 148 )
6X-RAY DIFFRACTION6chain 'A' and (resid 149 through 175 )
7X-RAY DIFFRACTION7chain 'A' and (resid 176 through 195 )

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