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Basic information

Entry
Database: PDB / ID: 8veh
TitleCrystal structure of outer membrane lipoprotein carrier protein (LolA) from Rickettsia bellii
ComponentsOuter membrane lipoprotein-sorting 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 / GLYCINE / TRIETHYLENE GLYCOL / Outer membrane lipoprotein-sorting protein LolA
Function and homology information
Biological speciesRickettsia bellii RML369-C (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.6 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 outer membrane lipoprotein carrier protein (LolA) from Rickettsia bellii
Authors: Lovell, S. / Cooper, A. / Liu, L. / Battaile, K.P.
History
DepositionDec 19, 2023Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 27, 2023Provider: 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-sorting protein LolA
B: Outer membrane lipoprotein-sorting protein LolA
C: Outer membrane lipoprotein-sorting protein LolA
D: Outer membrane lipoprotein-sorting protein LolA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)96,39210
Polymers96,0254
Non-polymers3676
Water1,08160
1
A: Outer membrane lipoprotein-sorting protein LolA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,0773
Polymers24,0061
Non-polymers712
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Outer membrane lipoprotein-sorting protein LolA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,0422
Polymers24,0061
Non-polymers351
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: Outer membrane lipoprotein-sorting protein LolA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,1173
Polymers24,0061
Non-polymers1112
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
D: Outer membrane lipoprotein-sorting protein LolA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,1562
Polymers24,0061
Non-polymers1501
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)77.802, 71.403, 78.502
Angle α, β, γ (deg.)90.00, 115.83, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
Outer membrane lipoprotein-sorting protein LolA


Mass: 24006.295 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rickettsia bellii RML369-C (bacteria) / Gene: lolA, RBE_0046 / Plasmid: RibeA.17554.a.VH3 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q1RKI7
#2: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Cl
#3: Chemical ChemComp-GLY / GLYCINE


Type: peptide linking / Mass: 75.067 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H5NO2
#4: Chemical ChemComp-PGE / TRIETHYLENE GLYCOL


Mass: 150.173 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H14O4
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 60 / Source method: isolated from a natural source / Formula: H2O
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: 2.04 Å3/Da / Density % sol: 39.82 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: Morpheus Fusion F5: 20% v/v PEG 500 MME; 10 % w/v PEG 20000, 0.04M Imidazole; 0.06M MES monohydrate (acid) pH 6.5, 0.02M DL-Glutamic acid monohydrate; 0.02M DL-Alanine; 0.02M Glycine; 0.02M ...Details: Morpheus Fusion F5: 20% v/v PEG 500 MME; 10 % w/v PEG 20000, 0.04M Imidazole; 0.06M MES monohydrate (acid) pH 6.5, 0.02M DL-Glutamic acid monohydrate; 0.02M DL-Alanine; 0.02M Glycine; 0.02M DL-Lysine monohydrochloride; 0.02M DL-Serine, 0.5% w/v 1,2,4-butanetriol, 0.5% w/v 1,2,6-hexanetriol, 0.5% w/v 1,5 -pentanediol, 0.5% w/v 1,1,1-tris(hydroxymethyl)propane, 0.5% w/v meso-erythritol, RibeA.17554.a.VH3.PW39215 at 28.3 mg/mL. Plate 13404 well F5 drop 2. Puck: PSL-0710, 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: Nov 19, 2023
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: 2.6→48.55 Å / Num. obs: 24006 / % possible obs: 99.9 % / Redundancy: 6.8 % / CC1/2: 0.997 / Rmerge(I) obs: 0.141 / Rpim(I) all: 0.058 / Rrim(I) all: 0.153 / Χ2: 1.02 / Net I/σ(I): 10.8 / Num. measured all: 164327
Reflection shellResolution: 2.6→2.72 Å / % possible obs: 100 % / Redundancy: 7.1 % / Rmerge(I) obs: 1.245 / Num. measured all: 20836 / Num. unique obs: 2916 / CC1/2: 0.6 / Rpim(I) all: 0.501 / Rrim(I) all: 1.344 / Χ2: 1 / Net I/σ(I) obs: 1.9

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Processing

Software
NameVersionClassification
PHENIX(1.21rc1_5177: ???)refinement
Aimlessdata scaling
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.6→48.55 Å / SU ML: 0.39 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 29.8 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2743 1256 5.24 %
Rwork0.2266 --
obs0.2291 23986 99.89 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.6→48.55 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6165 0 19 60 6244
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0046294
X-RAY DIFFRACTIONf_angle_d0.828515
X-RAY DIFFRACTIONf_dihedral_angle_d16.8832331
X-RAY DIFFRACTIONf_chiral_restr0.061978
X-RAY DIFFRACTIONf_plane_restr0.0061093
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.6-2.70.36961230.35792531X-RAY DIFFRACTION100
2.7-2.830.41221490.32552487X-RAY DIFFRACTION100
2.83-2.980.3551210.29282530X-RAY DIFFRACTION100
2.98-3.160.34321440.28652491X-RAY DIFFRACTION100
3.16-3.410.30041650.26922509X-RAY DIFFRACTION100
3.41-3.750.2861490.2212518X-RAY DIFFRACTION100
3.75-4.290.29031320.20352527X-RAY DIFFRACTION100
4.29-5.410.18571200.16842549X-RAY DIFFRACTION100
5.41-48.550.24211530.20772588X-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)
16.84571.0326-1.91383.5407-2.63744.3088-0.0784-2.11430.17120.4428-0.4485-0.3606-0.2827-0.19260.55050.6341-0.0521-0.03871.0276-0.0560.505228.1666.91368.388
26.09710.78232.59064.05280.36925.4101-0.1668-1.0687-1.01380.2803-0.00990.46930.8768-0.97430.22070.5187-0.08820.07020.82470.15660.494323.2970.17362.913
33.0834-1.5076-0.50862.09030.47383.1071-0.01840.1619-0.1938-0.2375-0.134-0.28440.31010.14990.08720.356-0.0197-0.0620.37440.01870.539540.21.90249.286
41.999821.999721.99982.0001-2.4326-3.16342.723110.8510.0097.2214-6.246-6.83042.44781.1710.4889-0.24460.7689-0.09830.76337.876-7.62318.028
55.40761.37042.83132.1781.64554.048-0.3040.2309-0.0160.16590.273-0.2721-0.71560.30940.00830.5232-0.0778-0.0610.41160.02950.348848.1284.86123.573
63.52350.80121.95373.8606-0.08674.1120.03660.3218-0.1325-0.0573-0.016-0.38370.16860.67110.00430.2883-0.01390.02420.5635-0.10450.512456.028-3.14226.637
74.7155-0.0438-0.29092.80180.42131.7328-0.73090.61051.1904-0.52930.25230.16380.117-0.22930.6780.7258-0.0347-0.16210.56240.18050.598543.53817.48517.136
85.09060.8765-2.39074.8518-0.00938.72490.7574-0.20950.2492-0.2031-0.44180.958-2.38060.3646-0.14030.6444-0.13080.06050.4323-0.09550.587737.35618.541-12.426
95.20951.4962-0.18682.8391-1.93545.48030.6538-0.2919-0.17590.0045-0.0102-0.0062-0.266-0.5424-0.62980.3758-0.0050.05640.25170.02490.495520.1132.886-7.955
102.22670.3507-1.53441.6107-1.9514.71870.3117-0.5129-0.68170.3103-0.2329-0.01030.76560.2467-0.08930.65750.0255-0.0480.54490.10170.543624.253-1.805-0.115
113.2586-0.0158-1.3395.1173-0.82655.1970.1277-0.5523-0.30110.6738-0.1393-0.2843-0.21720.6583-0.07230.352-0.0599-0.02280.41660.0240.323137.68210.039-13.079
123.95591.6288-0.48050.7601-0.21373.79420.22770.17860.23520.43560.25640.2954-0.4611-0.0475-0.14280.52970.02740.09990.29250.02250.488625.1666.86-12.345
132.3008-2.04420.20091.6389-0.75175.05850.4591-0.34720.20240.21640.2850.48140.3662-1.1457-0.68270.6056-0.06090.02910.66650.16860.487910.8674.0441.072
141.9493-1.0623-0.41553.92390.77692.52680.1172-0.25980.095-0.4942-0.1316-0.1154-0.3026-0.18070.00440.2637-0.0085-0.02140.26580.02130.297611.689-1.23531.735
152.64671.2217-0.82624.3848-0.1192.8273-0.04910.51090.2601-0.7558-0.41560.2743-0.1896-0.5688-0.00480.552-0.00780.02430.42230.06680.494917.291.51321.611
163.4781-1.09891.4885.76540.08975.1675-0.0089-0.23730.2323-0.63520.05670.1522-0.20360.2163-0.0540.3098-0.00940.04630.3591-0.00220.4656-0.3165.05532.032
173.0409-0.15460.67232.2594-0.13972.88120.0076-0.0389-0.0247-0.2624-0.1511-0.22820.1708-0.0390.11150.31090.00090.00970.2055-0.01950.412320.954-7.37931.396
181.99421.4924-1.10483.1491-0.10162.04290.0321-0.4749-0.10370.3433-0.0060.1469-0.1763-0.3265-0.05310.3510.013-0.0760.40950.02960.394733.3965.08254.779
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1( CHAIN D AND RESID 101:143 )D101 - 143
2X-RAY DIFFRACTION2( CHAIN D AND RESID 144:165 )D144 - 165
3X-RAY DIFFRACTION3( CHAIN D AND RESID 166:212 )D166 - 212
4X-RAY DIFFRACTION4( CHAIN C AND RESID 301:301 )C301
5X-RAY DIFFRACTION5( CHAIN A AND RESID 23:112 )A23 - 112
6X-RAY DIFFRACTION6( CHAIN A AND RESID 113:181 )A113 - 181
7X-RAY DIFFRACTION7( CHAIN A AND RESID 182:212 )A182 - 212
8X-RAY DIFFRACTION8( CHAIN B AND RESID 20:37 )B20 - 37
9X-RAY DIFFRACTION9( CHAIN B AND RESID 38:81 )B38 - 81
10X-RAY DIFFRACTION10( CHAIN B AND RESID 82:112 )B82 - 112
11X-RAY DIFFRACTION11( CHAIN B AND RESID 113:154 )B113 - 154
12X-RAY DIFFRACTION12( CHAIN B AND RESID 155:181 )B155 - 181
13X-RAY DIFFRACTION13( CHAIN B AND RESID 182:212 )B182 - 212
14X-RAY DIFFRACTION14( CHAIN C AND RESID 22:85 )C22 - 85
15X-RAY DIFFRACTION15( CHAIN C AND RESID 86:112 )C86 - 112
16X-RAY DIFFRACTION16( CHAIN C AND RESID 113:165 )C113 - 165
17X-RAY DIFFRACTION17( CHAIN C AND RESID 166:214 )C166 - 214
18X-RAY DIFFRACTION18( CHAIN D AND RESID 23:100 )D23 - 100

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