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

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Basic information

Entry
Database: PDB / ID: 9coz
TitleCrystal structure of outer membrane lipoprotein carrier protein (LolA) from Francisella philomiragia (Orthorhombic P Form)
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 / Outer membrane lipocarrier LolA family protein
Function and homology information
Biological speciesFrancisella philomiragia (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 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 Francisella philomiragia (Orthorhombic P Form)
Authors: Taylor, K.E. / Lovell, S. / Cooper, A. / Battaile, K.P. / Buchko, G.W.
History
DepositionJul 17, 2024Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 24, 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 lipocarrier LolA family protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,5025
Polymers22,1951
Non-polymers3074
Water1,65792
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)35.272, 62.107, 79.454
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#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
#2: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#3: Chemical ChemComp-MPD / (4S)-2-METHYL-2,4-PENTANEDIOL


Mass: 118.174 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H14O2 / Feature type: SUBJECT OF INVESTIGATION / Comment: precipitant*YM
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 92 / 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: 1.96 Å3/Da / Density % sol: 37.26 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: Morpheus C12: 20% (v/v) Ethylene glycol; 10 % (w/v) PEG 8000; 0.02M D-Glucose; 0.05M Sodium HEPES; 0.05M MOPS (acid) pH 7.5; 0.02M D-Mannose; 0.02M D-Galactose; 0.02M L-Fucose; 0.02M D- ...Details: Morpheus C12: 20% (v/v) Ethylene glycol; 10 % (w/v) PEG 8000; 0.02M D-Glucose; 0.05M Sodium HEPES; 0.05M MOPS (acid) pH 7.5; 0.02M D-Mannose; 0.02M D-Galactose; 0.02M L-Fucose; 0.02M D-Xylose; 0.02M N-Acetyl-D-Glucosamine; 0.2% w/v Lidocaine hydrochloride monohydrate, 0.2% w/v Procaine hydrochloride, 0.2%w/v Proparacaine hydrochloride, 0.2% w/v tetracaine hydrochloride . FrphA.20731.a.VL2.PB00125 at 13.9 mg/mL. plate 14180 well C12 drop2, Puck: PSL0901, 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: Jul 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: 1.7→48.93 Å / Num. obs: 19913 / % possible obs: 100 % / Redundancy: 13 % / CC1/2: 0.999 / Rmerge(I) obs: 0.107 / Rpim(I) all: 0.031 / Rrim(I) all: 0.112 / Χ2: 1.02 / Net I/σ(I): 14.1 / Num. measured all: 258287
Reflection shellResolution: 1.7→1.73 Å / % possible obs: 100 % / Redundancy: 13.6 % / Rmerge(I) obs: 2.052 / Num. measured all: 13912 / Num. unique obs: 1021 / CC1/2: 0.684 / Rpim(I) all: 0.575 / Rrim(I) all: 2.132 / Χ2: 1.04 / Net I/σ(I) obs: 1.5

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Processing

Software
NameVersionClassification
PHENIX(dev_5383: ???)refinement
Aimlessdata scaling
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.7→48.93 Å / SU ML: 0.25 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 23.71 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2269 998 5.03 %
Rwork0.1843 --
obs0.1865 19860 99.97 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.7→48.93 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1213 0 18 92 1323
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.011285
X-RAY DIFFRACTIONf_angle_d1.0141756
X-RAY DIFFRACTIONf_dihedral_angle_d15.618487
X-RAY DIFFRACTIONf_chiral_restr0.066214
X-RAY DIFFRACTIONf_plane_restr0.007221
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.7-1.790.38441300.31842637X-RAY DIFFRACTION100
1.79-1.90.27981460.21892640X-RAY DIFFRACTION100
1.9-2.050.26421200.22322688X-RAY DIFFRACTION100
2.05-2.250.2311450.17432653X-RAY DIFFRACTION100
2.25-2.580.22211440.18212688X-RAY DIFFRACTION100
2.58-3.250.2261460.18892727X-RAY DIFFRACTION100
3.25-48.930.20651670.16322829X-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)
13.8245-1.74621.8694.0718-0.88773.1521-0.10740.1696-0.1044-0.24720.1274-0.0446-0.39220.0777-0.02850.20750.00490.03030.18290.00660.14180.2446-11.635212.0619
23.32120.0713-1.38274.15980.55472.41390.1173-0.1067-0.12830.0104-0.16530.4639-0.2226-0.190.13580.18890.0186-0.0280.2807-0.00890.2455-12.0904-15.577415.9335
31.81290.21040.48134.18340.90072.0672-0.062-0.00860.0718-0.02580.00610.2657-0.0314-0.07340.02870.17160.00510.01560.2124-0.00080.2162-4.3471.34921.8602
42.4795-0.5761.07944.0796-0.3694.5872-0.15760.05350.0876-0.13840.0285-0.0551-0.2310.0197-0.01420.2320.01640.03520.19360.00740.17070.2454-5.472314.7855
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 52 through 78 )
2X-RAY DIFFRACTION2chain 'A' and (resid 79 through 120 )
3X-RAY DIFFRACTION3chain 'A' and (resid 121 through 183 )
4X-RAY DIFFRACTION4chain 'A' and (resid 184 through 205 )

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