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- PDB-3ksn: Crystal structure of the lipoprotein localization factor, LolA -

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Basic information

Entry
Database: PDB / ID: 3ksn
TitleCrystal structure of the lipoprotein localization factor, LolA
ComponentsOuter-membrane lipoprotein carrier protein
KeywordsPROTEIN TRANSPORT / lipoprotein carrier / Chaperone / Transport
Function / homology
Function and homology information


lipoprotein localization to outer membrane / lipoprotein transport / outer membrane-bounded periplasmic space
Similarity search - Function
Outer membrane lipoprotein carrier protein LolA, Proteobacteria / Outer 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
Similarity search - Domain/homology
Outer-membrane lipoprotein carrier protein
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.65 Å
AuthorsAhmadpour, F. / Gloyd, M. / Guarne, A. / Stewart, G. / Pathania, R. / Brown, E.D.
CitationJournal: To be Published
Title: Crystal structure of the lipoprotein localization factor, LolA
Authors: Ahmadpour, F. / Gloyd, M. / Guarne, A. / Stewart, G. / Pathania, R. / Brown, E.D.
History
DepositionNov 23, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 6, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 16, 2011Group: Atomic model
Revision 1.3Sep 6, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Outer-membrane lipoprotein carrier protein


Theoretical massNumber of molelcules
Total (without water)20,4001
Polymers20,4001
Non-polymers00
Water1,42379
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)60.357, 60.357, 79.251
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221
Components on special symmetry positions
IDModelComponents
11A-210-

HOH

21A-217-

HOH

31A-249-

HOH

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Components

#1: Protein Outer-membrane lipoprotein carrier protein / P20


Mass: 20400.348 Da / Num. of mol.: 1 / Fragment: Residues 22-203
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Strain: K12 / Gene: b0891, JW0874, lolA, lplA, yzzV / Plasmid: pDEST17 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P61316
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 79 / Source method: isolated from a natural source / Formula: H2O

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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: 39.78 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 4.4
Details: 25% PEG 1000, 20% PEG 8000, 0.1 M sodium acetate, dehydrated over 1M ammonium sulfate, pH 4.4, VAPOR DIFFUSION, HANGING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X29A / Wavelength: 1.0809 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Apr 24, 2008 / Details: mirrors
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0809 Å / Relative weight: 1
ReflectionResolution: 1.65→50 Å / Num. obs: 20611 / % possible obs: 99.6 % / Redundancy: 9.8 % / Biso Wilson estimate: 23.11 Å2 / Rmerge(I) obs: 0.047 / Rsym value: 0.035 / Net I/σ(I): 39.5
Reflection shellResolution: 1.65→1.71 Å / Redundancy: 9.8 % / Rmerge(I) obs: 0.534 / Mean I/σ(I) obs: 4.47 / Num. unique all: 2035 / Rsym value: 0.491 / % possible all: 99.7

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Processing

Software
NameVersionClassification
CBASSdata collection
PHASERphasing
PHENIX(phenix.refine: 1.4_159)refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1AU8

1au8


Resolution: 1.65→31.577 Å / SU ML: 0.24 / Cross valid method: THROUGHOUT / σ(F): 1.89 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2426 1052 5.12 %random
Rwork0.1936 ---
obs0.1961 20534 99.36 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 60.497 Å2 / ksol: 0.4 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-0.6185 Å2-0 Å2-0 Å2
2--0.6185 Å2-0 Å2
3----1.2371 Å2
Refinement stepCycle: LAST / Resolution: 1.65→31.577 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1409 0 0 79 1488
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0061441
X-RAY DIFFRACTIONf_angle_d1.0631955
X-RAY DIFFRACTIONf_dihedral_angle_d18.946516
X-RAY DIFFRACTIONf_chiral_restr0.067209
X-RAY DIFFRACTIONf_plane_restr0.004260
LS refinement shell

Refine-ID: X-RAY DIFFRACTION

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection obs% reflection obs (%)
1.65-1.72430.27141340.21362417255199
1.7243-1.81520.30841380.178123892527100
1.8152-1.92890.27761460.18992370251699
1.9289-2.07780.27041300.174124132543100
2.0778-2.28680.24461150.187324362551100
2.2868-2.61760.23751310.196524572588100
2.6176-3.29730.28031220.203724712593100
3.2973-31.58320.19671360.17832529266598

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