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- PDB-1ua8: Crystal structure of the lipoprotein localization factor, LolA -

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Basic information

Entry
Database: PDB / ID: 1ua8
TitleCrystal structure of the lipoprotein localization factor, LolA
ComponentsOuter-membrane lipoproteins carrier protein
KeywordsPROTEIN TRANSPORT / unclosed beta barrel
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: 1.9 Å
AuthorsTakeda, K. / Miyatake, H. / Yokota, N. / Matsuyama, S. / Tokuda, H. / Miki, K.
CitationJournal: Embo J. / Year: 2003
Title: Crystal structures of bacterial lipoprotein localization factors, LolA and LolB.
Authors: Takeda, K. / Miyatake, H. / Yokota, N. / Matsuyama, S. / Tokuda, H. / Miki, K.
History
DepositionMar 4, 2003Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jul 15, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 25, 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
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Outer-membrane lipoproteins carrier protein


Theoretical massNumber of molelcules
Total (without water)20,3431
Polymers20,3431
Non-polymers00
Water1,47782
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)60.59, 60.59, 79.03
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221

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Components

#1: Protein Outer-membrane lipoproteins carrier protein / Lipoprotein Localization Factor


Mass: 20343.291 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Plasmid: pMAN995 / Production host: Escherichia coli (E. coli) / References: UniProt: P61316
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 82 / 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: 2.03 Å3/Da / Density % sol: 38.91 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8
Details: PEG1500, Tris-HCl, Glycerol, pH 8.0, VAPOR DIFFUSION, SITTING DROP, temperature 293K
Crystal grow
*PLUS
Temperature: 20 ℃ / pH: 7.4 / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
120 mg/mlprotein1drop
210 mMTris-HCl1droppH7.4
315 %(w/v)PEG15001reservoir
420 mMTris-HCl1reservoirpH8.0
520 %(v/v)glycerol1reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL26B1 / Wavelength: 0.998 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Nov 20, 2000
RadiationMonochromator: Si 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.998 Å / Relative weight: 1
ReflectionResolution: 1.9→30 Å / Num. obs: 13592 / % possible obs: 99.4 % / Observed criterion σ(I): 0 / Redundancy: 9.1 % / Biso Wilson estimate: 17.5 Å2 / Rsym value: 0.039
Reflection shellResolution: 1.9→1.97 Å / Rsym value: 0.256 / % possible all: 99.5
Reflection
*PLUS
Rmerge(I) obs: 0.039
Reflection shell
*PLUS
% possible obs: 99.5 % / Rmerge(I) obs: 0.256

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Processing

Software
NameClassification
DENZOdata reduction
SCALEPACKdata scaling
CNSrefinement
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1IWL

1iwl


Resolution: 1.9→30 Å / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.259 679 -RANDOM
Rwork0.226 ---
obs-13592 99.4 %-
Displacement parametersBiso mean: 40.3 Å2
Baniso -1Baniso -2Baniso -3
1-2.86 Å2-0.33 Å20 Å2
2--2.86 Å20 Å2
3----5.71 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.3 Å0.25 Å
Luzzati d res low-5 Å
Luzzati sigma a0.28 Å0.2 Å
Refinement stepCycle: LAST / Resolution: 1.9→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1392 0 0 82 1474
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.006
X-RAY DIFFRACTIONc_angle_deg1.2
LS refinement shellResolution: 1.9→2.02 Å / Rfactor Rfree error: 0.035
RfactorNum. reflection% reflection
Rfree0.327 86 -
Rwork0.278 --
obs-2137 99.4 %
Refinement
*PLUS
% reflection Rfree: 5 %
Solvent computation
*PLUS
Displacement parameters
*PLUS
LS refinement shell
*PLUS
Lowest resolution: 1.97 Å

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