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- PDB-1iwm: Crystal Structure of the Outer Membrane Lipoprotein Receptor, LolB -

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Basic information

Entry
Database: PDB / ID: 1iwm
TitleCrystal Structure of the Outer Membrane Lipoprotein Receptor, LolB
ComponentsOuter Membrane Lipoprotein LolB
KeywordsPROTEIN TRANSPORT / UNCLOSED BETA BARREL / LIPOPROTEIN
Function / homology
Function and homology information


lipoprotein localization to outer membrane / lipoprotein metabolic process / cell outer membrane / protein transport / outer membrane-bounded periplasmic space
Similarity search - Function
Outer membrane lipoprotein LolB / Outer membrane lipoprotein LolB / Lipoprotein localisation LolA/LolB/LppX / outer membrane lipoprotein receptor (LolB), chain A / Lipoprotein localisation LolA/LolB/LppX / Clam / Prokaryotic membrane lipoprotein lipid attachment site profile. / Mainly Beta
Similarity search - Domain/homology
Outer-membrane lipoprotein LolB
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / 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
DepositionMay 17, 2002Deposition 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 1.3Nov 10, 2021Group: Database references / Derived calculations / Category: database_2 / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Dec 27, 2023Group: 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 LolB
B: Outer Membrane Lipoprotein LolB
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,8366
Polymers42,4512
Non-polymers3844
Water3,837213
1
A: Outer Membrane Lipoprotein LolB
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,4183
Polymers21,2261
Non-polymers1922
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Outer Membrane Lipoprotein LolB
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,4183
Polymers21,2261
Non-polymers1922
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)37.190, 112.440, 47.790
Angle α, β, γ (deg.)90.00, 111.40, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Outer Membrane Lipoprotein LolB


Mass: 21225.721 Da / Num. of mol.: 2 / Mutation: C1A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Plasmid: pYKT102 / Production host: Escherichia coli (E. coli) / References: UniProt: P61320
#2: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 213 / 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: 2.14 Å3/Da / Density % sol: 42.08 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 4.6
Details: PEGMME2000, sodium acetate, ammonium sulfate, pH 4.6, VAPOR DIFFUSION, SITTING DROP, temperature 293K
Crystal grow
*PLUS
Temperature: 20 ℃ / pH: 8 / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
120 mg/mlprotein1drop
210 mMTris-HCl1droppH8.0
330 %(w/v)PEG2000MME1reservoir
40.1 mMsodium acetate1reservoirpH4.6
50.2 Mammonium sulfate1reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL38B1 / 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: 28181 / % possible obs: 97.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.1 % / Biso Wilson estimate: 15.5 Å2 / Rsym value: 0.062
Reflection shellResolution: 1.9→1.97 Å / Rsym value: 0.279 / % possible all: 95
Reflection
*PLUS
Lowest resolution: 30 Å / Rmerge(I) obs: 0.062
Reflection shell
*PLUS
% possible obs: 95 % / Rmerge(I) obs: 0.279

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Processing

Software
NameVersionClassification
DENZOdata reduction
SCALEPACKdata scaling
SOLVEphasing
CNS1refinement
RefinementMethod to determine structure: MAD / Resolution: 1.9→30 Å / Isotropic thermal model: isotropi / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.249 1415 -RANDOM
Rwork0.215 ---
obs-28034 97.4 %-
Displacement parametersBiso mean: 26.6 Å2
Baniso -1Baniso -2Baniso -3
1-9.1 Å20 Å24.29 Å2
2---6.97 Å20 Å2
3----2.13 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.29 Å0.24 Å
Luzzati d res low-6 Å
Luzzati sigma a0.29 Å0.27 Å
Refinement stepCycle: LAST / Resolution: 1.9→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2872 0 20 213 3105
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.006
X-RAY DIFFRACTIONc_angle_deg1.3
LS refinement shellResolution: 1.9→2.02 Å / Rfactor Rfree error: 0.021
RfactorNum. reflection% reflection
Rfree0.324 233 -
Rwork0.3 --
obs-4479 94.1 %
Refinement
*PLUS
Highest resolution: 1.9 Å / Lowest resolution: 30 Å / % reflection Rfree: 5 %
Solvent computation
*PLUS
Displacement parameters
*PLUS
LS refinement shell
*PLUS
Lowest resolution: 1.97 Å

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