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- PDB-2zpd: Crystal structure of the R43L mutant of LolA in the open form -

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Open data


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Basic information

Entry
Database: PDB / ID: 2zpd
TitleCrystal structure of the R43L mutant of LolA in the open form
ComponentsOuter-membrane lipoprotein carrier protein
KeywordsPROTEIN TRANSPORT / unclosed beta barrel / 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: 1.85 Å
AuthorsTakeda, K. / Yokota, N. / Oguchi, Y. / Tokuda, H. / Miki, K.
CitationJournal: J.Biol.Chem. / Year: 2008
Title: Opening and closing of the hydrophobic cavity of LolA coupled to lipoprotein binding and release.
Authors: Oguchi, Y. / Takeda, K. / Watanabe, S. / Yokota, N. / Miki, K. / Tokuda, H.
History
DepositionJul 10, 2008Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Aug 5, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Feb 22, 2017Group: Database references
Revision 1.3Nov 10, 2021Group: Database references / Category: database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details
Revision 1.4Nov 1, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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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)21,3701
Polymers21,3701
Non-polymers00
Water1,964109
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)35.95, 63.01, 40.68
Angle α, β, γ (deg.)90.00, 100.14, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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


Mass: 21370.410 Da / Num. of mol.: 1 / Mutation: R43L
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: lolA, lplA, yzzV, b0891, JW0874 / Plasmid: pAMR43L / Production host: Escherichia coli (E. coli) / Strain (production host): TT106 / References: UniProt: P61316
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 109 / 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: 2.12 Å3/Da / Density % sol: 42.04 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 15% PEG 3350, 50mM MES (pH 6.5), 20% glycerol, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 90 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL44B2 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Mar 9, 2004
RadiationMonochromator: Si 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.85→60 Å / Num. all: 15490 / Num. obs: 14034 / % possible obs: 90.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.2 % / Biso Wilson estimate: 9.6 Å2 / Rsym value: 0.053 / Net I/σ(I): 11.1
Reflection shellResolution: 1.85→1.92 Å / Mean I/σ(I) obs: 1.4 / Num. unique all: 891 / Rsym value: 0.206 / % possible all: 57.5

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
CNSrefinement
HKL-2000data reduction
HKL-2000data scaling
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1UA8

1ua8


Resolution: 1.85→30 Å / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.231 701 -RANDOM
Rwork0.197 ---
all-15335 --
obs-13916 90.7 %-
Displacement parametersBiso mean: 22.1 Å2
Baniso -1Baniso -2Baniso -3
1-1.37 Å20 Å2-1.14 Å2
2---2.44 Å20 Å2
3---1.07 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.24 Å0.2 Å
Luzzati d res low-5 Å
Luzzati sigma a0.15 Å0.16 Å
Refinement stepCycle: LAST / Resolution: 1.85→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1433 0 0 109 1542
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.009
X-RAY DIFFRACTIONc_angle_deg1.4
LS refinement shellResolution: 1.85→1.92 Å / Rfactor Rfree error: 0.046
RfactorNum. reflection% reflection
Rfree0.301 43 -
Rwork0.246 --
obs-904 58.9 %

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