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- PDB-3wjt: Crystal structure of the L68D variant of mLolB -

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Basic information

Entry
Database: PDB / ID: 3wjt
TitleCrystal structure of the L68D variant of mLolB
ComponentsOuter-membrane lipoprotein LolB
KeywordsTRANSPORT PROTEIN / LolA/B Fold / Outer membrane
Function / homologyLipoprotein localisation LolA/LolB/LppX / outer membrane lipoprotein receptor (LolB), chain A / Clam / Mainly Beta / :
Function and homology information
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.55 Å
AuthorsTakeda, K. / Tokuda, H. / Miki, K.
CitationJournal: J.Biol.Chem. / Year: 2014
Title: Roles of the Protruding Loop of Factor B Essential for the Localization of Lipoproteins (LolB) in the Anchoring of Bacterial Triacylated Proteins to the Outer Membran
Authors: Hayashi, Y. / Tsurumizu, R. / Tsukahara, J. / Takeda, K. / Narita, S. / Mori, M. / Miki, K. / Tokuda, H.
History
DepositionOct 16, 2013Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Mar 5, 2014Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2014Group: Database references
Revision 1.2Nov 8, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / 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 / 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Outer-membrane lipoprotein LolB
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,8085
Polymers20,4851
Non-polymers3244
Water2,126118
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)35.291, 86.709, 111.071
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11A-204-

CL

21A-367-

HOH

31A-418-

HOH

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Components

#1: Protein Outer-membrane lipoprotein LolB


Mass: 20484.809 Da / Num. of mol.: 1 / Fragment: UNP residues 22-207 / Mutation: C1A, L68E
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Strain: ATCC 33849 / DSM 4235 / NCIB 12045 / K12 / DH1 / Gene: lolB, ECDH1ME8569_1148 / Plasmid: pRT102 / Production host: Escherichia coli (E. coli) / References: UniProt: C9QXY7
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 118 / 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 Å3/Da / Density % sol: 38.42 %
Crystal growTemperature: 277 K / pH: 8
Details: 180mM ammonium sulfate, 25%(w/v) PEG8000, 20mM Tris-HCl, 5.0%(v/v) glycerol, pH 8.0, VAPOR DIFFUSION, SITTING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 95 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL41XU / Wavelength: 1
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Apr 19, 2008 / Details: MIRRORS
RadiationMonochromator: SI 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.55→30 Å / Num. obs: 24057 / % possible obs: 96.1 % / Observed criterion σ(I): 0 / Redundancy: 10.1 % / Biso Wilson estimate: 20.1 Å2 / Rsym value: 0.053
Reflection shellResolution: 1.55→1.61 Å / Redundancy: 3.2 % / Rsym value: 0.256 / % possible all: 72.4

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Processing

Software
NameClassification
BSSdata collection
CNSrefinement
HKL-2000data reduction
HKL-2000data scaling
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: A CHAIN OF 1IWM

1iwm


Resolution: 1.55→28.17 Å / Rfactor Rfree error: 0.007 / Data cutoff high absF: 133040.49 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: ENGH & HUBER / Details: BULK SOLVENT MODEL USED
RfactorNum. reflection% reflectionSelection details
Rfree0.239 1168 4.9 %RANDOM
Rwork0.215 ---
obs0.215 24031 95.7 %-
all-24031 --
Solvent computationSolvent model: FLAT MODEL / Bsol: 61.4798 Å2 / ksol: 0.4 e/Å3
Displacement parametersBiso mean: 26.2 Å2
Baniso -1Baniso -2Baniso -3
1-1.88 Å20 Å20 Å2
2--2.3 Å20 Å2
3----4.18 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.23 Å0.19 Å
Luzzati d res low-5 Å
Luzzati sigma a0.2 Å0.16 Å
Refinement stepCycle: LAST / Resolution: 1.55→28.17 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1440 0 16 118 1574
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.012
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.4
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d26.6
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.87
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it2.941.5
X-RAY DIFFRACTIONc_mcangle_it4.272
X-RAY DIFFRACTIONc_scbond_it4.672
X-RAY DIFFRACTIONc_scangle_it6.712.5
Refine LS restraints NCSNCS model details: NONE
LS refinement shellResolution: 1.55→1.65 Å / Rfactor Rfree error: 0.026 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.317 152 5 %
Rwork0.282 2902 -
obs--74.1 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2water_rep.paramwater.top
X-RAY DIFFRACTION3ion.paramion.top
X-RAY DIFFRACTION4so4.paramso4.top
X-RAY DIFFRACTION5&_1_PARAMETER_INFILE_5&_1_TOPOLOGY_INFILE_5

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