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- PDB-6t1w: Structure of E. coli BamA in complex with lipoprotein RcsF -

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Basic information

Entry
Database: PDB / ID: 6t1w
TitleStructure of E. coli BamA in complex with lipoprotein RcsF
Components
  • Outer membrane lipoprotein RcsF
  • Outer membrane protein assembly factor BamA
KeywordsMEMBRANE PROTEIN / beta barrel assembly / lipoprotein / stress response
Function / homology
Function and homology information


: / positive regulation of phosphorelay signal transduction system / periplasmic side of cell outer membrane / outer membrane protein complex / Bam protein complex / Gram-negative-bacterium-type cell outer membrane assembly / cellular response to cell envelope stress / protein insertion into membrane / cell outer membrane / outer membrane-bounded periplasmic space ...: / positive regulation of phosphorelay signal transduction system / periplasmic side of cell outer membrane / outer membrane protein complex / Bam protein complex / Gram-negative-bacterium-type cell outer membrane assembly / cellular response to cell envelope stress / protein insertion into membrane / cell outer membrane / outer membrane-bounded periplasmic space / cell adhesion / intracellular signal transduction / membrane
Similarity search - Function
Outer membrane lipoprotein RcsF / RcsF lipoprotein / Hypothetical protein apc22750. Chain B / Translation Initiation Factor IF3 / Outer membrane protein assembly factor BamA / POTRA domain, BamA/TamA-like / Surface antigen variable number repeat / POTRA domain / POTRA domain profile. / Surface antigen D15-like ...Outer membrane lipoprotein RcsF / RcsF lipoprotein / Hypothetical protein apc22750. Chain B / Translation Initiation Factor IF3 / Outer membrane protein assembly factor BamA / POTRA domain, BamA/TamA-like / Surface antigen variable number repeat / POTRA domain / POTRA domain profile. / Surface antigen D15-like / Bacterial surface antigen (D15) / Omp85 superfamily domain / Prokaryotic membrane lipoprotein lipid attachment site profile. / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Outer membrane lipoprotein RcsF / Outer membrane protein assembly factor BamA / Outer membrane lipoprotein RcsF
Similarity search - Component
Biological speciesEscherichia coli K-12 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 3.79 Å
AuthorsLetoquart, J. / Remaut, H. / Collet, J.F.
Funding support Belgium, 2items
OrganizationGrant numberCountry
Research Foundation - Flanders Belgium
Walloon Excellence in Lifesciences & BIOtechnology Belgium
CitationJournal: Nat.Chem.Biol. / Year: 2020
Title: Structural insight into the formation of lipoprotein-beta-barrel complexes.
Authors: Rodriguez-Alonso, R. / Letoquart, J. / Nguyen, V.S. / Louis, G. / Calabrese, A.N. / Iorga, B.I. / Radford, S.E. / Cho, S.H. / Remaut, H. / Collet, J.F.
History
DepositionOct 7, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 13, 2020Provider: repository / Type: Initial release
Revision 1.1Jul 22, 2020Group: Database references / Category: citation / citation_author
Item: _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed ..._citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID / _citation_author.name
Revision 1.2Aug 26, 2020Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID
Revision 1.3Jan 24, 2024Group: 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 protein assembly factor BamA
B: Outer membrane protein assembly factor BamA
C: Outer membrane lipoprotein RcsF
D: Outer membrane lipoprotein RcsF


Theoretical massNumber of molelcules
Total (without water)209,6484
Polymers209,6484
Non-polymers00
Water00
1
A: Outer membrane protein assembly factor BamA
C: Outer membrane lipoprotein RcsF


Theoretical massNumber of molelcules
Total (without water)104,8242
Polymers104,8242
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Outer membrane protein assembly factor BamA
D: Outer membrane lipoprotein RcsF


Theoretical massNumber of molelcules
Total (without water)104,8242
Polymers104,8242
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)158.840, 142.530, 116.420
Angle α, β, γ (deg.)90.000, 102.610, 90.000
Int Tables number5
Space group name H-MC121

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Components

#1: Protein Outer membrane protein assembly factor BamA / Omp85


Mass: 90643.383 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli K-12 (bacteria) / Strain: K12 / Gene: bamA, yaeT, yzzN, yzzY, b0177, JW0172 / Production host: Escherichia coli BL21 (bacteria) / References: UniProt: P0A940
#2: Protein Outer membrane lipoprotein RcsF


Mass: 14180.471 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli K-12 (bacteria) / Production host: Escherichia coli BL21 (bacteria) / References: UniProt: E2QFC4, UniProt: P69411*PLUS

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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: 4.18 Å3/Da / Density % sol: 70.57 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 0.03 M sodium nitrate, 0.03 M sodium phosphate dibasic, 0.03 M ammonium sulfate, 0.10 M Tris-base [pH 8.5]; BICINE, 20 % (v/v) ethylene glycol; 10 % w/v PEG 8000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 1 / Wavelength: 1.77 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Feb 18, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.77 Å / Relative weight: 1
ReflectionResolution: 3.79→48.58 Å / Num. obs: 18489 / % possible obs: 92.8 % / Observed criterion σ(I): 1.2 / Redundancy: 34 % / Biso Wilson estimate: 149.4 Å2 / CC1/2: 0.99 / Rpim(I) all: 0.02 / Net I/σ(I): 15.8
Reflection shellResolution: 3.791→3.993 Å / Num. unique obs: 897 / CC1/2: 0.3 / Rpim(I) all: 0.788 / % possible all: 24.6

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
BUSTER2.10.3refinement
XDSdata reduction
PHASERphasing
PDB_EXTRACT3.25data extraction
STARANISOv3.309data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5D0O

5d0o


Resolution: 3.79→48.58 Å / Cor.coef. Fo:Fc: 0.859 / Cor.coef. Fo:Fc free: 0.873 / Cross valid method: THROUGHOUT / σ(F): 0 / SU Rfree Blow DPI: 0.974
RfactorNum. reflection% reflectionSelection details
Rfree0.317 973 5.26 %RANDOM
Rwork0.281 ---
obs0.283 18489 73.4 %-
Displacement parametersBiso max: 300 Å2 / Biso mean: 193.47 Å2 / Biso min: 20 Å2
Baniso -1Baniso -2Baniso -3
1--12.3494 Å20 Å2-3.3545 Å2
2---3.4476 Å20 Å2
3---15.7971 Å2
Refine analyzeLuzzati coordinate error obs: 0.81 Å
Refinement stepCycle: final / Resolution: 3.79→48.58 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10838 0 0 0 10838
Num. residues----1388
Refine LS restraints
Refine-IDTypeNumberRestraint functionWeightDev ideal
X-RAY DIFFRACTIONt_dihedral_angle_d3737SINUSOIDAL2
X-RAY DIFFRACTIONt_trig_c_planes
X-RAY DIFFRACTIONt_gen_planes1926HARMONIC5
X-RAY DIFFRACTIONt_it11092HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_chiral_improper_torsion1404SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact12114SEMIHARMONIC4
X-RAY DIFFRACTIONt_bond_d11092HARMONIC20.01
X-RAY DIFFRACTIONt_angle_deg15048HARMONIC21.15
X-RAY DIFFRACTIONt_omega_torsion2.94
X-RAY DIFFRACTIONt_other_torsion24.43
LS refinement shellResolution: 3.79→4.02 Å / Rfactor Rfree error: 0 / Total num. of bins used: 9
RfactorNum. reflection% reflection
Rfree0.2244 65 5.35 %
Rwork0.2179 1150 -
all0.2182 1215 -
obs--30.02 %

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