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- PDB-5ekq: The structure of the BamACDE subcomplex from E. coli -

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Basic information

Entry
Database: PDB / ID: 5ekq
TitleThe structure of the BamACDE subcomplex from E. coli
Components
  • Outer membrane protein assembly factor BamA
  • Outer membrane protein assembly factor BamC
  • Outer membrane protein assembly factor BamD
  • Outer membrane protein assembly factor BamE
KeywordsMEMBRANE PROTEIN / insertase / beta-barrel / outer membrane protein
Function / homology
Function and homology information


Bam protein complex / Gram-negative-bacterium-type cell outer membrane assembly / protein insertion into membrane / cell outer membrane / protein-macromolecule adaptor activity / cell adhesion / response to antibiotic / cell surface / membrane / identical protein binding
Similarity search - Function
Alpha-D-Glucose-1,6-Bisphosphate; Chain A, domain 4 - #50 / Beta-lactamase Inhibitory Protein; Chain:B, domain 1 / Beta-lactamase Inhibitory Protein; Chain:B, domain 1 - #10 / NlpB/DapX lipoprotein / Outer membrane protein assembly factor BamC / Outer membrane protein assembly factor BamC, C-terminal / NlpB/DapX lipoprotein / Outer membrane protein assembly factor BamD / Outer membrane protein assembly factor BamE / Lipoprotein SmpA/OmlA ...Alpha-D-Glucose-1,6-Bisphosphate; Chain A, domain 4 - #50 / Beta-lactamase Inhibitory Protein; Chain:B, domain 1 / Beta-lactamase Inhibitory Protein; Chain:B, domain 1 - #10 / NlpB/DapX lipoprotein / Outer membrane protein assembly factor BamC / Outer membrane protein assembly factor BamC, C-terminal / NlpB/DapX lipoprotein / Outer membrane protein assembly factor BamD / Outer membrane protein assembly factor BamE / Lipoprotein SmpA/OmlA / Outer membrane lipoprotein BamD-like / SmpA / OmlA family / Outer membrane lipoprotein / BamE-like / 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 / Alpha-D-Glucose-1,6-Bisphosphate; Chain A, domain 4 / Tetratricopeptide repeat domain / Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat / Prokaryotic membrane lipoprotein lipid attachment site profile. / Alpha Horseshoe / Tetratricopeptide-like helical domain superfamily / 2-Layer Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
Outer membrane protein assembly factor BamC / Outer membrane protein assembly factor BamE / Outer membrane protein assembly factor BamA / Outer membrane protein assembly factor BamD
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 3.392 Å
AuthorsBakelar, J. / Buchanan, S.K. / Noinaj, N.
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)1K22AI113078-01 United States
National Institutes of Health/National Institute of Diabetes and Digestive and Kidney Disease (NIH/NIDDK)Intramural Program United States
CitationJournal: Science / Year: 2016
Title: The structure of the beta-barrel assembly machinery complex.
Authors: Bakelar, J. / Buchanan, S.K. / Noinaj, N.
History
DepositionNov 4, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 20, 2016Provider: repository / Type: Initial release
Revision 1.1Sep 27, 2017Group: Author supporting evidence / Derived calculations / Category: pdbx_audit_support / pdbx_struct_oper_list
Item: _pdbx_audit_support.funding_organization / _pdbx_struct_oper_list.symmetry_operation
Revision 1.2Dec 11, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3Sep 27, 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

Downloads & links

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Assembly

Deposited unit
A: Outer membrane protein assembly factor BamA
D: Outer membrane protein assembly factor BamD
C: Outer membrane protein assembly factor BamC
E: Outer membrane protein assembly factor BamE


Theoretical massNumber of molelcules
Total (without water)159,1244
Polymers159,1244
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10070 Å2
ΔGint-55 kcal/mol
Surface area63010 Å2
MethodPISA
Unit cell
Length a, b, c (Å)234.848, 109.231, 103.988
Angle α, β, γ (deg.)90.00, 95.04, 90.00
Int Tables number5
Space group name H-MC121

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Components

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


Mass: 88514.742 Da / Num. of mol.: 1 / Fragment: UNP residues 21-810
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (strain K12) (bacteria)
Strain: K12 / Gene: bamA, yaeT, yzzN, yzzY, b0177, JW0172 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P0A940
#2: Protein Outer membrane protein assembly factor BamD


Mass: 25816.818 Da / Num. of mol.: 1 / Fragment: UNP residues 20-245
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (strain K12) (bacteria)
Strain: K12 / Gene: bamD, yfiO, b2595, JW2577 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P0AC02
#3: Protein Outer membrane protein assembly factor BamC


Mass: 34401.250 Da / Num. of mol.: 1 / Fragment: UNP residues 25-344
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (strain K12) (bacteria)
Strain: K12 / Gene: bamC, dapX, nlpB, b2477, JW2462 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P0A903
#4: Protein Outer membrane protein assembly factor BamE


Mass: 10391.554 Da / Num. of mol.: 1 / Fragment: UNP residues 20-113
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (strain K12) (bacteria)
Strain: K12 / Gene: bamE, smpA, b2617, JW2598 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P0A937

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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: 4.17 Å3/Da / Density % sol: 70.54 %
Crystal growTemperature: 294 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 100 mM Tris-HCl, pH 8.5, 200 mM MgCl2, 10 mM MnCl2, and 8% PEG 4000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å
DetectorType: RAYONIX MX300-HS / Detector: CCD / Date: Aug 19, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 3.392→50 Å / Num. obs: 36099 / % possible obs: 99.6 % / Redundancy: 6.3 % / Biso Wilson estimate: 133.43 Å2 / Rmerge(I) obs: 0.119 / Rpim(I) all: 0.058 / Rrim(I) all: 0.129 / Χ2: 1.596 / Net I/av σ(I): 21.346 / Net I/σ(I): 5.8 / Num. measured all: 226289
Reflection shell

Diffraction-ID: 1 / Rejects: 0

Resolution (Å)Redundancy (%)Num. unique allCC1/2Rpim(I) allΧ2% possible allRmerge(I) obsRrim(I) all
3.392-3.526.435850.4850.8750.95599.9
3.52-3.666.335920.6590.5620.979100
3.66-3.836.435940.8350.3421.04899.90.860.929
3.83-4.036.336210.9190.2361.08699.90.590.638
4.03-4.286.435900.9590.1511.22999.80.3810.411
4.28-4.616.435920.9870.0891.55699.70.2240.241
4.61-5.086.336020.9890.0671.79699.80.1690.183
5.08-5.816.336220.9880.0621.82599.40.1540.166
5.81-7.326.336340.9930.0462.24999.50.1120.122
7.32-505.736670.9960.0283.42698.50.0620.068

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
PHENIX(1.10_2142: ???)refinement
SCALEPACKdata scaling
PDB_EXTRACT3.15data extraction
PHASERphasing
DENZOdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB IDs 3TGO 4C4V 3Q6B 2KM7 3EFC

3tgo

4c4v

3q6b

2km7

3efc


Resolution: 3.392→29.914 Å / SU ML: 0.57 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 34.07 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2811 1994 5.54 %
Rwork0.2382 --
obs0.2405 36000 98.8 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 3.392→29.914 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9451 0 0 0 9451
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0039652
X-RAY DIFFRACTIONf_angle_d0.97313165
X-RAY DIFFRACTIONf_dihedral_angle_d17.1765691
X-RAY DIFFRACTIONf_chiral_restr0.0461459
X-RAY DIFFRACTIONf_plane_restr0.0051753
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.3921-3.47680.4391300.35672206X-RAY DIFFRACTION90
3.4768-3.57070.4291420.32812441X-RAY DIFFRACTION100
3.5707-3.67560.36831450.31832447X-RAY DIFFRACTION100
3.6756-3.7940.35831410.30222432X-RAY DIFFRACTION100
3.794-3.92930.35431430.27842423X-RAY DIFFRACTION100
3.9293-4.08630.31031440.27942461X-RAY DIFFRACTION100
4.0863-4.27170.32881430.26342418X-RAY DIFFRACTION100
4.2717-4.49620.28091420.23562440X-RAY DIFFRACTION100
4.4962-4.77690.25841450.22442457X-RAY DIFFRACTION100
4.7769-5.1440.28651430.2212454X-RAY DIFFRACTION100
5.144-5.65850.28751440.24372435X-RAY DIFFRACTION99
5.6585-6.47010.32241450.25452470X-RAY DIFFRACTION99
6.4701-8.12450.28191430.23552452X-RAY DIFFRACTION99
8.1245-29.91520.20581440.19562470X-RAY DIFFRACTION97

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