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- PDB-9cs2: E. coli BamA beta-barrel bound to cyclic peptide CP3 -

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Basic information

Entry
Database: PDB / ID: 9cs2
TitleE. coli BamA beta-barrel bound to cyclic peptide CP3
Components
  • Cyclic peptide CP3
  • Outer membrane protein assembly factor BamA
KeywordsMEMBRANE PROTEIN / 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
Similarity search - Function
Outer membrane protein assembly factor BamA / POTRA domain, BamA/TamA-like / Surface antigen variable number repeat / Surface antigen D15-like / POTRA domain / POTRA domain profile. / Bacterial surface antigen (D15) / Omp85 superfamily domain
Similarity search - Domain/homology
tetrabutylphosphonium / Outer membrane protein assembly factor BamA
Similarity search - Component
Biological speciesEscherichia coli O139:H28 (bacteria)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.784 Å
AuthorsWalker, M.E. / Gu, M. / Lu, J. / Klein, D.J.
Funding support United States, 1items
OrganizationGrant numberCountry
Other private United States
CitationJournal: Nat Commun / Year: 2025
Title: Antibacterial macrocyclic peptides reveal a distinct mode of BamA inhibition.
Authors: Walker, M.E. / Zhu, W. / Peterson, J.H. / Wang, H. / Patteson, J. / Soriano, A. / Zhang, H. / Mayhood, T. / Hou, Y. / Mesbahi-Vasey, S. / Gu, M. / Frost, J. / Lu, J. / Johnston, J. / ...Authors: Walker, M.E. / Zhu, W. / Peterson, J.H. / Wang, H. / Patteson, J. / Soriano, A. / Zhang, H. / Mayhood, T. / Hou, Y. / Mesbahi-Vasey, S. / Gu, M. / Frost, J. / Lu, J. / Johnston, J. / Hipolito, C. / Lin, S. / Painter, R.E. / Klein, D. / Walji, A. / Weinglass, A. / Kelly, T.M. / Saldanha, A. / Schubert, J. / Bernstein, H.D. / Walker, S.S.
History
DepositionJul 23, 2024Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 16, 2025Provider: repository / Type: Initial release
Revision 1.1Apr 23, 2025Group: Database references / Category: citation
Item: _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title

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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: Cyclic peptide CP3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,2134
Polymers45,6942
Non-polymers5192
Water4,125229
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)58.084, 78.987, 124.979
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number17
Space group name H-MP2221
Components on special symmetry positions
IDModelComponents
11A-902-

4NE

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Components

#1: Protein Outer membrane protein assembly factor BamA


Mass: 43542.238 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli O139:H28 (strain E24377A / ETEC) (bacteria)
Strain: E24377A / ETEC / Gene: bamA, yaeT, EcE24377A_0181 / Production host: Escherichia coli (E. coli) / References: UniProt: A7ZHR7
#2: Protein/peptide Cyclic peptide CP3


Mass: 2151.857 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#3: Chemical ChemComp-4NE / tetrabutylphosphonium


Mass: 259.431 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C16H36P
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 229 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
Has protein modificationY

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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: 3.14 Å3/Da / Density % sol: 60.79 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / Details: 2.5% w/v TBPB, 0.2 M sodium formate, 20% PEG3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 1.0001 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Sep 11, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0001 Å / Relative weight: 1
ReflectionResolution: 1.784→78.987 Å / Num. obs: 45901 / % possible obs: 82.6 % / Redundancy: 5 % / CC1/2: 0.999 / Rmerge(I) obs: 0.061 / Rpim(I) all: 0.03 / Rrim(I) all: 0.068 / Net I/σ(I): 12.4
Reflection shellResolution: 1.784→1.898 Å / Redundancy: 3.7 % / Rmerge(I) obs: 0.857 / Mean I/σ(I) obs: 1.4 / Num. unique obs: 2295 / CC1/2: 0.511 / Rpim(I) all: 0.505 / Rrim(I) all: 1 / % possible all: 24.7

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Processing

Software
NameVersionClassification
BUSTER2.11.8 (22-FEB-2023)refinement
autoPROCdata reduction
autoPROCdata scaling
DIMPLEphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.784→25.98 Å / Cor.coef. Fo:Fc: 0.935 / Cor.coef. Fo:Fc free: 0.922 / SU R Cruickshank DPI: 0.137 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.141 / SU Rfree Blow DPI: 0.132 / SU Rfree Cruickshank DPI: 0.13
RfactorNum. reflection% reflectionSelection details
Rfree0.2466 2256 4.92 %RANDOM
Rwork0.2156 ---
obs0.2171 45873 82.6 %-
Displacement parametersBiso mean: 37.3 Å2
Baniso -1Baniso -2Baniso -3
1-0.3133 Å20 Å20 Å2
2---0.3583 Å20 Å2
3---0.0449 Å2
Refine analyzeLuzzati coordinate error obs: 0.28 Å
Refinement stepCycle: LAST / Resolution: 1.784→25.98 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3188 0 62 231 3481
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.0093441HARMONIC2
X-RAY DIFFRACTIONt_angle_deg0.974697HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d1154SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes
X-RAY DIFFRACTIONt_gen_planes619HARMONIC5
X-RAY DIFFRACTIONt_it3441HARMONIC10
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_omega_torsion3.87
X-RAY DIFFRACTIONt_other_torsion16.92
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion413SEMIHARMONIC5
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_contact2931SEMIHARMONIC4
LS refinement shellResolution: 1.784→1.86 Å
RfactorNum. reflection% reflection
Rfree0.3251 -4.9 %
Rwork0.27 873 -
obs--14.67 %
Refinement TLS params.Method: refined / Origin x: -3.9467 Å / Origin y: -18.73 Å / Origin z: -12.1917 Å
111213212223313233
T0.0014 Å2-0.0425 Å20.011 Å2--0.0055 Å2-0.0012 Å2---0.0272 Å2
L0.7242 °20.172 °2-0.2539 °2-0.4049 °2-0.5315 °2--1.2995 °2
S0.0968 Å °-0.2322 Å °-0.064 Å °0.069 Å °-0.0661 Å °-0.0147 Å °-0.281 Å °-0.0128 Å °-0.0306 Å °
Refinement TLS groupSelection details: { A|* }

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