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- PDB-9cs1: E. coli BamA beta-barrel bound to darobactin and cyclic peptide CP2 -

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Basic information

Entry
Database: PDB / ID: 9cs1
TitleE. coli BamA beta-barrel bound to darobactin and cyclic peptide CP2
Components
  • Cyclic peptide CP2
  • Darobactin A
  • 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
Darobactin / tetrabutylphosphonium / Outer membrane protein assembly factor BamA
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
synthetic construct (others)
Photorhabdus khanii (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.147 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

Downloads & links

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Assembly

Deposited unit
A: Outer membrane protein assembly factor BamA
C: Cyclic peptide CP2
D: Darobactin A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,8505
Polymers46,3313
Non-polymers5192
Water1,22568
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3010 Å2
ΔGint-9 kcal/mol
Surface area18050 Å2
MethodPISA
Unit cell
Length a, b, c (Å)58.602, 82.625, 127.889
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

21A-1023-

HOH

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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 (E. coli) / Gene: bamA / Production host: Escherichia coli (E. coli) / References: UniProt: A7ZHR7
#2: Protein/peptide Cyclic peptide CP2


Mass: 1817.448 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#3: Protein/peptide Darobactin A


Type: Peptide-like / Class: Antibiotic / Mass: 971.047 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Photorhabdus khanii (bacteria) / References: Darobactin
#4: Chemical ChemComp-4NE / tetrabutylphosphonium


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


Mass: 18.015 Da / Num. of mol.: 68 / 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: 3.28 Å3/Da / Density % sol: 62.49 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop
Details: 6% v/v Tacsimate pH 6, 0.1 M MES pH 6, 2.5% w/v tetrabutylphosphonium bromide (TBPB), 7-10% w/v PEG 4000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: CLSI / Beamline: 08ID-1 / Wavelength: 1.18081 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: May 27, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.18081 Å / Relative weight: 1
ReflectionResolution: 2.147→82.625 Å / Num. obs: 28817 / % possible obs: 83 % / Redundancy: 8 % / CC1/2: 1 / Rmerge(I) obs: 0.044 / Rpim(I) all: 0.017 / Net I/σ(I): 24.6
Reflection shellResolution: 2.147→2.286 Å / Redundancy: 7.7 % / Rmerge(I) obs: 2.165 / Num. unique obs: 1442 / CC1/2: 0.521 / Rpim(I) all: 0.819 / Rrim(I) all: 2.32 / % possible all: 24.5

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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: 2.147→26.64 Å / Cor.coef. Fo:Fc: 0.916 / Cor.coef. Fo:Fc free: 0.906 / SU R Cruickshank DPI: 0.247 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.245 / SU Rfree Blow DPI: 0.196 / SU Rfree Cruickshank DPI: 0.199
RfactorNum. reflection% reflectionSelection details
Rfree0.2638 1470 5.11 %RANDOM
Rwork0.2461 ---
obs0.247 28791 83 %-
Displacement parametersBiso mean: 58.85 Å2
Baniso -1Baniso -2Baniso -3
1-2.0241 Å20 Å20 Å2
2--1.4557 Å20 Å2
3----3.4798 Å2
Refine analyzeLuzzati coordinate error obs: 0.33 Å
Refinement stepCycle: 1 / Resolution: 2.147→26.64 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2995 0 65 68 3128
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.0093177HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.094313HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d1022SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes
X-RAY DIFFRACTIONt_gen_planes551HARMONIC5
X-RAY DIFFRACTIONt_it3177HARMONIC10
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_omega_torsion3.98
X-RAY DIFFRACTIONt_other_torsion18.44
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion379SEMIHARMONIC5
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_contact2530SEMIHARMONIC4
LS refinement shellResolution: 2.15→2.23 Å / Total num. of bins used: 51
RfactorNum. reflection% reflection
Rfree0.3623 -3.65 %
Rwork0.2973 555 -
all0.2999 576 -
obs--16.29 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.84690.1852-0.14220.57770.33341.9895-0.0995-0.11940.04310.02340.03950.01010.54780.11480.060.06320.0240.0216-0.05840.0413-0.0792-27.0177-19.9685-13.2845
20.5204-0.27031.92462.8447-1.47750.722-0.250.0267-0.0809-0.32570.18010.17750.32810.02910.0699-0.0049-0.02870.01510.03330.03020.02-34.0949-14.2109-8.769
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1{ A|* }
2X-RAY DIFFRACTION2{ C|* }

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