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- PDB-7p1c: Crystal structure of E.coli BamA beta-barrel in complex with daro... -

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Basic information

Entry
Database: PDB / ID: 7p1c
TitleCrystal structure of E.coli BamA beta-barrel in complex with darobactin B
Components
  • Outer membrane protein assembly factor BamA
  • TRP-ASN-UX8-THR-LYS-ARG-PHE
KeywordsMEMBRANE PROTEIN / Beta-Barrel / outer membrane / protein insertion / protein folding / protein maturation / antibiotic / natural product / cyclized peptide
Function / homology
Function and homology information


Gram-negative-bacterium-type cell outer membrane assembly / protein insertion into membrane / cell outer membrane
Similarity search - Function
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
Similarity search - Domain/homology
: / Outer membrane protein assembly factor BamA
Similarity search - Component
Biological speciesEscherichia coli O157:H7 (bacteria)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å
AuthorsJakob, R.P. / Modaresi, S.M. / Hiller, S. / Maier, T.
CitationJournal: Microbiol Spectr / Year: 2021
Title: Mutasynthetic Production and Antimicrobial Characterization of Darobactin Analogs.
Authors: Bohringer, N. / Green, R. / Liu, Y. / Mettal, U. / Marner, M. / Modaresi, S.M. / Jakob, R.P. / Wuisan, Z.G. / Maier, T. / Iinishi, A. / Hiller, S. / Lewis, K. / Schaberle, T.F.
History
DepositionJul 1, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 6, 2022Provider: repository / Type: Initial release
Revision 1.1Jan 31, 2024Group: Data collection / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model / struct_conn
Item: _struct_conn.pdbx_leaving_atom_flag

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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: TRP-ASN-UX8-THR-LYS-ARG-PHE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,0069
Polymers44,8612
Non-polymers2,1457
Water1,54986
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)81.560, 80.372, 89.247
Angle α, β, γ (deg.)90.000, 107.940, 90.000
Int Tables number5
Space group name H-MI121

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Components

#1: Protein Outer membrane protein assembly factor BamA


Mass: 43805.457 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli O157:H7 (bacteria) / Gene: bamA, yaeT, Z0188, ECs0179 / Plasmid: pET15b / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P0A942
#2: Protein/peptide TRP-ASN-UX8-THR-LYS-ARG-PHE


Type: Peptide-like / Mass: 1055.189 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) / References: BIRD: PRD_002342
#3: Chemical
ChemComp-C8E / (HYDROXYETHYLOXY)TRI(ETHYLOXY)OCTANE


Mass: 306.438 Da / Num. of mol.: 7
Source method: isolated from a genetically manipulated source
Formula: C16H34O5 / Comment: C8E, detergent*YM
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 86 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 3.39 Å3/Da / Density % sol: 63.69 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 0.2M Calcium chloride dihydrate, 0.1M HEPES 7.5, 53% v/v PEG 400

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 1.00002 Å
DetectorType: DECTRIS PILATUS 2M-F / Detector: PIXEL / Date: Nov 23, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.00002 Å / Relative weight: 1
ReflectionResolution: 2.5→50.107 Å / Num. obs: 19080 / % possible obs: 99.86 % / Redundancy: 13.1 % / CC1/2: 0.998 / Rmerge(I) obs: 0.278 / Rpim(I) all: 0.113 / Net I/σ(I): 7.5
Reflection shellResolution: 2.5→2.59 Å / Redundancy: 13 % / Rmerge(I) obs: 2.952 / Mean I/σ(I) obs: 1.5 / Num. unique obs: 1887 / CC1/2: 0.789 / Rpim(I) all: 0.851 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX1.13_2998refinement
PDB_EXTRACT3.27data extraction
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 7NRF

7nrf


Resolution: 2.5→50.107 Å / SU ML: 0.29 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 26.31 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2494 921 4.83 %
Rwork0.2327 18138 -
obs0.2335 19059 99.86 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 240.98 Å2 / Biso mean: 64.4812 Å2 / Biso min: 23.5 Å2
Refinement stepCycle: final / Resolution: 2.5→50.107 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2909 0 379 90 3378
Biso mean--97 49.08 -
Num. residues----368
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork
2.5-2.63180.31941350.28972548
2.6318-2.79670.30021260.2732623
2.7967-3.01260.27921270.25792558
3.0126-3.31570.25021360.22572574
3.3157-3.79540.27771260.22062609
3.7954-4.78120.21711260.21342596
4.7812-50.1070.23451450.22852630
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)
10.7686-0.50370.44140.63-0.75831.0605-0.54530.18640.668-0.47290.266-0.425-0.07830.1043-0.01120.6319-0.0904-0.01030.3086-0.0160.533236.3636-1.78563.5457
20.45280.3067-0.32440.2395-0.01890.7867-0.1044-0.17110.7563-0.03110.1877-0.3462-0.65940.1490.07660.6030.04180.01670.1680.03680.505221.8710.8373-2.4549
31.37940.4927-0.26950.1596-0.01940.622-0.11630.35540.2945-0.41470.107-0.3761-0.4692-0.03170.00060.43870.0368-0.01860.3783-0.0190.366221.3138-12.06960.8665
41.88220.17520.77310.4217-0.47140.93870.0750.197-0.2108-0.11940.0189-0.21460.2073-0.06630.00010.328-00.01660.3033-0.05410.302722.3109-21.04694.5006
50.7920.50420.37930.53270.65890.8469-0.0253-0.1597-0.1132-0.0017-0.10530.04320.0001-0.2849-0.00040.2851-0.0171-0.00380.3539-0.03780.282721.3775-17.04214.7442
61.0621-0.4006-0.04470.41330.30382.14620.0923-0.2664-0.24780.32960.0465-0.15390.2658-0.04480.00510.2838-0.00960.00570.29460.00390.312230.9704-18.781121.1235
72.83180.9353-0.4330.89030.190.9426-0.1274-0.198-0.5277-0.60880.1798-0.32790.12580.3584-0.19980.53440.0364-0.06890.4149-0.06280.311136.205-17.199319.6759
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 424 through 446 )A424 - 446
2X-RAY DIFFRACTION2chain 'A' and (resid 447 through 483 )A447 - 483
3X-RAY DIFFRACTION3chain 'A' and (resid 484 through 537 )A484 - 537
4X-RAY DIFFRACTION4chain 'A' and (resid 538 through 589 )A538 - 589
5X-RAY DIFFRACTION5chain 'A' and (resid 590 through 675 )A590 - 675
6X-RAY DIFFRACTION6chain 'A' and (resid 676 through 789 )A676 - 789
7X-RAY DIFFRACTION7chain 'A' and (resid 790 through 810 )A790 - 810

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