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- PDB-6qgy: Crystal structure of E.coli BamA beta-barrel in complex with nano... -

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Basic information

Entry
Database: PDB / ID: 6qgy
TitleCrystal structure of E.coli BamA beta-barrel in complex with nanobody B12
Components
  • NanoB12
  • Outer membrane protein assembly factor BamA
KeywordsMEMBRANE PROTEIN / Beta-Barrel / outer membrane / protein insertion / protein folding / protein maturation
Function / homology
Function and homology information


Bam protein complex / Gram-negative-bacterium-type cell outer membrane assembly / protein insertion into membrane
Similarity search - Function
membrane protein fhac: a member of the omp85/tpsb transporter family / 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 / Porin ...membrane protein fhac: a member of the omp85/tpsb transporter family / 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 / Porin / Beta Barrel / Mainly Beta
Similarity search - Domain/homology
Outer membrane protein assembly factor BamA
Similarity search - Component
Biological speciesEscherichia coli O157:H7 (bacteria)
Lama glama (llama)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.509 Å
AuthorsHartmann, J.-B. / Kaur, H. / Jakob, R.P. / Zahn, M. / Zimmermann, I. / Seeger, M. / Maier, T. / Hiller, S.
CitationJournal: J.Biomol.Nmr / Year: 2019
Title: Identification of conformation-selective nanobodies against the membrane protein insertase BamA by an integrated structural biology approach.
Authors: Kaur, H. / Hartmann, J.B. / Jakob, R.P. / Zahn, M. / Zimmermann, I. / Maier, T. / Seeger, M.A. / Hiller, S.
History
DepositionJan 14, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 26, 2019Provider: repository / Type: Initial release
Revision 1.1Aug 21, 2019Group: Data collection / Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.2Jan 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
Revision 1.3Nov 20, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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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: NanoB12
C: Outer membrane protein assembly factor BamA
D: NanoB12
hetero molecules


Theoretical massNumber of molelcules
Total (without water)122,38414
Polymers119,3204
Non-polymers3,06410
Water5,711317
1
A: Outer membrane protein assembly factor BamA
B: NanoB12
hetero molecules


Theoretical massNumber of molelcules
Total (without water)61,1927
Polymers59,6602
Non-polymers1,5325
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
C: Outer membrane protein assembly factor BamA
D: NanoB12
hetero molecules


Theoretical massNumber of molelcules
Total (without water)61,1927
Polymers59,6602
Non-polymers1,5325
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)99.709, 86.664, 125.027
Angle α, β, γ (deg.)90.00, 105.26, 90.00
Int Tables number3
Space group name H-MP121
Components on special symmetry positions
IDModelComponents
11D-207-

HOH

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Components

#1: Protein Outer membrane protein assembly factor BamA


Mass: 46022.789 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli O157:H7 (bacteria) / Gene: bamA, yaeT, Z0188, ECs0179 / Plasmid: pET15a / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P0A942
#2: Antibody NanoB12


Mass: 13637.087 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Lama glama (llama) / Production host: Escherichia coli BL21(DE3) (bacteria)
#3: Chemical
ChemComp-C8E / (HYDROXYETHYLOXY)TRI(ETHYLOXY)OCTANE


Mass: 306.438 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: C16H34O5 / Comment: C8E, detergent*YM
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 317 / Source method: isolated from a natural source / Formula: H2O
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: 4.37 Å3/Da / Density % sol: 71.84 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 32% PEG 400, 0.2 M ammonium phosphate, 0.1 M ammonium sulfate, 0.1 M sodium citrate pH 4.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 0.99998 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Feb 2, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.99998 Å / Relative weight: 1
ReflectionResolution: 2.509→48.484 Å / Num. obs: 69491 / % possible obs: 98.5 % / Redundancy: 5.8 % / CC1/2: 0.998 / Rmerge(I) obs: 0.073 / Rpim(I) all: 0.051 / Net I/σ(I): 11.9
Reflection shellResolution: 2.51→2.57 Å / Redundancy: 5.3 % / Rmerge(I) obs: 0.973 / Mean I/σ(I) obs: 1.2 / Num. unique obs: 3901 / CC1/2: 0.621 / Rpim(I) all: 0.699 / % possible all: 86.3

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Processing

Software
NameVersionClassification
PHENIX(1.13_2998: ???)refinement
XDSdata reduction
Aimlessdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4n75

4n75


Resolution: 2.509→48.484 Å / SU ML: 0.38 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 28.64
RfactorNum. reflection% reflection
Rfree0.2442 3566 5.13 %
Rwork0.2224 --
obs0.2235 69491 98.38 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.509→48.484 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7729 0 107 337 8173
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0048050
X-RAY DIFFRACTIONf_angle_d0.59110899
X-RAY DIFFRACTIONf_dihedral_angle_d14.7924597
X-RAY DIFFRACTIONf_chiral_restr0.0461089
X-RAY DIFFRACTIONf_plane_restr0.0031418
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.5086-2.5430.38471190.3452108X-RAY DIFFRACTION78
2.543-2.57930.36261210.3292637X-RAY DIFFRACTION100
2.5793-2.61780.35521450.30562677X-RAY DIFFRACTION100
2.6178-2.65870.31971590.28492599X-RAY DIFFRACTION100
2.6587-2.70230.31181470.28872716X-RAY DIFFRACTION100
2.7023-2.74890.36681240.27792637X-RAY DIFFRACTION100
2.7489-2.79890.31011600.27152645X-RAY DIFFRACTION100
2.7989-2.85270.31431410.27612675X-RAY DIFFRACTION100
2.8527-2.9110.31171340.28092650X-RAY DIFFRACTION99
2.911-2.97420.31241550.28432659X-RAY DIFFRACTION100
2.9742-3.04340.31661570.30262606X-RAY DIFFRACTION99
3.0434-3.11950.35581450.29352677X-RAY DIFFRACTION99
3.1195-3.20380.28651440.25762688X-RAY DIFFRACTION100
3.2038-3.29810.2691270.24042624X-RAY DIFFRACTION99
3.2981-3.40450.24491390.24092659X-RAY DIFFRACTION99
3.4045-3.52620.25111330.23342651X-RAY DIFFRACTION99
3.5262-3.66730.25321460.21982550X-RAY DIFFRACTION96
3.6673-3.83410.23481610.20742639X-RAY DIFFRACTION99
3.8341-4.03620.231340.20172674X-RAY DIFFRACTION99
4.0362-4.28890.21241560.19072670X-RAY DIFFRACTION99
4.2889-4.61980.19381410.16682676X-RAY DIFFRACTION99
4.6198-5.08430.18611540.1742696X-RAY DIFFRACTION100
5.0843-5.8190.21281500.19662666X-RAY DIFFRACTION99
5.819-7.32720.21151460.21472646X-RAY DIFFRACTION97
7.3272-48.49270.25491280.23032800X-RAY DIFFRACTION100

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