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

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Basic information

Entry
Database: PDB / ID: 6qgx
TitleCrystal structure of E.coli BamA beta-barrel in complex with nanobody F7
Components
  • NanoF7
  • 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 / POTRA domain / POTRA domain profile. / Surface antigen D15-like / 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 / POTRA domain / POTRA domain profile. / Surface antigen D15-like / 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: 2.2 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

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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
B: NanoF7
hetero molecules


Theoretical massNumber of molelcules
Total (without water)63,09413
Polymers59,7232
Non-polymers3,37111
Water2,576143
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4930 Å2
ΔGint45 kcal/mol
Surface area24480 Å2
MethodPISA
Unit cell
Length a, b, c (Å)49.321, 80.335, 135.349
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Outer membrane protein assembly factor BamA


Mass: 46022.789 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 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P0A942
#2: Antibody NanoF7


Mass: 13700.338 Da / Num. of mol.: 1
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.: 11 / Source method: obtained synthetically / Formula: C16H34O5 / Comment: C8E, detergent*YM
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 143 / Source method: isolated from a natural source / Formula: H2O

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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: 2.24 Å3/Da / Density % sol: 45.21 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / Details: 33% PEG 400, 0.23 M NaCl, 0.05 M sodium acetate

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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: 2.2→49.34 Å / Num. obs: 27754 / % possible obs: 99.3 % / Redundancy: 6 % / CC1/2: 0.992 / Rmerge(I) obs: 0.104 / Rpim(I) all: 0.062 / Net I/σ(I): 10.4
Reflection shellResolution: 2.2→2.27 Å / Redundancy: 5.5 % / Rmerge(I) obs: 0.572 / Mean I/σ(I) obs: 1.8 / Num. unique obs: 2725 / CC1/2: 0.826 / Rpim(I) all: 0.374 / % possible all: 99.5

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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: 2.2→46.34 Å / SU ML: 0.3 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 30.18
RfactorNum. reflection% reflection
Rfree0.2659 1491 5.37 %
Rwork0.2289 --
obs0.2309 27754 98.78 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.2→46.34 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3877 0 101 146 4124
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0044078
X-RAY DIFFRACTIONf_angle_d0.5875500
X-RAY DIFFRACTIONf_dihedral_angle_d15.2492342
X-RAY DIFFRACTIONf_chiral_restr0.046552
X-RAY DIFFRACTIONf_plane_restr0.003710
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.2-2.2710.35241270.29722369X-RAY DIFFRACTION99
2.271-2.35220.31581460.28212362X-RAY DIFFRACTION99
2.3522-2.44640.31761580.27012335X-RAY DIFFRACTION100
2.4464-2.55770.30051170.26832358X-RAY DIFFRACTION100
2.5577-2.69250.3251270.26892403X-RAY DIFFRACTION99
2.6925-2.86120.30361230.26792366X-RAY DIFFRACTION99
2.8612-3.08210.30791430.25952379X-RAY DIFFRACTION99
3.0821-3.39210.26011360.23762361X-RAY DIFFRACTION99
3.3921-3.88280.27641440.2162393X-RAY DIFFRACTION99
3.8828-4.8910.22511320.17982432X-RAY DIFFRACTION98
4.891-46.35050.24171380.23082505X-RAY DIFFRACTION97
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)
14.5564-1.42473.14270.8177-0.983.4087-0.4051-0.6778-0.04721.18590.3088-0.40230.0119-0.05740.03281.07170.1113-0.00570.61490.06590.803215.274-4.009438.8363
20.78521.04361.45131.9041.81253.28720.08430.1058-0.35730.28220.3206-0.40840.38430.5146-0.4080.42150.0719-0.0550.5947-0.05930.655726.04642.958625.2989
34.9682-1.6551-3.06572.62972.64044.8721-0.1749-0.1737-0.2216-0.05960.2923-0.19510.110.5986-0.12830.3413-0.057-0.05610.37650.00680.399218.555719.079532.5406
43.3643-1.4429-0.74823.09112.26793.7304-0.13020.139-0.0349-0.43750.2195-0.3282-0.24940.2267-0.07420.5303-0.10490.02710.46740.04930.52516.668210.032110.8473
59.2181-1.1188-3.15315.07151.2334.3659-0.3132-1.1621-0.32870.8239-0.43991.0316-0.4672-0.38370.61270.4366-0.0243-0.0980.59030.02210.62840.615621.332138.2323
63.94850.239-2.97562.59250.80145.9307-0.0080.03920.1756-0.2514-0.00470.1225-0.1055-0.0621-0.00670.41420.0076-0.10730.3636-0.0340.48516.954516.376221.0029
71.00510.29960.4513.57340.78371.12260.0291-0.16180.28330.33930.13940.81640.082-0.797-0.03660.6685-0.1182-0.12880.824-0.08860.8071-5.6853-12.68290.8984
83.0382-0.25740.31096.44254.13722.65-0.3783-0.59080.5487-0.2548-0.46140.8657-0.0856-0.91820.96360.4629-0.042-0.04650.6606-0.09550.6489-5.2805-4.88373.7075
95.95230.1851-0.68914.50312.30815.251-0.26530.2603-0.2744-0.16470.2097-0.38340.36940.18310.10540.6031-0.04490.01050.5580.03050.36466.8417-4.5761-3.4598
103.31520.37151.08556.2794-4.7758.61820.2397-0.82980.43050.81980.32110.2835-0.9073-1.8891-0.55390.67480.0663-0.02640.884-0.08320.6068-5.26651.77733.0188
112.51060.48932.31584.34882.25733.019-0.0003-0.0783-0.0742-0.1764-0.1048-0.089-0.0849-0.15310.12240.4908-0.050.02980.5194-0.01580.42154.2812-7.6618-0.5573
124.8736-0.1454-2.12046.51640.84339.1902-0.2597-0.115-0.7064-1.0606-0.0642-0.15150.29640.24010.22650.9358-0.0249-0.07840.6508-0.09080.9001-0.9122-14.6532-13.4851
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 426 through 453 )
2X-RAY DIFFRACTION2chain 'A' and (resid 454 through 581 )
3X-RAY DIFFRACTION3chain 'A' and (resid 582 through 640 )
4X-RAY DIFFRACTION4chain 'A' and (resid 641 through 709 )
5X-RAY DIFFRACTION5chain 'A' and (resid 710 through 732 )
6X-RAY DIFFRACTION6chain 'A' and (resid 733 through 810 )
7X-RAY DIFFRACTION7chain 'B' and (resid -1 through 14 )
8X-RAY DIFFRACTION8chain 'B' and (resid 15 through 33 )
9X-RAY DIFFRACTION9chain 'B' and (resid 34 through 69 )
10X-RAY DIFFRACTION10chain 'B' and (resid 70 through 78 )
11X-RAY DIFFRACTION11chain 'B' and (resid 79 through 117 )
12X-RAY DIFFRACTION12chain 'B' and (resid 118 through 124 )

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