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- PDB-4pk1: Structure of BamB fused to a BamA POTRA domain fragment -

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Basic information

Entry
Database: PDB / ID: 4pk1
TitleStructure of BamB fused to a BamA POTRA domain fragment
ComponentsChimera protein of Outer membrane protein assembly factors BamA and BamB
KeywordsPROTEIN BINDING / BAM complex / fusion
Function / homology
Function and homology information


Bam protein complex / Gram-negative-bacterium-type cell outer membrane assembly / protein insertion into membrane / cell outer membrane / cell adhesion / identical protein binding / membrane
Similarity search - Function
membrane protein fhac / PQQ enzyme repeat / Outer membrane protein assembly factor BamB / Outer membrane protein assembly factor BamA / Pyrrolo-quinoline quinone repeat / PQQ-like domain / POTRA domain, BamA/TamA-like / Surface antigen variable number repeat / POTRA domain / POTRA domain profile. ...membrane protein fhac / PQQ enzyme repeat / Outer membrane protein assembly factor BamB / Outer membrane protein assembly factor BamA / Pyrrolo-quinoline quinone repeat / PQQ-like domain / POTRA domain, BamA/TamA-like / Surface antigen variable number repeat / POTRA domain / POTRA domain profile. / Pyrrolo-quinoline quinone beta-propeller repeat / beta-propeller repeat / Surface antigen D15-like / Bacterial surface antigen (D15) / Omp85 superfamily domain / Quinoprotein alcohol dehydrogenase-like superfamily / Ubiquitin-like (UB roll) / Prokaryotic membrane lipoprotein lipid attachment site profile. / WD40/YVTN repeat-like-containing domain superfamily / Roll / Alpha Beta
Similarity search - Domain/homology
Outer membrane protein assembly factor BamA / Outer membrane protein assembly factor BamB
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 3.1 Å
AuthorsJansen, K.B. / Sousa, M.C.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)R01 AI080709 United States
CitationJournal: J.Biol.Chem. / Year: 2015
Title: Crystal Structure of BamB Bound to a Periplasmic Domain Fragment of BamA, the Central Component of the beta-Barrel Assembly Machine.
Authors: Jansen, K.B. / Baker, S.L. / Sousa, M.C.
History
DepositionMay 13, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 10, 2014Provider: repository / Type: Initial release
Revision 1.1Dec 17, 2014Group: Database references
Revision 1.2Feb 4, 2015Group: Database references
Revision 1.3Sep 27, 2017Group: Author supporting evidence / Database references ...Author supporting evidence / Database references / Derived calculations / Source and taxonomy
Category: citation / entity_src_gen ...citation / entity_src_gen / pdbx_audit_support / pdbx_struct_assembly / pdbx_struct_oper_list
Item: _citation.journal_id_CSD / _entity_src_gen.pdbx_alt_source_flag ..._citation.journal_id_CSD / _entity_src_gen.pdbx_alt_source_flag / _pdbx_audit_support.funding_organization / _pdbx_struct_assembly.oligomeric_details / _pdbx_struct_oper_list.symmetry_operation
Revision 1.4Dec 11, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.5Dec 27, 2023Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Chimera protein of Outer membrane protein assembly factors BamA and BamB


Theoretical massNumber of molelcules
Total (without water)70,0381
Polymers70,0381
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)49.270, 91.410, 61.210
Angle α, β, γ (deg.)90.00, 92.85, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Chimera protein of Outer membrane protein assembly factors BamA and BamB / Omp85


Mass: 70037.844 Da / Num. of mol.: 1
Fragment: UNP P0A940 residues 175-424,UNP P77774 residues 21-392
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Strain: K12
Gene: bamA, yaeT, yzzN, yzzY, b0177, JW0172, bamB, yfgL, b2512, JW2496
Production host: Escherichia coli (E. coli) / References: UniProt: P0A940, UniProt: P77774

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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: 1.91 Å3/Da / Density % sol: 35.44 %
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop
Details: The BamA-BamB chimera protein was crystallized at 16 degC by sitting drop vapor diffusion method. Initial crystallizing conditions were refined in a hanging drop in the following solution: 1. ...Details: The BamA-BamB chimera protein was crystallized at 16 degC by sitting drop vapor diffusion method. Initial crystallizing conditions were refined in a hanging drop in the following solution: 1.4M Ammonium sulfate, 9% 2-propanol, and 0.1M Sodium acetate pH 5.5. We used 1.5 uL of the 20mg/ml protein mixed with 1.5 uL mother liquor in a reservoir filled with 500 uL precipitant solution

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Aug 6, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 3.1→19.9 Å / Num. obs: 9870 / % possible obs: 99.9 % / Redundancy: 3.7 % / Biso Wilson estimate: 68.7 Å2 / Net I/σ(I): 11
Reflection shellResolution: 3.1→3.15 Å / Redundancy: 3.6 % / Mean I/σ(I) obs: 1.9 / Num. unique all: 484 / % possible all: 100

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Processing

SoftwareName: PHENIX / Version: (phenix.refine: 1.9_1692) / Classification: refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.1→19.89 Å / Cross valid method: FREE R-VALUE
RfactorNum. reflection% reflection
Rfree0.281 517 5.29 %
Rwork0.251 --
obs-9778 98.9 %
Displacement parametersBiso mean: 87.84 Å2
Refinement stepCycle: LAST / Resolution: 3.1→19.89 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3762 0 0 0 3762
LS refinement shellResolution: 3.1→3.41 Å
RfactorNum. reflection% reflection
Rfree0.3797 112 -
Rwork0.2961 2243 -
obs--96 %

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