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- PDB-5ayw: Structure of a membrane complex -

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Basic information

Entry
Database: PDB / ID: 5ayw
TitleStructure of a membrane complex
Components
  • Outer membrane protein assembly factor BamA
  • Outer membrane protein assembly factor BamB
  • Outer membrane protein assembly factor BamC
  • Outer membrane protein assembly factor BamD
  • Outer membrane protein assembly factor BamE
KeywordsMEMBRANE PROTEIN / complex / membrane biogenesis
Function / homology
Function and homology information


Bam protein complex / Gram-negative-bacterium-type cell outer membrane assembly / protein insertion into membrane / cell outer membrane / protein-macromolecule adaptor activity / cell adhesion / response to antibiotic / cell surface / identical protein binding / membrane
Similarity search - Function
membrane protein fhac: a member of the omp85/tpsb transporter family / Beta-lactamase Inhibitory Protein; Chain:B, domain 1 / Beta-lactamase Inhibitory Protein; Chain:B, domain 1 - #10 / membrane protein fhac / PQQ enzyme repeat / Outer membrane protein assembly factor BamB / NlpB/DapX lipoprotein / Outer membrane protein assembly factor BamC / Outer membrane protein assembly factor BamC, C-terminal / NlpB/DapX lipoprotein ...membrane protein fhac: a member of the omp85/tpsb transporter family / Beta-lactamase Inhibitory Protein; Chain:B, domain 1 / Beta-lactamase Inhibitory Protein; Chain:B, domain 1 - #10 / membrane protein fhac / PQQ enzyme repeat / Outer membrane protein assembly factor BamB / NlpB/DapX lipoprotein / Outer membrane protein assembly factor BamC / Outer membrane protein assembly factor BamC, C-terminal / NlpB/DapX lipoprotein / Outer membrane protein assembly factor BamD / Outer membrane protein assembly factor BamE / Lipoprotein SmpA/OmlA / Outer membrane lipoprotein BamD-like / SmpA / OmlA family / Outer membrane lipoprotein / BamE-like / 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 / Porin / Tetratricopeptide repeat domain / Quinoprotein alcohol dehydrogenase-like superfamily / Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat / Ubiquitin-like (UB roll) / Prokaryotic membrane lipoprotein lipid attachment site profile. / Alpha Horseshoe / Tetratricopeptide-like helical domain superfamily / WD40/YVTN repeat-like-containing domain superfamily / Roll / Beta Barrel / 2-Layer Sandwich / Mainly Beta / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
Outer membrane protein assembly factor BamC / Outer membrane protein assembly factor BamE / Outer membrane protein assembly factor BamA / Outer membrane protein assembly factor BamD / Outer membrane protein assembly factor BamB
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.555 Å
AuthorsHuang, Y. / Han, L. / Zheng, J.
CitationJournal: Nat.Struct.Mol.Biol. / Year: 2016
Title: Structure of the BAM complex and its implications for biogenesis of outer-membrane proteins
Authors: Han, L. / Zheng, J. / Wang, Y. / Yang, X. / Liu, Y. / Sun, C. / Cao, B. / Zhou, H. / Ni, D. / Lou, J. / Zhao, Y. / Huang, Y.
History
DepositionSep 14, 2015Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Feb 24, 2016Provider: repository / Type: Initial release
Revision 1.1Mar 16, 2016Group: Database references
Revision 1.2Sep 27, 2017Group: Data collection / Derived calculations / Category: diffrn_detector / pdbx_struct_oper_list
Item: _diffrn_detector.detector / _pdbx_struct_oper_list.symmetry_operation
Revision 1.3Mar 20, 2024Group: 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

Downloads & links

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Assembly

Deposited unit
A: Outer membrane protein assembly factor BamA
B: Outer membrane protein assembly factor BamB
C: Outer membrane protein assembly factor BamC
D: Outer membrane protein assembly factor BamD
E: Outer membrane protein assembly factor BamE


Theoretical massNumber of molelcules
Total (without water)172,5485
Polymers172,5485
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area12380 Å2
ΔGint-62 kcal/mol
Surface area68520 Å2
Unit cell
Length a, b, c (Å)116.428, 116.428, 434.407
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212

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Components

#1: Protein Outer membrane protein assembly factor BamA / Omp85


Mass: 88443.656 Da / Num. of mol.: 1 / Fragment: UNP residues 22-810
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (strain K12) (bacteria)
Strain: K12 / Gene: bamA, yaeT, yzzN, yzzY, b0177, JW0172 / Production host: Escherichia coli (E. coli) / Strain (production host): C43 / References: UniProt: P0A940
#2: Protein Outer membrane protein assembly factor BamB


Mass: 41166.855 Da / Num. of mol.: 1 / Fragment: UNP residues 20-392
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (strain K12) (bacteria)
Strain: K12 / Gene: bamB, yfgL, b2512, JW2496 / Production host: Escherichia coli (E. coli) / Strain (production host): C43 / References: UniProt: P77774
#3: Protein Outer membrane protein assembly factor BamC


Mass: 5658.355 Da / Num. of mol.: 1 / Fragment: UNP residues 33-88
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (strain K12) (bacteria)
Strain: K12 / Gene: bamC, dapX, nlpB, b2477, JW2462 / Production host: Escherichia coli (E. coli) / Strain (production host): C43 / References: UniProt: P0A903
#4: Protein Outer membrane protein assembly factor BamD


Mass: 25816.818 Da / Num. of mol.: 1 / Fragment: UNP residues 20-245
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (strain K12) (bacteria)
Strain: K12 / Gene: bamD, yfiO, b2595, JW2577 / Production host: Escherichia coli (E. coli) / Strain (production host): C43 / References: UniProt: P0AC02
#5: Protein Outer membrane protein assembly factor BamE


Mass: 11462.772 Da / Num. of mol.: 1 / Fragment: UNP residues 20-113
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (strain K12) (bacteria)
Strain: K12 / Gene: bamE, smpA, b2617, JW2598 / Production host: Escherichia coli (E. coli) / Strain (production host): C43 / References: UniProt: P0A937

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 4.27 Å3/Da / Density % sol: 66.36 %
Crystal growTemperature: 289 K / Method: vapor diffusion / Details: Tris-HCl, NaCl, PEG 400

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.97853 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Sep 7, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97853 Å / Relative weight: 1
ReflectionResolution: 3.55→50 Å / Num. obs: 37045 / % possible obs: 99.5 % / Redundancy: 11.6 % / Net I/σ(I): 20

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Processing

Software
NameVersionClassification
PHENIX(phenix.refine: 1.9_1692)refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.555→34.568 Å / SU ML: 0.54 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 39.22 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.3141 2503 6.9 %
Rwork0.2711 --
obs0.2741 36273 97.78 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 3.555→34.568 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11497 0 0 0 11497
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00311739
X-RAY DIFFRACTIONf_angle_d0.66915963
X-RAY DIFFRACTIONf_dihedral_angle_d12.7324221
X-RAY DIFFRACTIONf_chiral_restr0.0261758
X-RAY DIFFRACTIONf_plane_restr0.0032106
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.555-3.62330.49331270.3961726X-RAY DIFFRACTION92
3.6233-3.69720.44621360.38631810X-RAY DIFFRACTION98
3.6972-3.77750.40781400.35071878X-RAY DIFFRACTION99
3.7775-3.86530.43511350.32671835X-RAY DIFFRACTION99
3.8653-3.96180.36811370.32141858X-RAY DIFFRACTION99
3.9618-4.06880.38741390.30811878X-RAY DIFFRACTION99
4.0688-4.18830.2931410.29791872X-RAY DIFFRACTION99
4.1883-4.32320.35031400.28721890X-RAY DIFFRACTION99
4.3232-4.47740.31411390.27481867X-RAY DIFFRACTION99
4.4774-4.65630.33641410.25841902X-RAY DIFFRACTION100
4.6563-4.86770.29461390.26431887X-RAY DIFFRACTION99
4.8677-5.12350.31911380.24251882X-RAY DIFFRACTION99
5.1235-5.44340.37511420.25621915X-RAY DIFFRACTION100
5.4434-5.86180.28091440.26911920X-RAY DIFFRACTION99
5.8618-6.44820.30031430.26771924X-RAY DIFFRACTION99
6.4482-7.37340.25741440.25931945X-RAY DIFFRACTION99
7.3734-9.26010.25681450.2311949X-RAY DIFFRACTION98
9.2601-34.56980.27221330.24531832X-RAY DIFFRACTION86

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