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- PDB-8us3: C2 Crystal structure of TamA from Pseudomonas aeruginosa at 3.1 Ang -

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Basic information

Entry
Database: PDB / ID: 8us3
TitleC2 Crystal structure of TamA from Pseudomonas aeruginosa at 3.1 Ang
ComponentsTranslocation and assembly module subunit TamA
KeywordsMEMBRANE PROTEIN / Omp85 / protein translocation
Function / homology
Function and homology information


TAM protein secretion complex / protein secretion / cell outer membrane
Similarity search - Function
TamA, POTRA domain 1 / POTRA domain TamA domain 1 / POTRA domain, BamA/TamA-like / Surface antigen variable number repeat / Surface antigen D15-like / Bacterial surface antigen (D15) / Omp85 superfamily domain
Similarity search - Domain/homology
Translocation and assembly module subunit TamA
Similarity search - Component
Biological speciesPseudomonas aeruginosa (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.1 Å
AuthorsMellouk, A. / Moraes, T.F. / Calmettes, C.
Funding support Canada, 1items
OrganizationGrant numberCountry
Natural Sciences and Engineering Research Council (NSERC, Canada) Canada
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2024
Title: POTRA domains of the TamA insertase interact with the outer membrane and modulate membrane properties.
Authors: Mellouk, A. / Jaouen, P. / Ruel, L.J. / Le, M. / Martini, C. / Moraes, T.F. / El Bakkouri, M. / Lague, P. / Boisselier, E. / Calmettes, C.
History
DepositionOct 27, 2023Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 26, 2024Provider: repository / Type: Initial release
Revision 1.1Jul 17, 2024Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID / _citation_author.name

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Translocation and assembly module subunit TamA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)61,9833
Polymers61,6521
Non-polymers3312
Water32418
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)140.400, 63.880, 81.360
Angle α, β, γ (deg.)90.000, 99.400, 90.000
Int Tables number5
Space group name H-MC121

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Components

#1: Protein Translocation and assembly module subunit TamA / Autotransporter assembly factor TamA


Mass: 61651.949 Da / Num. of mol.: 1 / Fragment: Mature TamA
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas aeruginosa (bacteria)
Strain: ATCC 15692 / DSM 22644 / CIP 104116 / JCM 14847 / LMG 12228 / 1C / PRS 101 / PAO1
Gene: PA2543 / Plasmid: pET / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): C43 / References: UniProt: Q9I0U1
#2: Chemical ChemComp-C8E / (HYDROXYETHYLOXY)TRI(ETHYLOXY)OCTANE


Mass: 306.438 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C16H34O5 / Comment: C8E, detergent*YM
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 18 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 2.92 Å3/Da / Density % sol: 57.87 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 7.2
Details: 12% peg 4K, 50 mM MgCl2, 70 mM Hepes pH 7.2, 4% isopropanol, 10% glycerol

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Data collection

DiffractionMean temperature: 77 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.97910 Ang
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Oct 12, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9791 Å / Relative weight: 1
ReflectionResolution: 3.1→48.6 Å / Num. obs: 13130 / % possible obs: 100 % / Redundancy: 2 % / Biso Wilson estimate: 68.282 Å2 / CC1/2: 0.9 / Rsym value: 0.04 / Net I/σ(I): 11.2
Reflection shell
Resolution (Å)Num. unique obsCC1/2Diffraction-ID
3.1-3.966740.81
3.9-4.933240.91
4.9-5.916380.991
5.9-6.98220.991
6.9-48.68050.991

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Processing

Software
NameVersionClassification
PHENIX1.19refinement
PDB_EXTRACT3.14data extraction
XDSdata reduction
XDSdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.1→48.6 Å / Cross valid method: FREE R-VALUE
RfactorNum. reflection% reflection
Rfree0.3 --
Rwork0.25 --
obs-13125 99.95 %
Displacement parametersBiso max: 214.1 Å2 / Biso min: 18.74 Å2
Refinement stepCycle: LAST / Resolution: 3.1→48.6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4303 0 22 18 4343

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