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- PDB-8us4: C2221 Crystal structure of TamA (Barrel only) from Pseudomonas ae... -

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Basic information

Entry
Database: PDB / ID: 8us4
TitleC2221 Crystal structure of TamA (Barrel only) from Pseudomonas aeruginosa at 3.15 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 PAO1 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.15 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)35,0276
Polymers34,0521
Non-polymers9755
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)97.975, 149.876, 53.620
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221

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Components

#1: Protein Translocation and assembly module subunit TamA


Mass: 34052.016 Da / Num. of mol.: 1 / Fragment: Mature TamA
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas aeruginosa PAO1 (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-PT / PLATINUM (II) ION


Mass: 195.078 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Pt
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: 2.89 Å3/Da / Density % sol: 57.44 %
Crystal growTemperature: 293 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: 3.15→48.988 Å / Num. obs: 12152 / % possible obs: 97.8 % / Redundancy: 3.9 % / Biso Wilson estimate: 88.521 Å2 / Rpim(I) all: 0.121 / Rrim(I) all: 0.244 / Rsym value: 0.168 / Net I/av σ(I): 1.996 / Net I/σ(I): 7.5
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsRpim(I) allRsym value% possible all
3.15-3.3940.581.257040.3830.5897.9
3.39-3.734.20.3761.763460.2460.37698.6
3.73-4.2840.284258940.1910.28498.4
4.28-5.393.70.1772.763490.1250.17797.2
5.39-48.983.50.0654.561210.050.06593.4

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Processing

Software
NameVersionClassification
XDS3.3.20data reduction
PHENIX1.19refinement
PDB_EXTRACT3.14data extraction
XDSdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.15→48.987 Å / Cross valid method: FREE R-VALUE
RfactorNum. reflection% reflection
Rfree0.35 --
Rwork0.3 --
obs-12152 92.09 %
Displacement parametersBiso max: 226.53 Å2 / Biso mean: 90.0774 Å2 / Biso min: 47.35 Å2
Refinement stepCycle: LAST / Resolution: 3.15→48.987 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2389 0 5 0 2394

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