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- PDB-8us2: P22121 Crystal structure of TamA from Pseudomonas aeruginosa at 3... -

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Basic information

Entry
Database: PDB / ID: 8us2
TitleP22121 Crystal structure of TamA from Pseudomonas aeruginosa at 3.95 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: 3.955 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
B: Translocation and assembly module subunit TamA


Theoretical massNumber of molelcules
Total (without water)123,3042
Polymers123,3042
Non-polymers00
Water00
1
A: Translocation and assembly module subunit TamA


Theoretical massNumber of molelcules
Total (without water)61,6521
Polymers61,6521
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Translocation and assembly module subunit TamA


Theoretical massNumber of molelcules
Total (without water)61,6521
Polymers61,6521
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)73.050, 155.502, 157.021
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP22121

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Components

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


Mass: 61651.949 Da / Num. of mol.: 2 / 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

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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: 3.62 Å3/Da / Density % sol: 65.99 %
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: 3.955→44.063 Å / Num. all: 16231 / Num. obs: 16231 / % possible obs: 99.7 % / Redundancy: 3.9 % / Biso Wilson estimate: 123.22 Å2 / Rpim(I) all: 0.155 / Rrim(I) all: 0.309 / Rsym value: 0.222 / Net I/av σ(I): 2.739 / Net I/σ(I): 7.2 / Num. measured all: 62873
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsRpim(I) allRsym value% possible all
3.955-4.1740.8710.835070.590.87199.7
4.17-4.423.90.618130040.4290.61899.8
4.42-4.7340.4451.423150.3130.44599.9
4.73-5.113.90.3891.620030.2720.38999.8
5.11-5.593.90.3941.616050.2690.39499.9
5.59-6.253.90.3391.97840.2260.33999.8
6.25-7.223.80.2232.824290.1510.22399.7
7.22-8.843.60.0946.88160.0650.09499.9
8.84-12.513.60.03914.88360.0250.03999.9
12.51-44.0633.30.03113.58700.0220.03194.9

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Processing

Software
NameVersionClassification
XDS3.3.20data reduction
PHENIX1.19refinement
PDB_EXTRACT3.14data extraction
SCALAdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.955→39.255 Å / SU ML: 0.87 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 45.57 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.3813 806 4.99 %
Rwork0.3021 15335 -
obs0.306 16141 99.32 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 550 Å2 / Biso mean: 159.9052 Å2 / Biso min: 6.18 Å2
Refinement stepCycle: final / Resolution: 3.955→39.255 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8008 0 0 0 8008
Num. residues----1025
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0048200
X-RAY DIFFRACTIONf_angle_d1.39911089
X-RAY DIFFRACTIONf_chiral_restr0.0571156
X-RAY DIFFRACTIONf_plane_restr0.0071481
X-RAY DIFFRACTIONf_dihedral_angle_d15.3413037
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.955-4.20210.44581340.37572492X-RAY DIFFRACTION99
4.2021-4.52610.40021350.31162498X-RAY DIFFRACTION99
4.5261-4.98070.35351330.28742524X-RAY DIFFRACTION100
4.9807-5.69960.38541280.29172554X-RAY DIFFRACTION100
5.6996-7.17370.3991360.32532578X-RAY DIFFRACTION100
7.1737-39.2550.35931400.27862689X-RAY DIFFRACTION99

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