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- PDB-9vnj: Crystal structure of the transmembrane domain of trimeric autotra... -

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Basic information

Entry
Database: PDB / ID: 9vnj
TitleCrystal structure of the transmembrane domain of trimeric autotransporter adhesin AtaA in complex with the N-terminal domain of TpgA
Components(Trimeric autotransporter ...) x 2
KeywordsCELL ADHESION / Outer membrane / Acinetobacter
Function / homology
Function and homology information


cell outer membrane / protein transport / periplasmic space / cell adhesion / cell surface
Similarity search - Function
Trimeric autotransporter adhesin YadA-like, head domain / YadA head domain repeat (2 copies) / ESPR domain / Extended Signal Peptide of Type V secretion system / Trimeric autotransporter adhesin YadA-like, stalk domain / Coiled stalk of trimeric autotransporter adhesin / Trimeric autotransporter adhesin YadA-like, C-terminal membrane anchor domain / YadA-like membrane anchor domain / Outer membrane protein, bacterial / : ...Trimeric autotransporter adhesin YadA-like, head domain / YadA head domain repeat (2 copies) / ESPR domain / Extended Signal Peptide of Type V secretion system / Trimeric autotransporter adhesin YadA-like, stalk domain / Coiled stalk of trimeric autotransporter adhesin / Trimeric autotransporter adhesin YadA-like, C-terminal membrane anchor domain / YadA-like membrane anchor domain / Outer membrane protein, bacterial / : / OmpA-like domain profile. / OmpA-like domain superfamily / OmpA family / OmpA-like domain / Lipoprotein SmpA/OmlA / Outer membrane protein assembly factor BamE domain / Serralysin-like metalloprotease, C-terminal / Pilin-like / BamE-like
Similarity search - Domain/homology
TRIETHYLENE GLYCOL / Trimeric autotransporter adhesin- and peptidoglycan-associated protein A / Trimeric autotransporter adhesin AtaA
Similarity search - Component
Biological speciesAcinetobacter sp. Tol 5 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.6 Å
AuthorsYoshimoto, S. / Suzuki, A. / Hiroshige, R. / Hori, K.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: Cell Surf / Year: 2025
Title: Insights into the complex formation of a trimeric autotransporter adhesin with a peptidoglycan-binding periplasmic protein.
Authors: Yoshimoto, S. / Sasahara, J. / Suzuki, A. / Kanie, J. / Koiwai, K. / Lupas, A.N. / Hori, K.
History
DepositionJun 30, 2025Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Oct 8, 2025Provider: repository / Type: Initial release
Revision 1.1Oct 29, 2025Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_last ..._citation.journal_volume / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Trimeric autotransporter adhesin AtaA
B: Trimeric autotransporter adhesin- and peptidoglycan-associated protein A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,64424
Polymers26,2212
Non-polymers2,42322
Water1,27971
1
A: Trimeric autotransporter adhesin AtaA
B: Trimeric autotransporter adhesin- and peptidoglycan-associated protein A
hetero molecules

A: Trimeric autotransporter adhesin AtaA
B: Trimeric autotransporter adhesin- and peptidoglycan-associated protein A
hetero molecules

A: Trimeric autotransporter adhesin AtaA
B: Trimeric autotransporter adhesin- and peptidoglycan-associated protein A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)85,93172
Polymers78,6636
Non-polymers7,26866
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-y,x-y,z1
crystal symmetry operation3_555-x+y,-x,z1
Unit cell
Length a, b, c (Å)61.939, 61.939, 428.920
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number155
Space group name H-MH32
Components on special symmetry positions
IDModelComponents
11A-3701-

CA

21A-3710-

MES

31B-201-

CA

41A-3825-

HOH

51A-3832-

HOH

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Components

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Trimeric autotransporter ... , 2 types, 2 molecules AB

#1: Protein Trimeric autotransporter adhesin AtaA / TAA AtaA / Type 5 secretion system autotransporter AtaA


Mass: 11123.314 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Acinetobacter sp. Tol 5 (bacteria) / Gene: ataA / Production host: Escherichia coli (E. coli) / References: UniProt: K7ZP88
#2: Protein Trimeric autotransporter adhesin- and peptidoglycan-associated protein A / TAA- and PGN-associated protein A / TpgA


Mass: 15097.733 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Acinetobacter sp. Tol 5 (bacteria) / Strain: Tol 5 / Gene: tpgA / Production host: Escherichia coli (E. coli) / References: UniProt: A0A160PB22

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Non-polymers , 6 types, 93 molecules

#3: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Ca
#4: Chemical ChemComp-C8E / (HYDROXYETHYLOXY)TRI(ETHYLOXY)OCTANE


Mass: 306.438 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C16H34O5 / Comment: C8E, detergent*YM
#5: Chemical
ChemComp-PGE / TRIETHYLENE GLYCOL


Mass: 150.173 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C6H14O4
#6: Chemical ChemComp-MES / 2-(N-MORPHOLINO)-ETHANESULFONIC ACID


Mass: 195.237 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H13NO4S / Comment: pH buffer*YM
#7: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Cl
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 71 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestN
Has protein modificationN

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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: 3.02 Å3/Da / Density % sol: 59.26 %
Crystal growTemperature: 293 K / Method: vapor diffusion / pH: 5 / Details: 35% PEG 400, 0.2 M MES, 0.4 M CaCl2

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: AR-NW12A / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 270 / Detector: CCD / Date: Jun 16, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.6→37.9246 Å / Num. obs: 10168 / % possible obs: 98.45 % / Redundancy: 8.4 % / CC1/2: 0.971 / Net I/σ(I): 45.6
Reflection shellResolution: 2.6→2.64 Å / Redundancy: 7.9 % / Num. unique obs: 477 / CC1/2: 0.971 / % possible all: 99

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Processing

Software
NameVersionClassification
PHENIX1.10.1_2155refinement
HKL-2000data scaling
MOLREPphasing
ARP/wARPmodel building
DENZOdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2GR7

2gr7


Resolution: 2.6→37.9246 Å / SU ML: 0.28 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 24.47 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2441 495 4.87 %
Rwork0.1945 --
obs0.1969 10168 98.45 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.6→37.9246 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1571 0 145 71 1787
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0131724
X-RAY DIFFRACTIONf_angle_d1.1692279
X-RAY DIFFRACTIONf_dihedral_angle_d27.605678
X-RAY DIFFRACTIONf_chiral_restr0.055228
X-RAY DIFFRACTIONf_plane_restr0.004287
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.6004-2.8620.30291220.20682304X-RAY DIFFRACTION97
2.862-3.27590.27481200.19182383X-RAY DIFFRACTION98
3.2759-4.12650.20041130.17832448X-RAY DIFFRACTION100
4.1265-37.92460.24651400.20462538X-RAY DIFFRACTION99

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