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- PDB-3wpo: Acinetobacter sp. Tol 5 AtaA YDD-DALL3 domains in C-terminal stal... -

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Basic information

Entry
Database: PDB / ID: 3wpo
TitleAcinetobacter sp. Tol 5 AtaA YDD-DALL3 domains in C-terminal stalk fused to GCN4 adaptors (CstalkC1i)
ComponentsTrimeric autotransporter adhesin
KeywordsCELL ADHESION / adhesin / trimeric autotransporter adhesin / TAA / nanofiber / DALL1 / DALL3 / YDD
Function / homology
Function and homology information


cell outer membrane / protein transport / cell adhesion / cell surface
Similarity search - Function
Trimeric autotransporter adhesin YadA-like, head domain / YadA head domain repeat (2 copies) / Trimeric autotransporter adhesin YadA-like, stalk domain / Coiled stalk of trimeric autotransporter adhesin / ESPR domain / Extended Signal Peptide of Type V secretion system / Trimeric autotransporter adhesin YadA-like, C-terminal membrane anchor domain / YadA-like membrane anchor domain / Pilin-like / Serralysin-like metalloprotease, C-terminal
Similarity search - Domain/homology
Trimeric autotransporter adhesin AtaA
Similarity search - Component
Biological speciesAcinetobacter (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.397 Å
AuthorsKoiwai, K. / Hartmann, M.D. / Yoshimoto, S. / Nur 'Izzah, N. / Suzuki, A. / Linke, D. / Lupas, A.N. / Hori, K.
CitationJournal: J.Biol.Chem. / Year: 2016
Title: Structural Basis for Toughness and Flexibility in the C-terminal Passenger Domain of an Acinetobacter Trimeric Autotransporter Adhesin.
Authors: Koiwai, K. / Hartmann, M.D. / Linke, D. / Lupas, A.N. / Hori, K.
History
DepositionJan 14, 2014Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Mar 4, 2015Provider: repository / Type: Initial release
Revision 1.1Dec 30, 2015Group: Database references
Revision 1.2Nov 20, 2019Group: Database references / Category: citation / struct_ref_seq_dif
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _struct_ref_seq_dif.details
Revision 1.3Nov 8, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Trimeric autotransporter adhesin
B: Trimeric autotransporter adhesin
C: Trimeric autotransporter adhesin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)67,2594
Polymers67,2243
Non-polymers351
Water2,054114
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area26570 Å2
ΔGint-207 kcal/mol
Surface area27760 Å2
MethodPISA
Unit cell
Length a, b, c (Å)159.750, 44.150, 95.730
Angle α, β, γ (deg.)90.000, 108.080, 90.000
Int Tables number5
Space group name H-MC121

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Components

#1: Protein Trimeric autotransporter adhesin


Mass: 22408.002 Da / Num. of mol.: 3 / Fragment: UNP residues 3334-3474
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Acinetobacter (bacteria) / Strain: Tol 5 / Gene: ataA / Plasmid: pIBA-GCN4tri / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) STAR / References: UniProt: K7ZP88
#2: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 114 / Source method: isolated from a natural source / Formula: H2O

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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: 2.39 Å3/Da / Density % sol: 48.47 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 0.1M MES, 0.5M Ammonium sulfate, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jun 20, 2013
RadiationMonochromator: Fixed exit Si (111) double crystal monochromator
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.397→39.687 Å / Num. all: 25148 / Num. obs: 25148 / % possible obs: 98.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Biso Wilson estimate: 44.03 Å2
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Highest resolution (Å)Rmerge F obsRmerge(I) obsMean I/σ(I) obsNum. measured obsNum. possibleNum. unique obsRrim(I) all% possible all
2.4-2.540.8740.7351.9113936404938590.86195.3
2.54-2.720.9220.483.0714466382738110.5699.6
2.72-2.930.9340.3344.7513303356835590.39199.7
2.93-3.210.9590.2147.3611673327932700.25399.7
3.21-3.590.9830.13311.8711608297729700.15599.8
3.59-4.140.9930.08915.869901265726370.10499.2
4.14-5.050.9970.05419.757832224222240.06599.2
5.05-7.090.9970.05320.266627177417690.06299.7
7.090.9990.03227.523533106810490.03898.2

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Processing

Software
NameVersionClassificationNB
XSCALEdata scaling
PHENIX1.8.1_1168refinement
PDB_EXTRACT3.14data extraction
XDSdata scaling
XDSdata reduction
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2YO2

2yo2


Resolution: 2.397→39.687 Å / FOM work R set: 0.7455 / SU ML: 0.37 / σ(F): 2.01 / Phase error: 31.6 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2797 1257 5 %
Rwork0.2119 --
all0.2153 25125 -
obs0.2153 25125 98.97 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 96.6 Å2 / Biso mean: 43.5 Å2 / Biso min: 16.92 Å2
Refinement stepCycle: LAST / Resolution: 2.397→39.687 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4355 0 1 114 4470
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0094376
X-RAY DIFFRACTIONf_angle_d1.1395918
X-RAY DIFFRACTIONf_chiral_restr0.081718
X-RAY DIFFRACTIONf_plane_restr0.004788
X-RAY DIFFRACTIONf_dihedral_angle_d16.5611628
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 9

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.3972-2.49320.36661300.27542482261294
2.4932-2.60660.32171400.26126492789100
2.6066-2.7440.31741390.25642643278299
2.744-2.91590.32821390.236926342773100
2.9159-3.1410.33311410.230426802821100
3.141-3.45690.26831390.208826552794100
3.4569-3.95670.27121420.190226882830100
3.9567-4.98350.24091400.17472670281099
4.9835-39.69270.2621470.21662767291499

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