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

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Basic information

Entry
Database: PDB / ID: 3wqa
TitleAcinetobacter sp. Tol 5 AtaA YDD-DALL3 domains in C-terminal stalk fused to GCN4 adaptors (CstalkC1ii)
ComponentsTrimeric autotransporter adhesin
KeywordsCELL ADHESION / adhesin / trimeric autotransporter adhesin / TAA / nanofiber
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) / 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 / Serralysin-like metalloprotease, C-terminal / Pilin-like
Similarity search - Domain/homology
NICKEL (II) ION / PHOSPHATE ION / Trimeric autotransporter adhesin AtaA
Similarity search - Component
Biological speciesAcinetobacter (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.401 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 24, 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 / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _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

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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)67,5087
Polymers67,2243
Non-polymers2844
Water4,900272
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area27970 Å2
ΔGint-226 kcal/mol
Surface area29310 Å2
MethodPISA
Unit cell
Length a, b, c (Å)86.110, 43.680, 95.564
Angle α, β, γ (deg.)90.00, 111.97, 90.00
Int Tables number4
Space group name H-MP1211

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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: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: PO4
#4: Chemical ChemComp-NI / NICKEL (II) ION


Mass: 58.693 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ni
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 272 / 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: 2.48 Å3/Da / Density % sol: 50.39 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 67mM MES, 0.67M 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: PSI 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: 2.4→88.56 Å / Num. all: 26029 / Num. obs: 26029 / % possible obs: 98.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Biso Wilson estimate: 29.39 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
2.4-2.540.7730.6411.8313461418340490.76596.8
2.54-2.720.9060.4212.8113427393439280.599.8
2.72-2.930.930.3014.212328369436760.35999.5
2.93-3.210.950.2076.3110796339333790.24999.6
3.21-3.590.9790.139.9710788309930880.15499.6
3.59-4.140.9880.09412.589001272927020.11399
4.14-5.050.9960.06514.847270234923190.07898.7
5.05-7.080.9970.06514.896095183318130.07898.9
7.080.9950.04818.533249110210750.05897.5

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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: 2.401→38.322 Å / FOM work R set: 0.7472 / SU ML: 0.41 / σ(F): 1.37 / Phase error: 31.98 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.307 1199 4.94 %RANDOM
Rwork0.2133 ---
obs0.2179 24248 92.39 %-
all-24248 --
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 99.1 Å2 / Biso mean: 26.68 Å2 / Biso min: 2.46 Å2
Refinement stepCycle: LAST / Resolution: 2.401→38.322 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4545 0 12 272 4829
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0084629
X-RAY DIFFRACTIONf_angle_d1.0896262
X-RAY DIFFRACTIONf_chiral_restr0.075752
X-RAY DIFFRACTIONf_plane_restr0.004827
X-RAY DIFFRACTIONf_dihedral_angle_d17.1411730
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 (%)
2.4006-2.49670.39621300.2842451258190
2.4967-2.61030.34461370.25292634277196
2.6103-2.74790.3571360.24162621275795
2.7479-2.920.30281340.21982624275895
2.92-3.14540.38061270.22682507263492
3.1454-3.46170.28681350.20272576271193
3.4617-3.96220.30151420.19192606274893
3.9622-4.99020.25921260.18192473259989
4.9902-38.32690.27651320.21612557268988

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