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

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Basic information

Entry
Database: PDB / ID: 3wpp
TitleAcinetobacter sp. Tol 5 AtaA YDD-DALL3 domains in C-terminal stalk fused to GCN4 adaptors (CstalkC1iii)
ComponentsTrimeric autotransporter adhesin
KeywordsCELL ADHESION / adhesin / trimeric autotransporter adhesin / TAA / nanofiber / YDD / DALL3
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
Trimeric autotransporter adhesin AtaA
Similarity search - Component
Biological speciesAcinetobacter (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.952 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 15, 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

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Assembly

Deposited unit
A: Trimeric autotransporter adhesin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,4432
Polymers22,4081
Non-polymers351
Water1,982110
1
A: Trimeric autotransporter adhesin
hetero molecules

A: Trimeric autotransporter adhesin
hetero molecules

A: Trimeric autotransporter adhesin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)67,3306
Polymers67,2243
Non-polymers1063
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_565-y,x-y+1,z1
crystal symmetry operation3_455-x+y-1,-x,z1
Buried area13650 Å2
ΔGint-122 kcal/mol
Surface area15760 Å2
MethodPISA
Unit cell
Length a, b, c (Å)43.460, 43.460, 825.360
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number155
Space group name H-MH32
Components on special symmetry positions
IDModelComponents
11A-3601-

CL

21A-3701-

HOH

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Components

#1: Protein Trimeric autotransporter adhesin


Mass: 22408.002 Da / Num. of mol.: 1 / 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.: 110 / 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: 3.35 Å3/Da / Density % sol: 63.25 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 0.67% PEG 2000 MME, 67mM HEPES, 667mM Succinic acid, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU FR-E SUPERBRIGHT / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS VII / Detector: IMAGE PLATE / Date: Mar 13, 2013
RadiationMonochromator: confocal mirror / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.95→19.64 Å / Num. all: 23200 / Num. obs: 23200 / % possible obs: 99.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0
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
1.95-2.070.9130.4694.0431306364435990.49998.8
2.07-2.210.9690.3256.5534528341034100.342100
2.21-2.380.9840.2339.3632429319031900.245100
2.38-2.610.9910.18311.8130204296929690.192100
2.61-2.910.9950.13216.2727591274727460.14100
2.91-3.350.9960.0923.6923483241024090.095100
3.35-4.070.9970.06531.0519418208520820.06899.9
4.07-5.640.9990.05234.0115709169716930.05599.8
5.640.9990.04133.399655115511020.04395.4

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Processing

Software
NameVersionClassificationNB
XSCALEdata scaling
REFMAC5.7.0032refinement
PDB_EXTRACT3.14data extraction
HKL-2000data collection
XDSdata reduction
XDSdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2YO2

2yo2


Resolution: 1.952→19.64 Å / Cor.coef. Fo:Fc: 0.936 / Cor.coef. Fo:Fc free: 0.917 / SU B: 3.638 / SU ML: 0.048 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.091 / ESU R Free: 0.083 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES: REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2053 1160 5 %RANDOM
Rwork0.1793 ---
all0.1806 23198 --
obs0.1806 23198 99.57 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 114.03 Å2 / Biso mean: 35.524 Å2 / Biso min: 15.24 Å2
Baniso -1Baniso -2Baniso -3
1-0.21 Å20.21 Å20 Å2
2--0.21 Å2-0 Å2
3----0.69 Å2
Refinement stepCycle: LAST / Resolution: 1.952→19.64 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms786 0 1 110 897
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.02800
X-RAY DIFFRACTIONr_bond_other_d0.0020.02777
X-RAY DIFFRACTIONr_angle_refined_deg1.381.931087
X-RAY DIFFRACTIONr_angle_other_deg0.8231785
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.3525107
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.7728.540
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.36615147
X-RAY DIFFRACTIONr_dihedral_angle_4_deg2.423151
X-RAY DIFFRACTIONr_chiral_restr0.0810.2132
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.02954
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02169
X-RAY DIFFRACTIONr_mcbond_it4.3383.199419
X-RAY DIFFRACTIONr_mcbond_other4.3383.184418
X-RAY DIFFRACTIONr_mcangle_it5.2424.767523
X-RAY DIFFRACTIONr_rigid_bond_restr3.80931575
X-RAY DIFFRACTIONr_sphericity_free29.456531
X-RAY DIFFRACTIONr_sphericity_bonded18.9951651
LS refinement shellResolution: 1.952→2.002 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.212 80 -
Rwork0.185 1518 -
all-1598 -
obs--97.68 %

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