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- PDB-3wp8: Acinetobacter sp. Tol 5 AtaA C-terminal Ylhead fused to GCN4 adap... -

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Basic information

Entry
Database: PDB / ID: 3wp8
TitleAcinetobacter sp. Tol 5 AtaA C-terminal Ylhead fused to GCN4 adaptors (Chead)
ComponentsTrimeric autotransporter adhesin
KeywordsCELL ADHESION / adhesin / trimeric autotransporter adhesin / TAA / nanofiber / Ylhead / FGG / beta roll / HIM1 / adhesion
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) / Serralysin-like metalloprotease, C-terminal / 2 Solenoid / Alkaline Protease, subunit P, domain 1 / 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 ...Trimeric autotransporter adhesin YadA-like, head domain / YadA head domain repeat (2 copies) / Serralysin-like metalloprotease, C-terminal / 2 Solenoid / Alkaline Protease, subunit P, domain 1 / 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 / Mainly Beta
Similarity search - Domain/homology
Trimeric autotransporter adhesin AtaA
Similarity search - Component
Biological speciesAcinetobacter (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.97 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 10, 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 22, 2017Group: Refinement description / Category: software
Item: _software.classification / _software.contact_author ..._software.classification / _software.contact_author / _software.contact_author_email / _software.date / _software.language / _software.location / _software.name / _software.type / _software.version
Revision 1.3Nov 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 1.4Nov 8, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Trimeric autotransporter adhesin


Theoretical massNumber of molelcules
Total (without water)34,3851
Polymers34,3851
Non-polymers00
Water3,261181
1
A: Trimeric autotransporter adhesin

A: Trimeric autotransporter adhesin

A: Trimeric autotransporter adhesin


Theoretical massNumber of molelcules
Total (without water)103,1553
Polymers103,1553
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_655-y+1,x-y,z1
crystal symmetry operation3_665-x+y+1,-x+1,z1
Buried area30860 Å2
ΔGint-232 kcal/mol
Surface area32530 Å2
MethodPISA
Unit cell
Length a, b, c (Å)54.406, 54.406, 210.732
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number173
Space group name H-MP63
Components on special symmetry positions
IDModelComponents
11A-3327-

HOH

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Components

#1: Protein Trimeric autotransporter adhesin


Mass: 34385.039 Da / Num. of mol.: 1 / Fragment: UNP residues 2905-3168 / Mutation: P3061G
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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 181 / 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: 2.62 Å3/Da / Density % sol: 53.02 % / Mosaicity: 0.954 °
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 3.6
Details: 3% PEG 6000, 1.0M NaCl, 0.1M Na-acetate, pH 3.6, vapor diffusion, hanging drop, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL38B1 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Oct 23, 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: 1.97→50 Å / Num. all: 24269 / Num. obs: 24269 / % possible obs: 99.2 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 11.2 % / Rmerge(I) obs: 0.069 / Χ2: 2.337 / Net I/σ(I): 14.8
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
2-2.07110.42124091.03199
2.07-2.1511.10.31724161.197199.1
2.15-2.2511.20.22624241.261199.3
2.25-2.3711.20.19124501.386199.4
2.37-2.5211.20.13923871.547199.5
2.52-2.7111.20.11324321.906199.5
2.71-2.9911.30.08724292.647199.6
2.99-3.4211.20.0824544.177199.6
3.42-4.3111.20.06324235.187199.5
4.31-5011.10.03824452.962198

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
REFMAC5.7.0032refinement
PDB_EXTRACT3.14data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3NTN

3ntn


Resolution: 1.97→19.24 Å / Cor.coef. Fo:Fc: 0.964 / Cor.coef. Fo:Fc free: 0.942 / Occupancy max: 1 / Occupancy min: 0.33 / SU B: 3.836 / SU ML: 0.11 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.154 / ESU R Free: 0.153 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES: REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2298 1241 5.1 %RANDOM
Rwork0.1755 ---
all0.1782 24217 --
obs0.1782 24217 97.85 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 98.23 Å2 / Biso mean: 41.2606 Å2 / Biso min: 14.69 Å2
Baniso -1Baniso -2Baniso -3
1-0.02 Å20.02 Å2-0 Å2
2--0.02 Å2-0 Å2
3----0.08 Å2
Refinement stepCycle: LAST / Resolution: 1.97→19.24 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2293 0 0 181 2474
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0180.0192308
X-RAY DIFFRACTIONr_bond_other_d0.0010.022244
X-RAY DIFFRACTIONr_angle_refined_deg1.7641.943124
X-RAY DIFFRACTIONr_angle_other_deg0.83335159
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.4155316
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.15227.52793
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.84815402
X-RAY DIFFRACTIONr_dihedral_angle_4_deg10.481154
X-RAY DIFFRACTIONr_chiral_restr0.1110.2385
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.022717
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02477
X-RAY DIFFRACTIONr_mcbond_it3.5313.7861267
X-RAY DIFFRACTIONr_mcbond_other3.5243.7841266
X-RAY DIFFRACTIONr_mcangle_it4.2825.6821582
LS refinement shellResolution: 1.973→2.024 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.26 69 -
Rwork0.226 1385 -
all-1454 -
obs--79.98 %

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