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- PDB-9t0n: Crystal structure of TagF (ACIAD2683) from Acinetobacter baylyi ADP1 -

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Basic information

Entry
Database: PDB / ID: 9t0n
TitleCrystal structure of TagF (ACIAD2683) from Acinetobacter baylyi ADP1
ComponentsType VI secretion-associated protein
KeywordsPROTEIN BINDING / Assembly checkpoint protein / Type VI secretion-associated protein / post-translational regulator / cytosolic protein
Function / homologyT6S-associated protein TagF / T6S-associated protein TagF superfamily / TagF N-terminal domain, Type VI secretion system-associated / ACETATE ION / : / Type VI secretion-associated protein
Function and homology information
Biological speciesAcinetobacter baylyi ADP1 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.8 Å
AuthorsEngelin, M.K. / Delbart, F. / Maier, T. / Basler, M.
Funding supportEuropean Union, Switzerland, 2items
OrganizationGrant numberCountry
European Research Council (ERC)865105European Union
Swiss National Science Foundation320030-227860 Switzerland
CitationJournal: To Be Published
Title: Spike-loading checkpoint controlling Type VI Secretion System assembly
Authors: Engelin, M.K. / Prakash, P. / Lin, L. / Muehlethaler, T. / Pereira, J. / Kuhn, E. / Delbart, F. / Maier, T. / Basler, M.
History
DepositionOct 17, 2025Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 12, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Type VI secretion-associated protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,81213
Polymers37,5161
Non-polymers1,29612
Water1,31573
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: assay for oligomerization, Flow-induced dispersion analysis (FIDA)
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1220 Å2
ΔGint-61 kcal/mol
Surface area15400 Å2
MethodPISA
Unit cell
Length a, b, c (Å)45.146, 74.909, 85.500
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Type VI secretion-associated protein


Mass: 37516.234 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Acinetobacter baylyi ADP1 (bacteria) / Gene: ACIAD2683 / Plasmid: pBXC3H / Production host: Escherichia coli MC1061 (bacteria) / Strain (production host): ME028 / References: UniProt: Q6F928
#2: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H3O2
#3: Chemical
ChemComp-CD / CADMIUM ION


Mass: 112.411 Da / Num. of mol.: 11 / Source method: obtained synthetically / Formula: Cd
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 73 / Source method: isolated from a natural source / Formula: H2O
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: 1.93 Å3/Da / Density % sol: 36.16 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 8
Details: 0.162 M CdSO4, 0.1 M Hepes 7.5 pH, 0.5 M NaOAc pH 8

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 1.000009 Å
DetectorType: DECTRIS PILATUS 2M-F / Detector: PIXEL / Date: Mar 20, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.000009 Å / Relative weight: 1
ReflectionResolution: 1.8→85.5 Å / Num. obs: 51891 / % possible obs: 100 % / Redundancy: 12.1 % / CC1/2: 0.998 / Net I/σ(I): 7.4
Reflection shellResolution: 1.8→1.84 Å / Redundancy: 12.3 % / Mean I/σ(I) obs: 0.5 / Num. unique obs: 1591 / CC1/2: 0.575 / % possible all: 100

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Processing

Software
NameVersionClassification
DIALS2.2data reduction
Aimless0.5.21data scaling
CRANK2phasing
PHENIX(2.0_5716)refinement
PDB_EXTRACTdata extraction
RefinementMethod to determine structure: SAD / Resolution: 1.8→56.34 Å / SU ML: 0.24 / Cross valid method: FREE R-VALUE / σ(F): 0.06 / Phase error: 27.75 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2452 2606 5.02 %
Rwork0.2095 --
obs0.2113 51891 99.99 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.8→56.34 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2614 0 15 73 2702
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0042676
X-RAY DIFFRACTIONf_angle_d0.7053629
X-RAY DIFFRACTIONf_dihedral_angle_d12.979988
X-RAY DIFFRACTIONf_chiral_restr0.04411
X-RAY DIFFRACTIONf_plane_restr0.005464
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.8-1.830.38211110.3282600X-RAY DIFFRACTION100
1.83-1.870.34641370.30682583X-RAY DIFFRACTION100
1.87-1.910.3261270.32616X-RAY DIFFRACTION100
1.91-1.950.31091090.26982606X-RAY DIFFRACTION100
1.95-1.990.29631460.25582592X-RAY DIFFRACTION100
1.99-2.040.26881530.23852593X-RAY DIFFRACTION100
2.04-2.10.27991270.22112596X-RAY DIFFRACTION100
2.1-2.160.26891620.21442546X-RAY DIFFRACTION100
2.16-2.230.2661390.212616X-RAY DIFFRACTION100
2.23-2.310.26131560.20332584X-RAY DIFFRACTION100
2.31-2.40.2531310.20542595X-RAY DIFFRACTION100
2.4-2.510.21771310.19942618X-RAY DIFFRACTION100
2.51-2.640.26431520.20042572X-RAY DIFFRACTION100
2.64-2.810.24451220.20792605X-RAY DIFFRACTION100
2.81-3.030.24071580.20842586X-RAY DIFFRACTION100
3.03-3.330.27341130.21452613X-RAY DIFFRACTION100
3.33-3.810.1991360.19732607X-RAY DIFFRACTION100
3.81-4.80.18951390.16882573X-RAY DIFFRACTION100
4.8-56.340.25891570.2152584X-RAY DIFFRACTION100
Refinement TLS params.Method: refined / Origin x: 45.4271 Å / Origin y: 2.7484 Å / Origin z: 2.5087 Å
111213212223313233
T0.1992 Å2-0.0297 Å20.0497 Å2-0.184 Å20.0487 Å2--0.2136 Å2
L0.8986 °20.1121 °20.2788 °2-2.0157 °21.3064 °2--2.8141 °2
S0.0465 Å °-0.0524 Å °-0.022 Å °0.2477 Å °-0.1035 Å °0.1671 Å °0.387 Å °-0.0849 Å °0.0288 Å °
Refinement TLS groupSelection details: all

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