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- PDB-9dv9: The AMP-bound structure of AckA from Treponema vincentii -

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Basic information

Entry
Database: PDB / ID: 9dv9
TitleThe AMP-bound structure of AckA from Treponema vincentii
ComponentsAcetate kinase
KeywordsTRANSFERASE / Acetate kinase / oral pathogen / AMP
Function / homology
Function and homology information


acetate kinase / acetate kinase activity / acetate metabolic process / acetyl-CoA biosynthetic process / magnesium ion binding / ATP binding / cytoplasm
Similarity search - Function
Acetate and butyrate kinases family signature 2. / Acetate/propionate kinase / Aliphatic acid kinase, short-chain, conserved site / Acetate and butyrate kinases family signature 1. / Aliphatic acid kinase, short-chain / Acetokinase family / ATPase, nucleotide binding domain
Similarity search - Domain/homology
ADENOSINE MONOPHOSPHATE / Acetate kinase
Similarity search - Component
Biological speciesTreponema pallidum (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.3 Å
AuthorsBrautigam, C.A. / Deka, R.K.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)AI56305 United States
CitationJournal: Plos One / Year: 2025
Title: Biophysical and biochemical evidence for the role of acetate kinases (AckAs) in an acetogenic pathway in pathogenic spirochetes.
Authors: Deka, R.K. / Tso, S.C. / Liu, W.Z. / Brautigam, C.A.
History
DepositionOct 5, 2024Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 22, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Acetate kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)53,0515
Polymers52,4831
Non-polymers5674
Water6,630368
1
A: Acetate kinase
hetero molecules

A: Acetate kinase
hetero molecules

A: Acetate kinase
hetero molecules


  • defined by author
  • Evidence: assay for oligomerization, Sedimentation velocity analytical ultracentrifugation, mass photometry were used to assess oligomerization state.
  • 159 kDa, 3 polymers
Theoretical massNumber of molelcules
Total (without water)159,15215
Polymers157,4493
Non-polymers1,70212
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
point symmetry operation2
Buried area8520 Å2
ΔGint-71 kcal/mol
Surface area34160 Å2
MethodPISA
Unit cell
Length a, b, c (Å)88.102, 105.232, 52.735
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21212
Space group name HallP22ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x+1/2,y+1/2,-z
#4: -x,-y,z

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Components

#1: Protein Acetate kinase / Acetokinase


Mass: 52483.117 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Treponema pallidum (bacteria) / Gene: ackA, TREVI0001_0924 / Production host: Escherichia coli (E. coli) / References: UniProt: C8PR54, acetate kinase
#2: Chemical ChemComp-AMP / ADENOSINE MONOPHOSPHATE


Mass: 347.221 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H14N5O7P / Feature type: SUBJECT OF INVESTIGATION / Comment: AMP*YM
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#4: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6O2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 368 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
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: 2.33 Å3/Da / Density % sol: 47.19 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 0.2 M Ammonium sulfate 0.1 M Bis-Tris pH 5.5 25% (w/v) PEG3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL12-2 / Wavelength: 0.97946 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Dec 7, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97946 Å / Relative weight: 1
ReflectionResolution: 1.3→23.1 Å / Num. obs: 120425 / % possible obs: 99.1 % / Redundancy: 4.3 % / Biso Wilson estimate: 12.59 Å2 / CC1/2: 1 / Net I/σ(I): 29.9
Reflection shellResolution: 1.3→1.32 Å / Num. unique obs: 5985 / CC1/2: 0.885

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
PHENIX1.20.1_4487refinement
HKL-3000data reduction
HKL-3000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.3→23.06 Å / SU ML: 0.1027 / Cross valid method: FREE R-VALUE / σ(F): 1.38 / Phase error: 14.6572
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1622 6136 5.1 %
Rwork0.1404 114230 -
obs0.1415 120366 98.98 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 19.32 Å2
Refinement stepCycle: LAST / Resolution: 1.3→23.06 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3495 0 36 368 3899
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00713807
X-RAY DIFFRACTIONf_angle_d0.97015186
X-RAY DIFFRACTIONf_chiral_restr0.08574
X-RAY DIFFRACTIONf_plane_restr0.0082675
X-RAY DIFFRACTIONf_dihedral_angle_d13.44851433
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.3-1.310.23871860.20863574X-RAY DIFFRACTION93.86
1.31-1.330.23032040.19553772X-RAY DIFFRACTION99.55
1.33-1.340.24351850.18553811X-RAY DIFFRACTION99.5
1.34-1.360.22812180.17093813X-RAY DIFFRACTION99.56
1.36-1.380.19872080.1683757X-RAY DIFFRACTION99.87
1.38-1.40.20512070.16243793X-RAY DIFFRACTION99.65
1.4-1.420.20862050.15973813X-RAY DIFFRACTION99.65
1.42-1.440.17812020.15663754X-RAY DIFFRACTION99.1
1.44-1.460.19561850.14623822X-RAY DIFFRACTION98.96
1.46-1.490.14812180.1313755X-RAY DIFFRACTION99.62
1.49-1.510.15481930.12343826X-RAY DIFFRACTION99.7
1.51-1.540.1472000.1233782X-RAY DIFFRACTION99.72
1.54-1.570.15832370.12233793X-RAY DIFFRACTION99.73
1.57-1.60.14861990.11723836X-RAY DIFFRACTION99.63
1.6-1.640.14082320.11953787X-RAY DIFFRACTION99.55
1.64-1.670.15561930.11993794X-RAY DIFFRACTION99.58
1.67-1.710.1462100.12213799X-RAY DIFFRACTION99.55
1.71-1.760.15242070.1253850X-RAY DIFFRACTION99.78
1.76-1.810.14991970.12453817X-RAY DIFFRACTION99.53
1.81-1.870.16011790.12773819X-RAY DIFFRACTION99.4
1.87-1.940.15072050.12563810X-RAY DIFFRACTION98.65
1.94-2.020.14092120.12873750X-RAY DIFFRACTION97.85
2.02-2.110.1311960.1283859X-RAY DIFFRACTION99.68
2.11-2.220.16542210.12913824X-RAY DIFFRACTION99.75
2.22-2.360.13512070.12873853X-RAY DIFFRACTION99.63
2.36-2.540.15952370.1363828X-RAY DIFFRACTION99.22
2.54-2.790.17232250.14273835X-RAY DIFFRACTION98.83
2.79-3.20.17651820.14993897X-RAY DIFFRACTION98.69
3.2-4.030.15861900.14693803X-RAY DIFFRACTION95.48
4.03-23.060.16911960.15774004X-RAY DIFFRACTION96.6

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