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- PDB-9dv8: The Apo structure of AckA from Treponema vincentii -

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Basic information

Entry
Database: PDB / ID: 9dv8
TitleThe Apo structure of AckA from Treponema vincentii
ComponentsAcetate kinase
KeywordsTRANSFERASE / Acetate kinase / oral pathogen
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
Biological speciesTreponema vincentii (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.36 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)52,8567
Polymers52,4831
Non-polymers3726
Water6,197344
1
A: Acetate kinase
hetero molecules

A: Acetate kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)105,71114
Polymers104,9662
Non-polymers74512
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_565-x,-y+1,z1
Buried area7280 Å2
ΔGint-38 kcal/mol
Surface area35030 Å2
MethodPISA
Unit cell
Length a, b, c (Å)88.132, 105.050, 52.731
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 vincentii (bacteria) / Gene: ackA, TREVI0001_0924 / Production host: Escherichia coli (E. coli) / References: UniProt: C8PR54, acetate kinase
#2: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C2H6O2
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 344 / 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: 2.33 Å3/Da / Density % sol: 47.11 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting 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: APS / Beamline: 19-ID / Wavelength: 0.97918 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Dec 8, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97918 Å / Relative weight: 1
ReflectionResolution: 1.36→28.4 Å / Num. obs: 105432 / % possible obs: 99.7 % / Redundancy: 5.2 % / Biso Wilson estimate: 13.09 Å2 / CC1/2: 0.999 / Net I/σ(I): 26.6
Reflection shellResolution: 1.36→1.38 Å / Num. unique obs: 5219 / CC1/2: 0.848

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.36→28.4 Å / SU ML: 0.1178 / Cross valid method: FREE R-VALUE / σ(F): 1.37 / Phase error: 13.8265
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1621 5240 4.97 %
Rwork0.1411 100127 -
obs0.1421 105367 99.68 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 19.47 Å2
Refinement stepCycle: LAST / Resolution: 1.36→28.4 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3495 0 24 346 3865
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00743655
X-RAY DIFFRACTIONf_angle_d0.93984950
X-RAY DIFFRACTIONf_chiral_restr0.0789555
X-RAY DIFFRACTIONf_plane_restr0.0076638
X-RAY DIFFRACTIONf_dihedral_angle_d13.56191357
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.36-1.380.22021550.1883243X-RAY DIFFRACTION97.64
1.38-1.390.23771610.18483312X-RAY DIFFRACTION99.66
1.39-1.410.17561720.16863278X-RAY DIFFRACTION99.91
1.41-1.430.19731860.16593360X-RAY DIFFRACTION99.72
1.43-1.450.21631570.17333281X-RAY DIFFRACTION99.71
1.45-1.470.20591890.17663290X-RAY DIFFRACTION99.86
1.47-1.490.21121780.15633292X-RAY DIFFRACTION99.83
1.49-1.510.18561660.14463348X-RAY DIFFRACTION99.77
1.51-1.530.19371810.13693259X-RAY DIFFRACTION99.83
1.53-1.560.17051600.13253342X-RAY DIFFRACTION99.91
1.56-1.580.15661950.1223277X-RAY DIFFRACTION99.88
1.58-1.610.1481720.123323X-RAY DIFFRACTION99.83
1.61-1.640.14821660.11983329X-RAY DIFFRACTION99.89
1.64-1.680.17111630.12273303X-RAY DIFFRACTION99.6
1.68-1.710.14771820.12523325X-RAY DIFFRACTION99.43
1.71-1.750.15811870.12763309X-RAY DIFFRACTION99.89
1.75-1.80.16291640.13253324X-RAY DIFFRACTION99.77
1.8-1.850.17971730.13193315X-RAY DIFFRACTION99.94
1.85-1.90.14821710.13133363X-RAY DIFFRACTION99.89
1.9-1.960.16281870.133336X-RAY DIFFRACTION99.86
1.96-2.030.15751850.12883315X-RAY DIFFRACTION99.86
2.03-2.110.15141620.12643370X-RAY DIFFRACTION99.75
2.11-2.210.16031740.1293332X-RAY DIFFRACTION99.66
2.21-2.330.13411810.1253356X-RAY DIFFRACTION99.83
2.33-2.470.13551790.12833346X-RAY DIFFRACTION99.86
2.47-2.660.14691730.13743400X-RAY DIFFRACTION99.97
2.66-2.930.15261990.14923391X-RAY DIFFRACTION99.83
2.93-3.350.16911660.15383378X-RAY DIFFRACTION99.22
3.35-4.220.16021860.14543433X-RAY DIFFRACTION99.67
4.22-28.40.17531700.15853597X-RAY DIFFRACTION99

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