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- PDB-23vl: Crystal structure of AS-like domain of APS kinase from Entamoeba ... -

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Basic information

Entry
Database: PDB / ID: 23vl
TitleCrystal structure of AS-like domain of APS kinase from Entamoeba histolytica
Componentsadenylyl-sulfate kinase
KeywordsSULFATE ACTIVATION / SULFURYLASE-LIKE DOMAIN / SULFURYLASE-lLIKE
Function / homology
Function and homology information


: / : / adenylyl-sulfate kinase / adenylylsulfate kinase activity / sulfate adenylyltransferase (ATP) activity / ATP binding / cytoplasm
Similarity search - Function
: / ATP-sulfurylase PUA-like domain / PUA-like domain / : / Adenylyl-sulfate kinase / Adenylylsulphate kinase / PUA-like superfamily / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
adenylyl-sulfate kinase
Similarity search - Component
Biological speciesEntamoeba histolytica (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsHatanaka, R. / Yuasa, H. / Inoguchi, A. / Matsui, H. / Osumi, Y. / Mi-ichi, F. / Kishikawa, J. / Shiba, T.
Funding support Japan, 1items
OrganizationGrant numberCountry
Japan Society for the Promotion of Science (JSPS)Grant-in-Aid for Scientific Research(B), 25K02488 Japan
CitationJournal: J Struct Biol X / Year: 2026
Title: Structural insights into interdomain interactions in Entamoeba histolytica APS kinase.
Authors: Hatanaka, R. / Osumi, Y. / Matsui, H. / Inoguchi, A. / Yuasa, H. / Mi-ichi, F. / Kishikawa, J. / Shiba, T.
History
DepositionFeb 20, 2026Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jun 3, 2026Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: adenylyl-sulfate kinase


Theoretical massNumber of molelcules
Total (without water)35,3571
Polymers35,3571
Non-polymers00
Water72140
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)53.634, 55.695, 105.765
Angle α, β, γ (deg.)90, 90, 90
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein adenylyl-sulfate kinase / AS-like domain of APS kinase


Mass: 35356.680 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Entamoeba histolytica (eukaryote) / Gene: CL6EHI_179080 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A5K1U9J0, adenylyl-sulfate kinase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 40 / Source method: isolated from a natural source / Formula: H2O
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: 2.23 Å3/Da / Density % sol: 44.94 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 0.2 M Ammonium tartrate dibasic pH 7.0 20% w/v Polyethylene glycol 3,350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL44XU / Wavelength: 0.9 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jul 21, 2024
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9 Å / Relative weight: 1
ReflectionResolution: 2.1→50 Å / Num. obs: 18967 / % possible obs: 98.5 % / Redundancy: 6.15 % / CC1/2: 0.998 / Rmerge(I) obs: 0.127 / Net I/σ(I): 13
Reflection shellResolution: 2.1→2.22 Å / Mean I/σ(I) obs: 2 / Num. unique obs: 2951 / CC1/2: 0.743 / % possible all: 96.4

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Processing

Software
NameVersionClassification
REFMAC5.8.0430refinement
XDSdata reduction
XDSdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.1→19.93 Å / Cor.coef. Fo:Fc: 0.951 / Cor.coef. Fo:Fc free: 0.917 / Cross valid method: THROUGHOUT
RfactorNum. reflection% reflectionSelection details
Rfree0.28579 914 -RANDOM
Rwork0.22624 ---
obs0.22911 17995 98.47 %-
Displacement parametersBiso mean: 54.847 Å2
Baniso -1Baniso -2Baniso -3
1--0.07 Å20 Å2-0 Å2
2--0.05 Å2-0 Å2
3---0.02 Å2
Refinement stepCycle: LAST / Resolution: 2.1→19.93 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2244 0 0 40 2284
LS refinement shellResolution: 2.1→2.2 Å /
Rfactor% reflection
Rfree0.392 -
Rwork0.417 -
obs-92.89 %

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