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- PDB-23vk: Crystal structure of full-length of APS kinase from Entamoeba his... -

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Basic information

Entry
Database: PDB / ID: 23vk
TitleCrystal structure of full-length of APS kinase from Entamoeba histolytica
Componentsadenylyl-sulfate kinase
KeywordsTRANSFERASE / KINASE / sulfate activation
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 / SAD / Resolution: 2.595 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

Downloads & links

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Assembly

Deposited unit
A: adenylyl-sulfate kinase
B: adenylyl-sulfate kinase
C: adenylyl-sulfate kinase
D: adenylyl-sulfate kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)222,8368
Polymers222,4514
Non-polymers3844
Water23413
1
A: adenylyl-sulfate kinase
B: adenylyl-sulfate kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)111,4184
Polymers111,2262
Non-polymers1922
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4260 Å2
ΔGint-46 kcal/mol
Surface area40510 Å2
MethodPISA
2
C: adenylyl-sulfate kinase
D: adenylyl-sulfate kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)111,4184
Polymers111,2262
Non-polymers1922
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4350 Å2
ΔGint-45 kcal/mol
Surface area40220 Å2
MethodPISA
Unit cell
Length a, b, c (Å)144.449, 158.387, 226.163
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11D-602-

HOH

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Components

#1: Protein
adenylyl-sulfate kinase


Mass: 55612.859 Da / Num. of mol.: 4
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: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: SO4 / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 13 / 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: 2.91 Å3/Da / Density % sol: 57.7 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8
Details: 10 mM Tris-HCl (pH 8.0) 100 mM NaCl 1 mM TCEP 5 mM APS 5 mM AMP-PNP 5 mM MgCl2 0.24 M K2SO4 16% PEG3400

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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: Oct 28, 2023
RadiationMonochromator: SI111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9 Å / Relative weight: 1
ReflectionResolution: 2.59→50 Å / Num. obs: 79795 / % possible obs: 99.5 % / Redundancy: 6.1 % / CC1/2: 0.999 / Rmerge(I) obs: 0.066 / Net I/σ(I): 14.36
Reflection shellResolution: 2.59→2.75 Å / Mean I/σ(I) obs: 0.8 / Num. unique obs: 12586 / CC1/2: 0.531

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Processing

Software
NameVersionClassification
REFMAC5.8.0430refinement
XDSdata reduction
XDSdata scaling
CRANK2phasing
BUCCANEERmodel building
RefinementMethod to determine structure: SAD / Resolution: 2.595→19.97 Å / Cor.coef. Fo:Fc: 0.962 / Cor.coef. Fo:Fc free: 0.951 / Cross valid method: FREE R-VALUE / ESU R: 0.513 / ESU R Free: 0.303
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2648 3995 5.019 %
Rwork0.2265 75601 -
all0.228 --
obs-79596 99.308 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 111.398 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å2-0 Å2
2---0.001 Å2-0 Å2
3---0.001 Å2
Refinement stepCycle: LAST / Resolution: 2.595→19.97 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms14065 0 20 13 14098
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0040.01214376
X-RAY DIFFRACTIONr_bond_other_d0.0010.01614028
X-RAY DIFFRACTIONr_angle_refined_deg1.2851.82419499
X-RAY DIFFRACTIONr_angle_other_deg0.7691.76132523
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.89951798
X-RAY DIFFRACTIONr_dihedral_angle_2_deg11.572564
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.224102584
X-RAY DIFFRACTIONr_dihedral_angle_6_deg13.51510572
X-RAY DIFFRACTIONr_chiral_restr0.070.22259
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0216289
X-RAY DIFFRACTIONr_gen_planes_other0.0050.022943
X-RAY DIFFRACTIONr_nbd_refined0.2210.23009
X-RAY DIFFRACTIONr_symmetry_nbd_other0.2140.213060
X-RAY DIFFRACTIONr_nbtor_refined0.1750.27091
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0820.27552
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1370.2315
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.1140.227
X-RAY DIFFRACTIONr_nbd_other0.2370.2117
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1180.27
X-RAY DIFFRACTIONr_mcbond_it7.38810.9147216
X-RAY DIFFRACTIONr_mcbond_other7.38710.9147216
X-RAY DIFFRACTIONr_mcangle_it11.33719.6229006
X-RAY DIFFRACTIONr_mcangle_other11.33619.6229007
X-RAY DIFFRACTIONr_scbond_it7.56211.4277160
X-RAY DIFFRACTIONr_scbond_other7.5511.4317145
X-RAY DIFFRACTIONr_scangle_it11.81220.80710493
X-RAY DIFFRACTIONr_scangle_other11.79820.81510470
X-RAY DIFFRACTIONr_lrange_it15.98104.34715515
X-RAY DIFFRACTIONr_lrange_other15.981104.34715516
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRfactor allNum. reflection allFsc freeFsc work% reflection obs (%)WRfactor Rwork
2.595-2.6620.4882680.49553220.49557840.8490.85796.64590.531
2.662-2.7330.4832760.4653540.46156330.8620.87899.94670.484
2.733-2.8110.4812820.4551950.45154800.8770.87899.94530.461
2.811-2.8960.4282690.40450480.40553180.8880.90199.98120.399
2.896-2.9880.3733020.33948610.34151650.9110.92599.96130.321
2.988-3.0910.392290.31447790.31750160.8910.93199.84050.298
3.091-3.2050.3412540.29645740.29848320.9210.94299.91720.281
3.205-3.3320.3672480.30644430.3146960.9160.93999.89350.294
3.332-3.4760.3282120.29342610.29444910.9310.9599.59920.279
3.476-3.640.3272060.27440650.27642780.9280.95899.83640.26
3.64-3.8290.2811900.26139410.26241350.9480.96299.90330.248
3.829-4.0520.2992020.24236580.24538700.9460.96599.74160.234
4.052-4.320.2521950.20534890.20836890.9620.97599.86450.202
4.32-4.6480.2161820.17932660.18134540.9720.9899.82630.183
4.648-5.0640.2181680.18130010.18331770.9710.97999.74820.19
5.064-5.6170.2771340.19227860.19529280.9570.97999.72680.202
5.617-6.4020.2531180.20124740.20326040.9620.97899.53920.215
6.402-7.6460.2361210.19521390.19722760.9670.97799.2970.215
7.646-10.0990.186820.14717380.14918330.9770.98799.29080.179
10.099-19.970.139570.18412070.18212790.9890.97998.82720.228

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