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- PDB-8j5h: Crystal structure of kinase AbmG in complex with 4'-hydroxy-4'-th... -

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Basic information

Entry
Database: PDB / ID: 8j5h
TitleCrystal structure of kinase AbmG in complex with 4'-hydroxy-4'-thiocytidine
ComponentsDeoxyadenosine/deoxycytidine kinase
KeywordsTRANSFERASE / Albomycin / biosynthesis
Function / homology
Function and homology information


deoxynucleoside kinase activity / phosphorylation / nucleotide binding / cytoplasm
Similarity search - Function
: / Deoxynucleoside kinase domain / Deoxynucleoside kinase / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
NITRATE ION / : / Deoxyadenosine/deoxycytidine kinase
Similarity search - Component
Biological speciesStreptomyces sp. ATCC 700974 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.4 Å
AuthorsUshimaru, R. / Mori, T. / Liu, H.-w. / Abe, I.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: J.Am.Chem.Soc. / Year: 2025
Title: Biosynthesis of the Thiofuranose Core in Albomycin Requires a Versatile Enzyme AbmG That Catalyzes Net Dehydration via Cryptic Phosphorylation
Authors: Zheng, Z. / Ushimaru, R. / Mori, T. / Ruszczycky, M.W. / Abe, I. / Liu, H.W.
History
DepositionApr 22, 2023Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Apr 24, 2024Provider: repository / Type: Initial release
Revision 1.1Nov 5, 2025Group: Database references / Structure summary / Category: citation / citation_author / pdbx_entry_details
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.title / _citation.year / _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Deoxyadenosine/deoxycytidine kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,7423
Polymers27,4051
Non-polymers3372
Water4,378243
1
A: Deoxyadenosine/deoxycytidine kinase
hetero molecules

A: Deoxyadenosine/deoxycytidine kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)55,4846
Polymers54,8102
Non-polymers6754
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_555x,-y,-z1
Buried area3460 Å2
ΔGint-20 kcal/mol
Surface area20210 Å2
MethodPISA
Unit cell
Length a, b, c (Å)70.152, 77.572, 83.945
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221
Space group name HallC2c2
Symmetry operation#1: x,y,z
#2: x,-y,-z
#3: -x,y,-z+1/2
#4: -x,-y,z+1/2
#5: x+1/2,y+1/2,z
#6: x+1/2,-y+1/2,-z
#7: -x+1/2,y+1/2,-z+1/2
#8: -x+1/2,-y+1/2,z+1/2

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Components

#1: Protein Deoxyadenosine/deoxycytidine kinase / AbmG


Mass: 27404.893 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptomyces sp. ATCC 700974 (bacteria)
Production host: Escherichia coli (E. coli) / References: UniProt: A0A370RDE4
#2: Chemical ChemComp-TV0 / 4-azanyl-1-[(2~{R},3~{R},4~{S},5~{S})-5-(hydroxymethyl)-3,4,5-tris(oxidanyl)thiolan-2-yl]pyrimidin-2-one


Mass: 275.282 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C9H13N3O5S / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-NO3 / NITRATE ION


Mass: 62.005 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: NO3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 243 / 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: 2.08 Å3/Da / Density % sol: 40.97 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 0.03 M citrate, 0.07 M Bis-Tris propane, 28% PEG3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-1A / Wavelength: 1 Å
DetectorType: DECTRIS EIGER X 4M / Detector: PIXEL / Date: Nov 30, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.4→44.22 Å / Num. obs: 45024 / % possible obs: 99.4 % / Redundancy: 6.9 % / CC1/2: 1 / Rmerge(I) obs: 0.046 / Net I/σ(I): 21.3
Reflection shellResolution: 1.4→1.42 Å / Redundancy: 7 % / Rmerge(I) obs: 0.422 / Mean I/σ(I) obs: 3.9 / Num. unique obs: 2233 / CC1/2: 0.921 / % possible all: 98.3

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Processing

Software
NameVersionClassification
PHENIX1.19.2_4158refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.4→44.22 Å / SU ML: 0.1162 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 17.5866
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1904 1998 4.44 %
Rwork0.1737 43006 -
obs0.1744 45004 99.22 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 15.86 Å2
Refinement stepCycle: LAST / Resolution: 1.4→44.22 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1772 0 22 243 2037
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00581892
X-RAY DIFFRACTIONf_angle_d0.91312575
X-RAY DIFFRACTIONf_chiral_restr0.0716289
X-RAY DIFFRACTIONf_plane_restr0.0086340
X-RAY DIFFRACTIONf_dihedral_angle_d4.6878270
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.4-1.440.22581400.20392995X-RAY DIFFRACTION98.25
1.44-1.470.24121390.19713000X-RAY DIFFRACTION98.19
1.47-1.520.24761390.18213006X-RAY DIFFRACTION98.5
1.52-1.570.20771410.17943020X-RAY DIFFRACTION98.78
1.57-1.620.1911410.17983055X-RAY DIFFRACTION98.79
1.62-1.690.17781410.17543047X-RAY DIFFRACTION99.1
1.69-1.760.21141430.1763047X-RAY DIFFRACTION99.32
1.76-1.860.20891410.18353061X-RAY DIFFRACTION99.44
1.86-1.970.19141440.17533068X-RAY DIFFRACTION99.54
1.97-2.130.20731440.17043086X-RAY DIFFRACTION99.78
2.13-2.340.17181430.16553103X-RAY DIFFRACTION99.75
2.34-2.680.18871450.17343114X-RAY DIFFRACTION99.97
2.68-3.370.20091470.17363143X-RAY DIFFRACTION99.91
3.37-44.220.16071500.16623261X-RAY DIFFRACTION99.68

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