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- PDB-8j5e: Crystal structure of kinase AbmG in complex with 4'-thiocytidine -

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Basic information

Entry
Database: PDB / ID: 8j5e
TitleCrystal structure of kinase AbmG in complex with 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
: / Deoxyadenosine/deoxycytidine kinase
Similarity search - Component
Biological speciesStreptomyces sp. ATCC 700974 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 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)27,6642
Polymers27,4051
Non-polymers2591
Water4,684260
1
A: Deoxyadenosine/deoxycytidine kinase
hetero molecules

A: Deoxyadenosine/deoxycytidine kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)55,3284
Polymers54,8102
Non-polymers5192
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_555x,-y,-z1
Buried area3080 Å2
ΔGint-25 kcal/mol
Surface area19780 Å2
MethodPISA
Unit cell
Length a, b, c (Å)70.642, 78.108, 84.089
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
Details: Author's provided sample sequence corresponds to the reference sequence (A0A370RDE4) in the UniProt database.
Source: (gene. exp.) Streptomyces sp. ATCC 700974 (bacteria)
Production host: Escherichia coli (E. coli) / References: UniProt: A0A370RDE4
#2: Chemical ChemComp-TQR / 4-azanyl-1-[(2~{R},3~{R},4~{S},5~{R})-5-(hydroxymethyl)-3,4-bis(oxidanyl)thiolan-2-yl]pyrimidin-2-one


Mass: 259.282 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C9H13N3O4S / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 260 / 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: 2.12 Å3/Da / Density % sol: 41.88 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: 0.2 M magnesium nitrate, 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: 1.1 Å
DetectorType: DECTRIS EIGER X 4M / Detector: PIXEL / Date: Nov 7, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.1 Å / Relative weight: 1
ReflectionResolution: 1.7→44.47 Å / Num. obs: 25964 / % possible obs: 99.9 % / Redundancy: 14.9 % / Biso Wilson estimate: 16.24 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.108 / Net I/σ(I): 16.9
Reflection shellResolution: 1.7→1.73 Å / Redundancy: 11.1 % / Rmerge(I) obs: 0.682 / Mean I/σ(I) obs: 3.3 / Num. unique obs: 1332 / CC1/2: 0.871 / % possible all: 99.1

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Processing

Software
NameVersionClassification
PHENIX1.19.2_4158refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.7→44.47 Å / SU ML: 0.1682 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 19.7351
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2139 2000 7.71 %
Rwork0.171 23939 -
obs0.1743 25939 99.94 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 20.23 Å2
Refinement stepCycle: LAST / Resolution: 1.7→44.47 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1825 0 17 260 2102
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00691899
X-RAY DIFFRACTIONf_angle_d0.98082575
X-RAY DIFFRACTIONf_chiral_restr0.0558286
X-RAY DIFFRACTIONf_plane_restr0.0082340
X-RAY DIFFRACTIONf_dihedral_angle_d4.9596269
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.7-1.740.25811400.20621676X-RAY DIFFRACTION99.23
1.74-1.790.25331400.19651683X-RAY DIFFRACTION100
1.79-1.840.24531420.18651681X-RAY DIFFRACTION99.95
1.84-1.90.23311410.18331699X-RAY DIFFRACTION100
1.9-1.970.22711420.18171694X-RAY DIFFRACTION100
1.97-2.050.23161410.17321691X-RAY DIFFRACTION100
2.05-2.140.20351410.16151690X-RAY DIFFRACTION100
2.14-2.250.20111430.15261705X-RAY DIFFRACTION100
2.25-2.40.20981430.17171711X-RAY DIFFRACTION100
2.4-2.580.23821410.17361689X-RAY DIFFRACTION100
2.58-2.840.22631440.18621729X-RAY DIFFRACTION100
2.84-3.250.22031440.17081725X-RAY DIFFRACTION100
3.25-4.10.18131460.14911742X-RAY DIFFRACTION100
4.1-44.470.20381520.17441824X-RAY DIFFRACTION100

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