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- PDB-8j5g: Crystal structure of kinase AbmG in complex with 4'-hydroxy-4'-th... -

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Basic information

Entry
Database: PDB / ID: 8j5g
TitleCrystal structure of kinase AbmG in complex with 4'-hydroxy-4'-thiocytidine 5'-diphosphate
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: 1.5 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)27,8392
Polymers27,4041
Non-polymers4351
Water5,423301
1
A: Deoxyadenosine/deoxycytidine kinase
hetero molecules

A: Deoxyadenosine/deoxycytidine kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)55,6784
Polymers54,8082
Non-polymers8702
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_555x,-y,-z1
Buried area2990 Å2
ΔGint-27 kcal/mol
Surface area19400 Å2
MethodPISA
Unit cell
Length a, b, c (Å)71.415, 78.344, 83.414
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
Components on special symmetry positions
IDModelComponents
11A-526-

HOH

21A-583-

HOH

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Components

#1: Protein Deoxyadenosine/deoxycytidine kinase / AbmG


Mass: 27403.908 Da / Num. of mol.: 1 / Mutation: E188Q
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-TT9 / [(2~{S},3~{S},4~{R},5~{R})-5-(4-azanyl-2-oxidanylidene-pyrimidin-1-yl)-2-(hydroxymethyl)-3,4-bis(oxidanyl)thiolan-2-yl] phosphono hydrogen phosphate


Mass: 435.241 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C9H15N3O11P2S / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 301 / 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: 2.13 Å3/Da / Density % sol: 42.22 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 0.03 M citrate, 0.07 M Bis-Tris propane, 28% PEG 3350

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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: 1.5→44.6 Å / Num. obs: 37780 / % possible obs: 100 % / Redundancy: 7.5 % / Biso Wilson estimate: 12.55 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.084 / Net I/σ(I): 13.4
Reflection shellResolution: 1.5→1.53 Å / Redundancy: 7.7 % / Rmerge(I) obs: 0.625 / Mean I/σ(I) obs: 3.2 / Num. unique obs: 1824 / CC1/2: 0.933 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX1.19.2_4158refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.5→44.6 Å / SU ML: 0.1467 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 18.7237
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1962 1998 5.29 %
Rwork0.168 35743 -
obs0.1694 37741 99.95 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 16.51 Å2
Refinement stepCycle: LAST / Resolution: 1.5→44.6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1831 0 26 301 2158
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00591921
X-RAY DIFFRACTIONf_angle_d1.05372614
X-RAY DIFFRACTIONf_chiral_restr0.0539289
X-RAY DIFFRACTIONf_plane_restr0.0093344
X-RAY DIFFRACTIONf_dihedral_angle_d5.1054276
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.5-1.540.23671390.20582501X-RAY DIFFRACTION99.81
1.54-1.580.25451400.19242507X-RAY DIFFRACTION99.92
1.58-1.630.20781420.18222530X-RAY DIFFRACTION99.96
1.63-1.680.22051410.17222529X-RAY DIFFRACTION100
1.68-1.740.22261420.17122535X-RAY DIFFRACTION99.96
1.74-1.810.20781420.16842534X-RAY DIFFRACTION100
1.81-1.890.17721410.17232537X-RAY DIFFRACTION99.96
1.89-1.990.20061420.16782541X-RAY DIFFRACTION99.89
1.99-2.110.19381430.16112553X-RAY DIFFRACTION99.93
2.11-2.280.20691420.16062532X-RAY DIFFRACTION100
2.28-2.510.18411440.16742568X-RAY DIFFRACTION99.96
2.51-2.870.21961430.17832570X-RAY DIFFRACTION99.96
2.87-3.610.18431460.16612603X-RAY DIFFRACTION99.96
3.61-44.60.17531510.15682703X-RAY DIFFRACTION99.96

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