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- PDB-9emx: Nucleoside 2'deoxyribosyltransferase from Chroococcidiopsis therm... -

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Basic information

Entry
Database: PDB / ID: 9emx
TitleNucleoside 2'deoxyribosyltransferase from Chroococcidiopsis thermalis PCC 7203 Double Mutant Y7F A9S bound to Cordycepin
ComponentsNucleoside 2-deoxyribosyltransferase
KeywordsTRANSFERASE / Mutant / Clofarabine / Ligand
Function / homologydeoxyribonucleoside monophosphate catabolic process / 5-hydroxymethyl-dUMP N-hydrolase activity / : / Nucleoside 2-deoxyribosyltransferase / Nucleoside 2-deoxyribosyltransferase / transferase activity / metal ion binding / 3'-DEOXYADENOSINE / Nucleoside 2-deoxyribosyltransferase
Function and homology information
Biological speciesChroococcidiopsis thermalis PCC 7203 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.77 Å
AuthorsTang, P. / Harding, C.J. / Czekster, C.M.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
Other privateIBioIC 2020-2-1 United Kingdom
CitationJournal: To Be Published
Title: Engineered nucleoside 2'-deoxyribonsyltransferase enzymes enable scalable synthesis of diverse nucleoside analogues
Authors: Tang, P. / Harding, C.J. / Czekster, C.M.
History
DepositionMar 11, 2024Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 7, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Nucleoside 2-deoxyribosyltransferase
B: Nucleoside 2-deoxyribosyltransferase
C: Nucleoside 2-deoxyribosyltransferase
D: Nucleoside 2-deoxyribosyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)72,2868
Polymers71,2814
Non-polymers1,0054
Water8,089449
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration, The corresponding mass of ~62kDa calculated from a calibration curve of Superdex 75 Increase 10/300 GL
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area13740 Å2
ΔGint-66 kcal/mol
Surface area22390 Å2
Unit cell
Length a, b, c (Å)97.380, 97.380, 66.456
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number145
Space group name H-MP32

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Components

#1: Protein
Nucleoside 2-deoxyribosyltransferase


Mass: 17820.344 Da / Num. of mol.: 4 / Mutation: Y7F A9S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Chroococcidiopsis thermalis PCC 7203 (bacteria)
Strain: PCC 7203 / Gene: Chro_1188 / Production host: Escherichia coli B (bacteria) / References: UniProt: K9TVX3
#2: Chemical
ChemComp-3AD / 3'-DEOXYADENOSINE


Mass: 251.242 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C10H13N5O3 / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 449 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationY

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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: 2.55 Å3/Da / Density % sol: 51.81 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 0.1 M Bis-Tris Propane, pH 8.33, 21.429% PEG Smear High, 0.05 M MgCl2

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Data collection

DiffractionMean temperature: 298 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I24 / Wavelength: 0.97 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Jul 2, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97 Å / Relative weight: 1
ReflectionResolution: 1.77→84.33 Å / Num. obs: 68981 / % possible obs: 99.64 % / Redundancy: 9.8 % / CC1/2: 0.991 / Rmerge(I) obs: 0.181 / Rpim(I) all: 0.059 / Rrim(I) all: 0.191 / Net I/σ(I): 5.9
Reflection shellResolution: 1.77→1.8 Å / Redundancy: 5.8 % / Rmerge(I) obs: 1.052 / Mean I/σ(I) obs: 0.2 / Num. unique obs: 3232 / CC1/2: 0.158 / Rpim(I) all: 0.459 / Rrim(I) all: 1.153 / % possible all: 92.21

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Processing

Software
NameVersionClassification
PHENIX1.19.2-4158refinement
xia23.14.0data reduction
DIALS3.14.1-1-ge7f638df6-releasedata scaling
PHENIX1.19.2-4158phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.77→42.17 Å / SU ML: 0.33 / Cross valid method: FREE R-VALUE / σ(F): 1.96 / Phase error: 33.17 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2111 1930 2.97 %
Rwork0.1884 --
obs0.1891 64882 93.98 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.77→42.17 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4958 0 72 449 5479
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_dihedral_angle_d5.77670
X-RAY DIFFRACTIONf_chiral_restr0.055746
X-RAY DIFFRACTIONf_plane_restr0.01907
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.77-1.810.4836750.45262509X-RAY DIFFRACTION52
1.81-1.860.3778980.38963492X-RAY DIFFRACTION73
1.86-1.920.36681190.37324384X-RAY DIFFRACTION92
1.92-1.980.39161590.37884760X-RAY DIFFRACTION100
1.98-2.050.44941220.3984779X-RAY DIFFRACTION100
2.05-2.130.32071320.29664819X-RAY DIFFRACTION100
2.13-2.230.22951360.1934775X-RAY DIFFRACTION100
2.23-2.340.25751620.21334767X-RAY DIFFRACTION100
2.34-2.490.22581660.19974782X-RAY DIFFRACTION100
2.49-2.680.22471560.18874803X-RAY DIFFRACTION100
2.68-2.950.1791350.17754763X-RAY DIFFRACTION100
2.95-3.380.18271440.1764779X-RAY DIFFRACTION100
3.38-4.260.18291490.13834778X-RAY DIFFRACTION100
4.26-42.170.16281770.14124762X-RAY DIFFRACTION100
Refinement TLS params.Method: refined / Origin x: 34.7117 Å / Origin y: -1.1599 Å / Origin z: -2.4913 Å
111213212223313233
T0.2871 Å20.0166 Å2-0.0045 Å2-0.2836 Å2-0.0035 Å2--0.2905 Å2
L0.2536 °20.0183 °20.1314 °2-0.5214 °2-0.055 °2--0.2348 °2
S-0.0215 Å °-0.0387 Å °-0.0107 Å °-0.0618 Å °-0.0214 Å °0.0263 Å °-0.0184 Å °-0.0266 Å °0.0001 Å °
Refinement TLS groupSelection details: all

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