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

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Basic information

Entry
Database: PDB / ID: 9emw
TitleNucleoside 2'deoxyribosyltransferase from Chroococcidiopsis thermalis PCC 7203 Y7F Mutant bound to ImmH-Forodesine
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 / Chem-IMH / Nucleoside 2-deoxyribosyltransferase
Function and homology information
Biological speciesChroococcidiopsis thermalis PCC 7203 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.51 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 14, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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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)71,7588
Polymers70,6934
Non-polymers1,0654
Water93752
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 area15050 Å2
ΔGint-76 kcal/mol
Surface area21470 Å2
Unit cell
Length a, b, c (Å)135.760, 135.760, 87.550
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number173
Space group name H-MP63

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Components

#1: Protein
Nucleoside 2-deoxyribosyltransferase


Mass: 17673.146 Da / Num. of mol.: 4 / Mutation: Y7F
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-IMH / 1,4-DIDEOXY-4-AZA-1-(S)-(9-DEAZAHYPOXANTHIN-9-YL)-D-RIBITOL / Forodesine / Immucillin H


Mass: 266.253 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C11H14N4O4 / Feature type: SUBJECT OF INVESTIGATION / Comment: inhibitor*YM
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 52 / 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: 3.31 Å3/Da / Density % sol: 62.89 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 0.1 M Tris pH 8.0, 0.002 M Zinc chloride, 20% w/v PEG6000

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Data collection

DiffractionMean temperature: 298 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.9795 Å
DetectorType: DECTRIS EIGER2 XE 16M / Detector: PIXEL / Date: May 31, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 2.44→70.21 Å / Num. obs: 33966 / % possible obs: 99.12 % / Redundancy: 16.1 % / CC1/2: 0.997 / Rmerge(I) obs: 0.16 / Rpim(I) all: 0.038 / Rrim(I) all: 0.165 / Net I/σ(I): 9.4
Reflection shellResolution: 2.44→2.48 Å / Rmerge(I) obs: 1.833 / Mean I/σ(I) obs: 0.3 / Num. unique obs: 1529 / CC1/2: 0.295 / Rpim(I) all: 0.859 / Rrim(I) all: 2.036

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Processing

Software
NameVersionClassification
REFMAC5.8.0430refinement
xia23.10.dev0data reduction
DIALS3.devdata scaling
PHENIX1.19.2-4158phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.51→70.21 Å / Cor.coef. Fo:Fc: 0.951 / Cor.coef. Fo:Fc free: 0.805 / SU B: 11.957 / SU ML: 0.24 / Cross valid method: THROUGHOUT / ESU R: 0.349 / ESU R Free: 0.266 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.25261 1565 5 %RANDOM
Rwork0.18718 ---
obs0.19026 29897 99.82 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 71.296 Å2
Baniso -1Baniso -2Baniso -3
1-1.19 Å20.59 Å20 Å2
2--1.19 Å2-0 Å2
3----3.85 Å2
Refinement stepCycle: 1 / Resolution: 2.51→70.21 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5033 0 0 52 5085
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0125169
X-RAY DIFFRACTIONr_bond_other_d0.0030.0164814
X-RAY DIFFRACTIONr_angle_refined_deg2.3851.8117031
X-RAY DIFFRACTIONr_angle_other_deg0.9031.75911050
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.5535609
X-RAY DIFFRACTIONr_dihedral_angle_2_deg12.929531
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.05310834
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.1140.2749
X-RAY DIFFRACTIONr_gen_planes_refined0.010.026156
X-RAY DIFFRACTIONr_gen_planes_other0.0040.021269
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it8.2566.8182448
X-RAY DIFFRACTIONr_mcbond_other8.256.8162447
X-RAY DIFFRACTIONr_mcangle_it10.98412.293053
X-RAY DIFFRACTIONr_mcangle_other10.98212.2913054
X-RAY DIFFRACTIONr_scbond_it12.0667.632721
X-RAY DIFFRACTIONr_scbond_other12.0647.6292721
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other16.34713.7473979
X-RAY DIFFRACTIONr_long_range_B_refined20.05371.245661
X-RAY DIFFRACTIONr_long_range_B_other20.05471.265660
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.51→2.575 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.36 108 -
Rwork0.366 2162 -
obs--97.72 %

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