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- PDB-9gn4: Nucleoside-2'-deoxyribosyltransferase from Lactobacillus leichman... -

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Basic information

Entry
Database: PDB / ID: 9gn4
TitleNucleoside-2'-deoxyribosyltransferase from Lactobacillus leichmannii. Y7F/D72N mutant with cytidine
ComponentsNucleoside deoxyribosyltransferase
KeywordsTRANSFERASE / Nucleoside-2'-deoxyribosyltransferase
Function / homologynucleoside deoxyribosyltransferase / nucleotide salvage / nucleoside deoxyribosyltransferase activity / Nucleoside 2-deoxyribosyltransferase / Nucleoside 2-deoxyribosyltransferase / 4-AMINO-1-BETA-D-RIBOFURANOSYL-2(1H)-PYRIMIDINONE / Nucleoside deoxyribosyltransferase
Function and homology information
Biological speciesLactobacillus leichmannii (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.48 Å
AuthorsAscham, A. / Salihovic, A. / Burley, G. / Grogan, G.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: Chem Sci / Year: 2025
Title: Biocatalytic synthesis of ribonucleoside analogues using nucleoside transglycosylase-2.
Authors: Salihovic, A. / Ascham, A. / Rosenqvist, P.S. / Taladriz-Sender, A. / Hoskisson, P.A. / Hodgson, D.R.W. / Grogan, G. / Burley, G.A.
History
DepositionAug 30, 2024Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 25, 2024Provider: repository / Type: Initial release
Revision 1.1Jan 1, 2025Group: Database references / Category: citation / citation_author
Item: _citation.journal_id_ISSN / _citation.pdbx_database_id_PubMed ..._citation.journal_id_ISSN / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID
Revision 1.2Jan 29, 2025Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.year

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Nucleoside deoxyribosyltransferase
B: Nucleoside deoxyribosyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,6494
Polymers36,1632
Non-polymers4862
Water1,982110
1
A: Nucleoside deoxyribosyltransferase
B: Nucleoside deoxyribosyltransferase
hetero molecules

A: Nucleoside deoxyribosyltransferase
B: Nucleoside deoxyribosyltransferase
hetero molecules

A: Nucleoside deoxyribosyltransferase
B: Nucleoside deoxyribosyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)109,94812
Polymers108,4886
Non-polymers1,4596
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_555z,x,y1
crystal symmetry operation9_555y,z,x1
Buried area20790 Å2
ΔGint-119 kcal/mol
Surface area32170 Å2
Unit cell
Length a, b, c (Å)150.134, 150.134, 150.134
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number199
Space group name H-MI213

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Components

#1: Protein Nucleoside deoxyribosyltransferase / N-deoxyribosyltransferase


Mass: 18081.369 Da / Num. of mol.: 2 / Mutation: Y7F, D72N
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Lactobacillus leichmannii (bacteria) / Gene: ntd / Production host: Escherichia coli (E. coli)
References: UniProt: Q9R5V5, nucleoside deoxyribosyltransferase
#2: Chemical ChemComp-CTN / 4-AMINO-1-BETA-D-RIBOFURANOSYL-2(1H)-PYRIMIDINONE / CYTIDINE


Mass: 243.217 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C9H13N3O5 / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 110 / 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: 3.9 Å3/Da / Density % sol: 68.45 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7 / Details: 25% tascimate, pH 7.0

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Data collection

DiffractionMean temperature: 120 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.976277 Å
DetectorType: DECTRIS EIGER2 XE 16M / Detector: PIXEL / Date: Jun 26, 2024
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.976277 Å / Relative weight: 1
ReflectionResolution: 2.48→61.37 Å / Num. obs: 20103 / % possible obs: 100 % / Redundancy: 41.6 % / Biso Wilson estimate: 47 Å2 / CC1/2: 1 / Rmerge(I) obs: 0.16 / Rpim(I) all: 0.14 / Net I/σ(I): 26.1
Reflection shellResolution: 2.48→2.58 Å / Rmerge(I) obs: 1.56 / Mean I/σ(I) obs: 3.9 / Num. unique obs: 2256 / CC1/2: 0.9 / Rpim(I) all: 0.34

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Processing

Software
NameVersionClassification
REFMAC5.8.0430refinement
XDSdata reduction
SCALAdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.48→61.37 Å / Cor.coef. Fo:Fc: 0.965 / Cor.coef. Fo:Fc free: 0.958 / SU B: 5.473 / SU ML: 0.123 / Cross valid method: THROUGHOUT / ESU R: 0.232 / ESU R Free: 0.177 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.18773 1044 5.2 %RANDOM
Rwork0.16316 ---
obs0.16446 19055 99.97 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 50.313 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refinement stepCycle: 1 / Resolution: 2.48→61.37 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2519 0 34 111 2664
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0122621
X-RAY DIFFRACTIONr_bond_other_d0.0010.0162370
X-RAY DIFFRACTIONr_angle_refined_deg1.71.8153563
X-RAY DIFFRACTIONr_angle_other_deg0.6221.7565470
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.3435312
X-RAY DIFFRACTIONr_dihedral_angle_2_deg10.85355
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.98310409
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.1020.2374
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.023061
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02597
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_it4.5485.0941254
X-RAY DIFFRACTIONr_mcbond_other4.5485.0931254
X-RAY DIFFRACTIONr_mcangle_it5.8399.1451564
X-RAY DIFFRACTIONr_mcangle_other5.8399.1451565
X-RAY DIFFRACTIONr_scbond_it6.0785.581367
X-RAY DIFFRACTIONr_scbond_other6.0765.5841368
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other8.09210.0682000
X-RAY DIFFRACTIONr_long_range_B_refined9.49951.372912
X-RAY DIFFRACTIONr_long_range_B_other9.47450.672893
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.48→2.545 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.246 94 -
Rwork0.206 1391 -
obs--100 %

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