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- PDB-9gn2: Nucleoside-2'-deoxyribosyltransferase from Lactobacillus leichman... -

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Basic information

Entry
Database: PDB / ID: 9gn2
TitleNucleoside-2'-deoxyribosyltransferase from Lactobacillus leichmannii. Complex with ribose and cytosine
ComponentsNucleoside deoxyribosyltransferase
KeywordsTRANSFERASE / Nucleoside-2'-deoxyribosyltransferase
Function / homologynucleoside deoxyribosyltransferase / nucleotide salvage / nucleoside deoxyribosyltransferase activity / Nucleoside 2-deoxyribosyltransferase / Nucleoside 2-deoxyribosyltransferase / 6-AMINOPYRIMIDIN-2(1H)-ONE / alpha-D-ribofuranose / Nucleoside deoxyribosyltransferase
Function and homology information
Biological speciesLactobacillus leichmannii (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.41 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

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)36,4584
Polymers36,1972
Non-polymers2612
Water1,15364
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)109,37412
Polymers108,5906
Non-polymers7846
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_555z,x,y1
crystal symmetry operation9_555y,z,x1
Unit cell
Length a, b, c (Å)148.981, 148.981, 148.981
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number199
Space group name H-MI213
Components on special symmetry positions
IDModelComponents
11B-229-

HOH

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Components

#1: Protein Nucleoside deoxyribosyltransferase


Mass: 18098.354 Da / Num. of mol.: 2
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
#2: Chemical ChemComp-CYT / 6-AMINOPYRIMIDIN-2(1H)-ONE / CYTOSINE


Mass: 111.102 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H5N3O / Feature type: SUBJECT OF INVESTIGATION
#3: Sugar ChemComp-RIB / alpha-D-ribofuranose / alpha-D-ribose / D-ribose / ribose


Type: D-saccharide, alpha linking / Mass: 150.130 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C5H10O5 / Feature type: SUBJECT OF INVESTIGATION
IdentifierTypeProgram
DRibfaCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
a-D-ribofuranoseCOMMON NAMEGMML 1.0
a-D-RibfIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
RibSNFG CARBOHYDRATE SYMBOLGMML 1.0
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 64 / 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: 3.81 Å3/Da / Density % sol: 67.69 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7 / Details: 35% 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: 0.976269 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: 0.976269 Å / Relative weight: 1
ReflectionResolution: 2.41→60.82 Å / Num. obs: 21394 / % possible obs: 100 % / Redundancy: 40.5 % / Biso Wilson estimate: 68 Å2 / CC1/2: 1 / Rmerge(I) obs: 0.07 / Rpim(I) all: 0.02 / Net I/σ(I): 35
Reflection shellResolution: 2.41→2.5 Å / Redundancy: 40.6 % / Rmerge(I) obs: 1.65 / Mean I/σ(I) obs: 3 / Num. unique obs: 2231 / CC1/2: 0.87 / Rpim(I) all: 0.37 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5refinement
XDSdata reduction
SCALAdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.41→60.82 Å / Cross valid method: FREE R-VALUE
RfactorNum. reflection% reflection
Rwork0.19 --
obs-21394 100 %
Refinement stepCycle: LAST / Resolution: 2.41→60.82 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2532 0 17 64 2613

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