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- PDB-9f09: Nucleoside-2'-deoxyribosyltransferase from Lactobacillus leichman... -

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Basic information

Entry
Database: PDB / ID: 9f09
TitleNucleoside-2'-deoxyribosyltransferase from Lactobacillus leichmannii. Complex with 2-deoxyribose, 7-Bromo-1H-imidazo[4,5-b]pyridine and 2'-deoxycytidine
ComponentsNucleoside deoxyribosyltransferase
KeywordsTRANSFERASE / Nucleoside-2'-deoxyribosyltransferase
Function / homologynucleoside deoxyribosyltransferase / nucleotide salvage / nucleoside deoxyribosyltransferase activity / Nucleoside 2-deoxyribosyltransferase / Nucleoside 2-deoxyribosyltransferase / 2-deoxy-beta-D-erythro-pentofuranose / : / 2'-DEOXYCYTIDINE / Nucleoside deoxyribosyltransferase
Function and homology information
Biological speciesLactobacillus leichmannii (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.37 Å
AuthorsAscham, A. / Salihovic, A. / Burley, G. / Grogan, G.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: Chem Sci / Year: 2024
Title: Gram-scale enzymatic synthesis of 2'-deoxyribonucleoside analogues using nucleoside transglycosylase-2.
Authors: Salihovic, A. / Ascham, A. / Taladriz-Sender, A. / Bryson, S. / Withers, J.M. / McKean, I.J.W. / Hoskisson, P.A. / Grogan, G. / Burley, G.A.
History
DepositionApr 15, 2024Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 4, 2024Provider: 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 deoxyribosyltransferase
B: Nucleoside deoxyribosyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,9546
Polymers36,1972
Non-polymers7574
Water1,00956
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)110,86218
Polymers108,5906
Non-polymers2,27212
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)148.885, 148.885, 148.885
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number199
Space group name H-MI213
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21A

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: MET / Beg label comp-ID: MET / End auth comp-ID: TYR / End label comp-ID: TYR / Auth asym-ID: A / Label asym-ID: A / Auth seq-ID: 1 - 157 / Label seq-ID: 1 - 157

Dom-ID
1
2

NCS ensembles : (Details: Local NCS retraints between domains: 1 2)

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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-DCZ / 2'-DEOXYCYTIDINE


Type: DNA OH 5 prime terminus / Mass: 227.217 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C9H13N3O4 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-A1H8P / 7-bromanyl-3~{H}-imidazo[4,5-b]pyridine


Mass: 198.020 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H4BrN3 / Feature type: SUBJECT OF INVESTIGATION
#4: Sugar ChemComp-2DR / 2-deoxy-beta-D-erythro-pentofuranose / 2-deoxy-beta-D-ribofuranose / 2-deoxy-beta-D-erythro-pentose / 2-deoxy-D-erythro-pentose / 2-deoxy-erythro-pentose


Type: D-saccharide, beta linking / Mass: 134.130 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C5H10O4 / Feature type: SUBJECT OF INVESTIGATION
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 56 / 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: 3.8 Å3/Da / Density % sol: 67.62 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7 / Details: 0.2 M sodium citrate; 20% PEG 3350 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: Jan 20, 2024
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.976277 Å / Relative weight: 1
ReflectionResolution: 2.37→60.856 Å / Num. obs: 22441 / % possible obs: 100 % / Redundancy: 41.7 % / Biso Wilson estimate: 56 Å2 / CC1/2: 1 / Rmerge(I) obs: 0.09 / Rpim(I) all: 0.02 / Net I/σ(I): 33.3
Reflection shellResolution: 2.37→2.46 Å / Redundancy: 43.5 % / Rmerge(I) obs: 1.48 / Mean I/σ(I) obs: 3.6 / Num. unique obs: 2337 / CC1/2: 0.91 / Rpim(I) all: 0.32

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Processing

Software
NameVersionClassification
REFMAC5.8.0425refinement
XDSdata reduction
SCALAdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.37→60.856 Å / Cor.coef. Fo:Fc: 0.964 / Cor.coef. Fo:Fc free: 0.951 / SU B: 6.086 / SU ML: 0.141 / Cross valid method: FREE R-VALUE / ESU R: 0.219 / ESU R Free: 0.179
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.211 1133 5.049 %
Rwork0.184 21306 -
all0.185 --
obs-22439 99.982 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 59.782 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refinement stepCycle: LAST / Resolution: 2.37→60.856 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2524 0 44 56 2624
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0122638
X-RAY DIFFRACTIONr_bond_other_d0.0010.0162384
X-RAY DIFFRACTIONr_angle_refined_deg1.6951.8233582
X-RAY DIFFRACTIONr_angle_other_deg0.6051.7655502
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.4015312
X-RAY DIFFRACTIONr_dihedral_angle_2_deg9.98655
X-RAY DIFFRACTIONr_dihedral_angle_other_2_deg19.764202
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.84910418
X-RAY DIFFRACTIONr_dihedral_angle_6_deg13.03410130
X-RAY DIFFRACTIONr_chiral_restr0.0940.2371
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.023082
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02597
X-RAY DIFFRACTIONr_nbd_refined0.2270.2538
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1970.22167
X-RAY DIFFRACTIONr_nbtor_refined0.1910.21285
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0870.21349
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2430.267
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_other0.4420.22
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.1540.213
X-RAY DIFFRACTIONr_nbd_other0.2410.277
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1870.23
X-RAY DIFFRACTIONr_mcbond_it5.5145.9031254
X-RAY DIFFRACTIONr_mcbond_other5.4945.9021254
X-RAY DIFFRACTIONr_mcangle_it7.31710.5961564
X-RAY DIFFRACTIONr_mcangle_other7.31510.5961565
X-RAY DIFFRACTIONr_scbond_it6.426.4441384
X-RAY DIFFRACTIONr_scbond_other6.4196.4441384
X-RAY DIFFRACTIONr_scangle_it8.79511.6412018
X-RAY DIFFRACTIONr_scangle_other8.79311.6412019
X-RAY DIFFRACTIONr_lrange_it10.62957.8232971
X-RAY DIFFRACTIONr_lrange_other10.62857.8252972
X-RAY DIFFRACTIONr_ncsr_local_group_10.0820.055164
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDRefine-IDTypeRms dev position (Å)Weight position
11AX-RAY DIFFRACTIONLocal ncs0.081940.05009
12AX-RAY DIFFRACTIONLocal ncs0.081940.05009
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRfactor allNum. reflection allFsc freeFsc work% reflection obs (%)WRfactor Rwork
2.37-2.4320.315770.2415800.24316590.9410.96999.87940.209
2.432-2.4980.276800.2315250.23216050.9590.9711000.197
2.498-2.570.311830.24714580.25115410.9460.9691000.211
2.57-2.6490.246530.22614610.22715140.9680.9731000.191
2.649-2.7360.338630.23514040.23914670.9360.9711000.2
2.736-2.8320.263650.21213450.21414100.9560.9741000.182
2.832-2.9390.212790.19313050.19413840.9720.9761000.168
2.939-3.0580.23600.20312680.20513280.960.9731000.181
3.058-3.1940.262790.22811880.2312670.9570.9681000.207
3.194-3.3490.264630.2111300.21411930.9560.9721000.196
3.349-3.530.236540.20711100.20811640.9710.9771000.194
3.53-3.7430.23480.1910540.19211020.980.9791000.183
3.743-4.0010.199630.1779670.17810300.9780.9861000.172
4.001-4.320.152530.1459170.1469700.9870.9891000.142
4.32-4.730.17510.1298220.1318730.9850.991000.128
4.73-5.2840.132470.1527810.158280.9910.9871000.15
5.284-6.0940.242350.1796690.1827040.9670.9831000.178
6.094-7.4440.196310.1675930.1686240.9760.9841000.168
7.444-10.450.179330.1454500.1474830.9780.9881000.153
10.45-60.8560.238160.2422790.2422950.9690.9621000.252

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