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

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Basic information

Entry
Database: PDB / ID: 9ezk
TitleNucleoside-2'-deoxyribosyltransferase from Lactobacillus leichmannii (apo).
ComponentsNucleoside deoxyribosyltransferase
KeywordsTRANSFERASE / Nucleoside-2'-deoxyribosyltransferase
Function / homologynucleoside deoxyribosyltransferase / nucleotide salvage / nucleoside deoxyribosyltransferase activity / Nucleoside 2-deoxyribosyltransferase / Nucleoside 2-deoxyribosyltransferase / Nucleoside deoxyribosyltransferase
Function and homology information
Biological speciesLactobacillus leichmannii (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.79 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 12, 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


Theoretical massNumber of molelcules
Total (without water)36,1972
Polymers36,1972
Non-polymers00
Water18010
1
A: Nucleoside deoxyribosyltransferase
B: Nucleoside deoxyribosyltransferase

A: Nucleoside deoxyribosyltransferase
B: Nucleoside deoxyribosyltransferase

A: Nucleoside deoxyribosyltransferase
B: Nucleoside deoxyribosyltransferase


Theoretical massNumber of molelcules
Total (without water)108,5906
Polymers108,5906
Non-polymers00
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_555z,x,y1
crystal symmetry operation9_555y,z,x1
Buried area17080 Å2
ΔGint-127 kcal/mol
Surface area33270 Å2
Unit cell
Length a, b, c (Å)149.270, 149.270, 149.270
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: PRO / Beg label comp-ID: PRO / End auth comp-ID: VAL / End label comp-ID: VAL / Auth asym-ID: A / Label asym-ID: A / Auth seq-ID: 2 - 156 / Label seq-ID: 2 - 156

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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 10 / Source method: isolated from a natural source / Formula: H2O
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: 3.83 Å3/Da / Density % sol: 67.87 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 20 mM NaH2PO4 buffer; 0.2M sodium citrate; 20% (w/v) PEG 3350

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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: 2.79→60.94 Å / Num. obs: 13954 / % possible obs: 100 % / Redundancy: 40.8 % / Biso Wilson estimate: 75 Å2 / CC1/2: 1 / Rmerge(I) obs: 0.15 / Rpim(I) all: 0.03 / Net I/σ(I): 22.6
Reflection shellResolution: 2.79→2.94 Å / Rmerge(I) obs: 2.2 / Mean I/σ(I) obs: 2.3 / Num. unique obs: 2028 / CC1/2: 0.82 / Rpim(I) all: 0.49

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Processing

Software
NameVersionClassification
REFMAC5.8.0425refinement
XDSdata reduction
SCALAdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.79→52.831 Å / Cor.coef. Fo:Fc: 0.964 / Cor.coef. Fo:Fc free: 0.937 / SU B: 12.347 / SU ML: 0.23 / Cross valid method: THROUGHOUT / ESU R: 0.433 / ESU R Free: 0.294
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflectionSelection details
Rfree0.2374 723 5.182 %RANDOM
Rwork0.1717 13228 --
all0.175 ---
obs-13951 99.971 %-
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: 77.264 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refinement stepCycle: LAST / Resolution: 2.79→52.831 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2500 0 0 10 2510
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0122566
X-RAY DIFFRACTIONr_bond_other_d0.0010.0162308
X-RAY DIFFRACTIONr_angle_refined_deg1.8381.8183490
X-RAY DIFFRACTIONr_angle_other_deg0.6351.7525322
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.3825311
X-RAY DIFFRACTIONr_dihedral_angle_2_deg10.25255
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.39610400
X-RAY DIFFRACTIONr_dihedral_angle_6_deg13.95410129
X-RAY DIFFRACTIONr_chiral_restr0.0870.2365
X-RAY DIFFRACTIONr_chiral_restr_other0.0380.21
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.023027
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02585
X-RAY DIFFRACTIONr_nbd_refined0.2160.2484
X-RAY DIFFRACTIONr_symmetry_nbd_other0.2020.22052
X-RAY DIFFRACTIONr_nbtor_refined0.1920.21235
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0840.21274
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1610.252
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.0980.212
X-RAY DIFFRACTIONr_nbd_other0.2510.265
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.0430.21
X-RAY DIFFRACTIONr_mcbond_it6.9637.7421250
X-RAY DIFFRACTIONr_mcbond_other6.9637.7421250
X-RAY DIFFRACTIONr_mcangle_it8.88213.9471559
X-RAY DIFFRACTIONr_mcangle_other8.88213.9471560
X-RAY DIFFRACTIONr_scbond_it8.3888.1991316
X-RAY DIFFRACTIONr_scbond_other8.3888.1991316
X-RAY DIFFRACTIONr_scangle_it10.68814.9131931
X-RAY DIFFRACTIONr_scangle_other10.68614.9111932
X-RAY DIFFRACTIONr_lrange_it11.35774.7172792
X-RAY DIFFRACTIONr_lrange_other11.35574.7282793
X-RAY DIFFRACTIONr_ncsr_local_group_10.080.054953
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDRefine-IDTypeRms dev position (Å)Weight position
11AX-RAY DIFFRACTIONLocal ncs0.079760.05009
12AX-RAY DIFFRACTIONLocal ncs0.079760.05009
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
2.79-2.8620.439540.2629720.27110260.90.9571000.239
2.862-2.9410.385410.2829520.2869930.9090.9541000.254
2.941-3.0260.33450.2649260.2689710.9410.9581000.235
3.026-3.1180.3530.2538830.2569360.9410.9581000.22
3.118-3.220.405300.2548760.269060.9130.9611000.223
3.22-3.3330.297530.228320.2258850.9460.9691000.194
3.333-3.4580.24520.1987810.28330.9660.9791000.171
3.458-3.5990.223540.1647650.1688200.9710.98499.87810.142
3.599-3.7580.226320.1637600.1657920.9750.9841000.142
3.758-3.940.241300.167210.1647510.9660.9831000.141
3.94-4.1520.186470.146780.1437250.9810.9881000.123
4.152-4.4030.168320.1186590.1216910.9860.9911000.109
4.403-4.7040.178310.1085950.1126260.9880.9931000.103
4.704-5.0780.193260.1395830.1416090.9740.991000.135
5.078-5.5570.265310.1375250.1435560.9720.991000.133
5.557-6.2050.201360.1474670.1515030.9790.9871000.143
6.205-7.1480.275220.1614210.1654430.9460.9841000.159
7.148-8.7150.247230.1613670.1663900.9640.9831000.165
8.715-12.160.23200.1742820.1783020.9770.9871000.188
12.16-52.8310.223110.2731830.2691940.9760.9611000.29

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