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- PDB-9f08: Nucleoside-2'-deoxyribosyltransferase from Lactobacillus leichman... -

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Basic information

Entry
Database: PDB / ID: 9f08
TitleNucleoside-2'-deoxyribosyltransferase from Lactobacillus leichmannii. Covalent complex with 2-deoxyribose.
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 / Nucleoside deoxyribosyltransferase
Function and homology information
Biological speciesLactobacillus leichmannii (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.371 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)36,4654
Polymers36,1972
Non-polymers2682
Water64936
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)109,39512
Polymers108,5906
Non-polymers8056
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_555-z+1/2,-x,y+1/21
crystal symmetry operation10_545-y,z-1/2,-x+1/21
Buried area17310 Å2
ΔGint-132 kcal/mol
Surface area32640 Å2
MethodPISA
Unit cell
Length a, b, c (Å)148.461, 148.461, 148.461
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: 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.: 2 / Source method: obtained synthetically / Formula: C5H10O4 / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 36 / 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: 3.77 Å3/Da / Density % sol: 67.35 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7 / Details: 35% tascimate

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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→60.61 Å / Num. obs: 22224 / % possible obs: 100 % / Redundancy: 41.2 % / CC1/2: 1 / Rmerge(I) obs: 0.06 / Rpim(I) all: 0.01 / Net I/σ(I): 42.5
Reflection shellResolution: 2.37→2.46 Å / Rmerge(I) obs: 0.96 / Mean I/σ(I) obs: 5.1 / Num. unique obs: 2312 / CC1/2: 0.95 / Rpim(I) all: 0.22

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Processing

Software
NameVersionClassification
REFMAC5.8.0425refinement
XDSdata reduction
SCALAdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.371→60.61 Å / Cor.coef. Fo:Fc: 0.959 / Cor.coef. Fo:Fc free: 0.944 / SU B: 6.41 / SU ML: 0.15 / Cross valid method: FREE R-VALUE / ESU R: 0.234 / ESU R Free: 0.192
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2284 1115 5.02 %
Rwork0.199 21097 -
all0.201 --
obs-22212 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: 63.329 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refinement stepCycle: LAST / Resolution: 2.371→60.61 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2523 0 16 37 2576
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0122607
X-RAY DIFFRACTIONr_bond_other_d0.0010.0162365
X-RAY DIFFRACTIONr_angle_refined_deg1.6611.8273537
X-RAY DIFFRACTIONr_angle_other_deg0.5781.7675463
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.675312
X-RAY DIFFRACTIONr_dihedral_angle_2_deg9.85655
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.14610422
X-RAY DIFFRACTIONr_dihedral_angle_6_deg13.76410131
X-RAY DIFFRACTIONr_chiral_restr0.0930.2369
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.023043
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02585
X-RAY DIFFRACTIONr_nbd_refined0.220.2516
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1940.22147
X-RAY DIFFRACTIONr_nbtor_refined0.1870.21286
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0910.21304
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.190.270
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.1140.215
X-RAY DIFFRACTIONr_nbd_other0.2520.273
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1290.25
X-RAY DIFFRACTIONr_mcbond_it5.7886.3231254
X-RAY DIFFRACTIONr_mcbond_other5.7836.3221254
X-RAY DIFFRACTIONr_mcangle_it7.33111.3591564
X-RAY DIFFRACTIONr_mcangle_other7.32911.3581565
X-RAY DIFFRACTIONr_scbond_it6.2476.741353
X-RAY DIFFRACTIONr_scbond_other6.2456.7391354
X-RAY DIFFRACTIONr_scangle_it8.3612.2421973
X-RAY DIFFRACTIONr_scangle_other8.35812.2411974
X-RAY DIFFRACTIONr_lrange_it9.6161.2512914
X-RAY DIFFRACTIONr_lrange_other9.61361.2582912
X-RAY DIFFRACTIONr_ncsr_local_group_10.0750.055103
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDRefine-IDTypeRms dev position (Å)Weight position
11AX-RAY DIFFRACTIONLocal ncs0.075360.05009
12AX-RAY DIFFRACTIONLocal ncs0.075360.05009
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.37-60.610.252160.241275X-RAY DIFFRACTION100
2.371-2.4320.37670.251532X-RAY DIFFRACTION99.8751
2.432-2.4990.281780.2541500X-RAY DIFFRACTION100
2.499-2.5710.35890.2721472X-RAY DIFFRACTION100
2.571-2.650.329460.2681452X-RAY DIFFRACTION100
2.65-2.7370.384590.2611393X-RAY DIFFRACTION100
2.737-2.8320.289720.2331335X-RAY DIFFRACTION100
2.832-2.9390.223770.221279X-RAY DIFFRACTION100
2.939-3.0590.281580.2141245X-RAY DIFFRACTION100
3.059-3.1950.254770.231190X-RAY DIFFRACTION100
3.195-3.350.244690.2261130X-RAY DIFFRACTION100
3.35-3.5310.228480.2131090X-RAY DIFFRACTION100
3.531-3.7440.23540.1991042X-RAY DIFFRACTION100
3.744-4.0010.184580.18964X-RAY DIFFRACTION100
4.001-4.320.194500.172908X-RAY DIFFRACTION100
4.32-4.730.208550.156831X-RAY DIFFRACTION100
4.73-5.2850.199460.177753X-RAY DIFFRACTION100
5.285-6.0950.246320.196683X-RAY DIFFRACTION100
6.095-7.4460.238310.182579X-RAY DIFFRACTION100
7.446-10.4510.177330.159444X-RAY DIFFRACTION100

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