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- PDB-6qai: 2-desoxiribosyltransferase from Leishmania mexicana -

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Basic information

Entry
Database: PDB / ID: 6qai
Title2-desoxiribosyltransferase from Leishmania mexicana
Components2-Deoxyribosyltransferase
KeywordsTRANSFERASE / deoxyribosyltransferase / enzymatic synthesis / oligomeric assembly / purine nucleoside analogues / protein crystallography
Function / homology: / Nucleoside 2-deoxyribosyltransferase / Nucleoside 2-deoxyribosyltransferase / Rossmann fold - #450 / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta / Nucleoside 2-deoxyribosyltransferase
Function and homology information
Biological speciesLeishmania mexicana (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.66 Å
AuthorsCrespo, N. / Mancheno, J.M.
Funding support Spain, 2items
OrganizationGrant numberCountry
Spanish Ministry of Economy and CompetitivenessBFU2010-17929/BMC Spain
Spanish Ministry of Economy and CompetitivenessSAF2015-64629-C2-2-R Spain
CitationJournal: Appl.Microbiol.Biotechnol. / Year: 2017
Title: 2'-Deoxyribosyltransferase from Leishmania mexicana, an efficient biocatalyst for one-pot, one-step synthesis of nucleosides from poorly soluble purine bases.
Authors: Crespo, N. / Sanchez-Murcia, P.A. / Gago, F. / Cejudo-Sanches, J. / Galmes, M.A. / Fernandez-Lucas, J. / Mancheno, J.M.
History
DepositionDec 19, 2018Deposition site: PDBE / Processing site: PDBE
SupersessionDec 26, 2018ID: 5NBR
Revision 1.0Dec 26, 2018Provider: repository / Type: Initial release
Revision 1.1Jan 24, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: 2-Deoxyribosyltransferase
B: 2-Deoxyribosyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,4855
Polymers34,1192
Non-polymers3663
Water4,035224
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: equilibrium centrifugation
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4590 Å2
ΔGint-23 kcal/mol
Surface area13100 Å2
MethodPISA
Unit cell
Length a, b, c (Å)80.209, 46.265, 87.987
Angle α, β, γ (deg.)90.00, 115.06, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-45-

ILE

21A-45-

ILE

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Components

#1: Protein 2-Deoxyribosyltransferase


Mass: 17059.373 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Leishmania mexicana (eukaryote) / Gene: LMXM_23_1580 / Production host: Escherichia coli (E. coli) / References: UniProt: E9AWJ0
#2: Chemical ChemComp-TRS / 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL / TRIS BUFFER


Mass: 122.143 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C4H12NO3 / Comment: pH buffer*YM
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 224 / Source method: isolated from a natural source / Formula: H2O

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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: 2.17 Å3/Da / Density % sol: 43.25 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop
Details: 25% PEG 3350, 0.2 M magnesium chloride, 0.1 M Tris-HCl, pH 8.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALBA / Beamline: XALOC / Wavelength: 0.9793 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Feb 8, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
ReflectionResolution: 1.66→39.85 Å / Num. obs: 33859 / % possible obs: 97.7 % / Redundancy: 6.8 % / Rpim(I) all: 0.028 / Rrim(I) all: 0.052 / Net I/σ(I): 18.3
Reflection shellResolution: 1.66→1.7 Å

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Processing

Software
NameVersionClassification
PHENIX(1.14_3260: ???)refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2A0K

2a0k


Resolution: 1.66→39.85 Å / SU ML: 0.2 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 20.57
RfactorNum. reflection% reflection
Rfree0.1995 2000 5.91 %
Rwork0.169 --
obs0.1708 33853 97.41 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.66→39.85 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2345 0 24 224 2593
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0082452
X-RAY DIFFRACTIONf_angle_d0.8953334
X-RAY DIFFRACTIONf_dihedral_angle_d3.7121993
X-RAY DIFFRACTIONf_chiral_restr0.055366
X-RAY DIFFRACTIONf_plane_restr0.006436
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.66-1.70150.3021370.24252206X-RAY DIFFRACTION96
1.7015-1.74750.22441430.22052223X-RAY DIFFRACTION96
1.7475-1.79890.26511350.21692244X-RAY DIFFRACTION96
1.7989-1.8570.23391460.20122248X-RAY DIFFRACTION96
1.857-1.92340.2051430.19062252X-RAY DIFFRACTION97
1.9234-2.00040.24681340.1972249X-RAY DIFFRACTION97
2.0004-2.09140.24451500.19312245X-RAY DIFFRACTION97
2.0914-2.20170.21971420.1792292X-RAY DIFFRACTION98
2.2017-2.33960.20471400.17262247X-RAY DIFFRACTION98
2.3396-2.52020.19231440.17222288X-RAY DIFFRACTION98
2.5202-2.77380.20341500.18472305X-RAY DIFFRACTION98
2.7738-3.1750.22211470.18672308X-RAY DIFFRACTION99
3.175-3.99960.18761420.15682340X-RAY DIFFRACTION99
3.9996-39.86360.16481470.13932406X-RAY DIFFRACTION99
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
12.9880.7772-0.60495.6911-0.61253.13050.08110.18070.2308-0.1892-0.04130.1204-0.2224-0.0851-0.00550.1180.0076-0.01630.12030.02130.1924-24.4917-0.884479.1135
23.5624-1.6118-0.25344.56050.44113.2712-0.1062-0.06880.22070.09150.06020.3197-0.5008-0.7354-0.03240.21340.0861-0.04520.2661-0.02510.2612-35.8773-0.017185.1042
31.0059-0.2022-0.39941.44190.73863.89180.0362-0.51330.02260.18230.1687-0.223-0.0960.6634-0.1110.1759-0.008-0.02410.3278-0.04780.2245-19.4538-4.820696.7774
46.91010.1619-2.51488.4571-4.33214.0550.02230.0034-0.4503-0.17990.09170.5910.47140.1659-0.12970.21460.0096-0.02970.0768-0.00960.3124-22.6391-18.204481.448
51.49190.123-1.69572.7269-0.97242.1866-0.1283-0.8511-0.08040.90010.05210.30970.06-0.12990.01270.5201-0.03070.12170.8271-0.06620.3093-32.0377-1.009118.2717
63.9557-0.7537-3.55631.73772.34924.9467-0.1786-1.4055-0.79341.4002-0.12040.18120.85610.46390.27210.6467-0.06010.04040.61550.07840.2639-27.4283-11.7608111.8464
71.9888-0.04670.55362.9831.30834.60030.0902-0.56380.29770.121-0.26870.3086-0.8309-0.6919-0.22850.3050.06840.05320.4296-0.12990.2457-33.73844.9053103.1622
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 6 through 36 )
2X-RAY DIFFRACTION2chain 'A' and (resid 37 through 66 )
3X-RAY DIFFRACTION3chain 'A' and (resid 67 through 145 )
4X-RAY DIFFRACTION4chain 'A' and (resid 146 through 158 )
5X-RAY DIFFRACTION5chain 'B' and (resid 8 through 36 )
6X-RAY DIFFRACTION6chain 'B' and (resid 37 through 53 )
7X-RAY DIFFRACTION7chain 'B' and (resid 54 through 157 )

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