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- PDB-6evs: Characterization of 2-deoxyribosyltransferase from psychrotoleran... -

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Basic information

Entry
Database: PDB / ID: 6evs
TitleCharacterization of 2-deoxyribosyltransferase from psychrotolerant bacterium Bacillus psychrosaccharolyticus: a suitable biocatalyst for the industrial synthesis of antiviral and antitumoral nucleosides
ComponentsN-deoxyribosyltransferase
KeywordsTRANSFERASE / 2-Deoxyribosyltransferase / Enzymatic synthesis / Oligomeric assembly / Protein crystallography / Purine nucleoside analogues
Function / homologynucleoside deoxyribosyltransferase / nucleoside deoxyribosyltransferase activity / Nucleoside 2-deoxyribosyltransferase / Nucleoside 2-deoxyribosyltransferase / Nucleoside 2'-deoxyribosyltransferase
Function and homology information
Biological speciesBacillus psychrosaccharolyticus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsFresco-Tabohada, A. / Fernandez-Lucas, J. / Acebal, C. / Arroyo, M. / Ramon, F. / Mancheno, J.M. / de la Mata, I.
CitationJournal: Catalysts / Year: 2019
Title: 2'-Deoxyribosyltransferase from Bacillus psychrosaccharolyticus: A Mesophilic-Like Biocatalyst for the Synthesis of Modified Nucleosides from a Psychrotolerant Bacterium
Authors: Fresco-Tabohada, A. / Fernandez-Lucas, J. / Acebal, C. / Arroyo, M. / Ramon, F. / de la Mata, I. / Mancheno, J.M.
History
DepositionNov 2, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 14, 2018Provider: repository / Type: Initial release
Revision 1.1May 29, 2019Group: Data collection / Database references / Category: citation / citation_author / pdbx_database_proc
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.title / _citation.year / _citation_author.name
Revision 1.2Jan 17, 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

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Assembly

Deposited unit
A: N-deoxyribosyltransferase
B: N-deoxyribosyltransferase


Theoretical massNumber of molelcules
Total (without water)32,8292
Polymers32,8292
Non-polymers00
Water1,874104
1
A: N-deoxyribosyltransferase
B: N-deoxyribosyltransferase

A: N-deoxyribosyltransferase
B: N-deoxyribosyltransferase

A: N-deoxyribosyltransferase
B: N-deoxyribosyltransferase


Theoretical massNumber of molelcules
Total (without water)98,4876
Polymers98,4876
Non-polymers00
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-y,x-y,z1
crystal symmetry operation3_555-x+y,-x,z1
Buried area15800 Å2
ΔGint-119 kcal/mol
Surface area31110 Å2
MethodPISA
Unit cell
Length a, b, c (Å)107.547, 107.547, 61.244
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number146
Space group name H-MH3
Components on special symmetry positions
IDModelComponents
11A-261-

HOH

21A-262-

HOH

31B-241-

HOH

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Components

#1: Protein N-deoxyribosyltransferase


Mass: 16414.510 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus psychrosaccharolyticus (bacteria)
Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: A0A3G5BRZ6*PLUS, nucleoside deoxyribosyltransferase
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 104 / 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: 2.08 Å3/Da / Density % sol: 40.76 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop
Details: in 3 M sodium nitrate, 0.1 M sodium acetate trihydrate, pH 4.6

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.9792 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Feb 9, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 1.9→37.07 Å / Num. obs: 20796 / % possible obs: 100 % / Redundancy: 5.2 % / Biso Wilson estimate: 32.7 Å2 / CC1/2: 0.988 / Rpim(I) all: 0.02 / Rrim(I) all: 0.05 / Net I/σ(I): 14.8
Reflection shellResolution: 1.9→2 Å / Redundancy: 4.9 % / Rmerge(I) obs: 0.534 / Mean I/σ(I) obs: 2.9 / Num. unique obs: 2998 / Rpim(I) all: 0.267 / Rrim(I) all: 0.598 / Rsym value: 0.534 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX(1.12_2829: ???)refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1S2G

1s2g


Resolution: 1.9→37.07 Å / SU ML: 0.23 / Cross valid method: FREE R-VALUE / σ(F): 1.98 / Phase error: 26.95
RfactorNum. reflection% reflection
Rfree0.2165 1067 5.13 %
Rwork0.1774 --
obs0.1793 20783 99.92 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.9→37.07 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2248 0 0 104 2352
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0092328
X-RAY DIFFRACTIONf_angle_d0.9273171
X-RAY DIFFRACTIONf_dihedral_angle_d3.0491602
X-RAY DIFFRACTIONf_chiral_restr0.055335
X-RAY DIFFRACTIONf_plane_restr0.007409
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.9003-1.98680.32071490.27222438X-RAY DIFFRACTION100
1.9868-2.09150.26111250.232482X-RAY DIFFRACTION100
2.0915-2.22260.27521450.20292448X-RAY DIFFRACTION100
2.2226-2.39410.23121380.19132466X-RAY DIFFRACTION100
2.3941-2.6350.23631280.17982463X-RAY DIFFRACTION100
2.635-3.01610.21941320.18152466X-RAY DIFFRACTION100
3.0161-3.79940.17961220.16472479X-RAY DIFFRACTION100
3.7994-37.07680.20131280.16072474X-RAY DIFFRACTION100
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)
15.94771.009-0.3174.8195-0.20663.1239-0.01890.3477-0.1222-0.3493-0.02660.38560.143-0.45420.02340.2795-0.0557-0.06750.3623-0.00940.2528-20.048-6.17212.2171
22.89060.6367-0.7413.7098-1.73073.00270.06850.1742-0.7165-0.61050.12520.07240.6396-0.321-0.14010.3411-0.0657-0.11720.3173-0.03280.4624-12.6658-14.821610.5283
31.8232-3.47021.27767.2022-4.59868.79730.6761-0.1668-0.4451.0180.60471.69660.1279-1.7912-1.22470.82420.00130.02891.0434-0.00161.0517-28.6973-4.182214.7495
42.14780.13390.88282.85780.02432.85190.07780.19010.1537-0.1455-0.00920.6442-0.3125-0.5878-0.04870.24340.0652-0.01550.36640.04520.4639-18.13775.46549.4173
57.20640.0788-1.51933.56860.60534.7845-0.1198-0.554-0.23640.62010.30890.6636-0.1814-0.5346-0.14250.35850.03010.11990.48840.05270.4715-20.9093-0.918138.1371
62.9928-0.5746-0.16041.2136-1.56283.48710.0911-0.08040.05260.26990.21260.5974-0.1287-0.4805-0.17340.25820.01270.05360.3605-0.01030.506-18.20437.644928.9344
72.95-0.0855-1.01092.4218-1.24764.4159-0.0873-0.4397-0.62760.34920.03410.71340.4637-0.40060.06730.3277-0.05350.08350.34710.06920.5376-15.2948-11.1630.7157
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 2 through 35 )
2X-RAY DIFFRACTION2chain 'A' and (resid 36 through 72 )
3X-RAY DIFFRACTION3chain 'A' and (resid 73 through 79 )
4X-RAY DIFFRACTION4chain 'A' and (resid 80 through 138 )
5X-RAY DIFFRACTION5chain 'B' and (resid 2 through 35 )
6X-RAY DIFFRACTION6chain 'B' and (resid 36 through 79 )
7X-RAY DIFFRACTION7chain 'B' and (resid 80 through 138 )

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