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- PDB-1f8y: CRYSTAL STRUCTURE ANALYSIS OF NUCLEOSIDE 2-DEOXYRIBOSYLTRANSFERAS... -

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Basic information

Entry
Database: PDB / ID: 1f8y
TitleCRYSTAL STRUCTURE ANALYSIS OF NUCLEOSIDE 2-DEOXYRIBOSYLTRANSFERASE COMPLEXED WITH 5-METHYL-2'-DEOXYPSEUDOURIDINE
ComponentsNUCLEOSIDE 2-DEOXYRIBOSYLTRANSFERASE
KeywordsTRANSFERASE / active site / alpha/beta protein / biocatalyst / nucleoside
Function / homology
Function and homology information


nucleoside deoxyribosyltransferase / nucleotide salvage / nucleoside deoxyribosyltransferase activity
Similarity search - Function
Nucleoside 2-deoxyribosyltransferase / Nucleoside 2-deoxyribosyltransferase / Rossmann fold - #450 / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
2'-deoxy-1-methyl-pseudouridine / Nucleoside deoxyribosyltransferase
Similarity search - Component
Biological speciesLactobacillus leichmannii (bacteria)
MethodX-RAY DIFFRACTION / Resolution: 2.4 Å
AuthorsArmstrong, S.R. / Cook, W.J. / Short, S.A. / Ealick, S.E.
CitationJournal: Structure / Year: 1996
Title: Crystal structures of nucleoside 2-deoxyribosyltransferase in native and ligand-bound forms reveal architecture of the active site.
Authors: Armstrong, S.R. / Cook, W.J. / Short, S.A. / Ealick, S.E.
History
DepositionJul 5, 2000Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 9, 2000Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 7, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / entity / pdbx_entity_nonpoly / struct_site
Item: _chem_comp.name / _chem_comp.pdbx_synonyms ..._chem_comp.name / _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _entity.pdbx_description / _pdbx_entity_nonpoly.name / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: NUCLEOSIDE 2-DEOXYRIBOSYLTRANSFERASE
B: NUCLEOSIDE 2-DEOXYRIBOSYLTRANSFERASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,6814
Polymers36,1972
Non-polymers4842
Water1,36976
1
A: NUCLEOSIDE 2-DEOXYRIBOSYLTRANSFERASE
B: NUCLEOSIDE 2-DEOXYRIBOSYLTRANSFERASE
hetero molecules

A: NUCLEOSIDE 2-DEOXYRIBOSYLTRANSFERASE
B: NUCLEOSIDE 2-DEOXYRIBOSYLTRANSFERASE
hetero molecules

A: NUCLEOSIDE 2-DEOXYRIBOSYLTRANSFERASE
B: NUCLEOSIDE 2-DEOXYRIBOSYLTRANSFERASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)110,04312
Polymers108,5906
Non-polymers1,4536
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation6_555z+1/2,-x+1/2,-y1
crystal symmetry operation12_554-y+1/2,-z,x-1/21
Unit cell
Length a, b, c (Å)149.600, 149.600, 149.600
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number199
Space group name H-MI213
DetailsThe biological assembly is a hexamer. Each pair of monomers is related by a noncrystallographic twofold symmetry axis.

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Components

#1: Protein NUCLEOSIDE 2-DEOXYRIBOSYLTRANSFERASE


Mass: 18098.354 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Lactobacillus leichmannii (bacteria)
References: UniProt: Q9R5V5, nucleoside deoxyribosyltransferase
#2: Chemical ChemComp-5MD / 2'-deoxy-1-methyl-pseudouridine / 5-METHYL-2'-DEOXYPSEUDOURIDINE


Type: DNA linking / Mass: 242.229 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H14N2O5
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 76 / 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: 3.85 Å3/Da / Density % sol: 68.07 %
Crystal growTemperature: 296 K / Method: vapor diffusion, hanging drop / pH: 5.4
Details: Ammonium Sulfate, Citrate Buffer, pH 5.4, VAPOR DIFFUSION, HANGING DROP, temperature 296K
Crystal grow
*PLUS
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
140 mg/mlprotein1drop
25 %satammonium sulfate1drop
30.05 Mcitrate1drop
45 %satammonium sulfate1reservoir
50.05 Mcitrate1reservoir

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Data collection

DiffractionMean temperature: 296 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.5418
DetectorType: SDMS / Detector: AREA DETECTOR / Date: Jan 1, 1992
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.4→100 Å / Num. all: 21897 / Num. obs: 21897 / % possible obs: 93 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.6 % / Rmerge(I) obs: 0.075
Reflection
*PLUS
Num. measured all: 101311

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Processing

Software
NameClassification
X-PLORmodel building
X-PLORrefinement
SDMSdata reduction
SDMSdata scaling
X-PLORphasing
RefinementResolution: 2.4→5 Å / σ(F): 2 / σ(I): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflectionSelection details
Rfree0.218 1792 RANDOM
Rwork0.16 --
obs0.16 17921 -
all-17921 -
Refinement stepCycle: LAST / Resolution: 2.4→5 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2536 0 34 76 2646
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.008
X-RAY DIFFRACTIONx_angle_deg1.56

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