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- PDB-1f8x: CRYSTAL STRUCTURE OF NUCLEOSIDE 2-DEOXYRIBOSYLTRANSFERASE -

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Basic information

Entry
Database: PDB / ID: 1f8x
TitleCRYSTAL STRUCTURE OF NUCLEOSIDE 2-DEOXYRIBOSYLTRANSFERASE
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
Nucleoside deoxyribosyltransferase
Similarity search - Component
Biological speciesLactobacillus leichmannii (bacteria)
MethodX-RAY DIFFRACTION / Resolution: 2.5 Å
AuthorsArmstrong, S.R. / Cook, W.J. / Short, S.A. / Ealick, S.E.
Citation
Journal: 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.
#1: Journal: J.Biol.Chem. / Year: 1990
Title: Crystallization and Preliminary X-ray Investigation of Recombinant Lactobacillus leichmannii Nucleoside Deoxyribosyltransferase
Authors: Cook, W.J. / Short, S.A. / Ealick, S.E.
History
DepositionJul 5, 2000Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 26, 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 / Category: chem_comp_atom / chem_comp_bond / database_2
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: NUCLEOSIDE 2-DEOXYRIBOSYLTRANSFERASE
B: NUCLEOSIDE 2-DEOXYRIBOSYLTRANSFERASE


Theoretical massNumber of molelcules
Total (without water)36,1972
Polymers36,1972
Non-polymers00
Water1,44180
1
A: NUCLEOSIDE 2-DEOXYRIBOSYLTRANSFERASE
B: NUCLEOSIDE 2-DEOXYRIBOSYLTRANSFERASE

A: NUCLEOSIDE 2-DEOXYRIBOSYLTRANSFERASE
B: NUCLEOSIDE 2-DEOXYRIBOSYLTRANSFERASE

A: NUCLEOSIDE 2-DEOXYRIBOSYLTRANSFERASE
B: NUCLEOSIDE 2-DEOXYRIBOSYLTRANSFERASE


Theoretical massNumber of molelcules
Total (without water)108,5906
Polymers108,5906
Non-polymers00
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)151.000, 151.000, 151.000
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number199
Space group name H-MI213

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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: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 80 / 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: 3

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Sample preparation

CrystalDensity Matthews: 3.96 Å3/Da / Density % sol: 68.95 %
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

Diffraction
IDMean temperature (K)Crystal-ID
12961
22961
32961
Diffraction source
SourceTypeIDWavelength
ROTATING ANODERIGAKU11.5418
ROTATING ANODERIGAKU21.5418
ROTATING ANODERIGAKU31.5418
Detector
TypeIDDetectorDate
SIEMENS-NICOLET X1001AREA DETECTORJan 1, 1989
SIEMENS-NICOLET X1002AREA DETECTORJan 1, 1989
SDMS3AREA DETECTORJan 1, 1993
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.5→100 Å / Num. all: 223078 / Num. obs: 19875 / % possible obs: 95 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 11.2 % / Rmerge(I) obs: 0.115

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Processing

Software
NameClassification
PHASESphasing
X-PLORrefinement
SDMSdata reduction
SDMSdata scaling
RefinementResolution: 2.5→5 Å / σ(F): 2 / σ(I): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflectionSelection details
Rfree0.24 1584 random
Rwork0.166 --
all-15845 -
obs-0 -
Refinement stepCycle: LAST / Resolution: 2.5→5 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2536 0 0 80 2616
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.007
X-RAY DIFFRACTIONx_angle_deg1.54

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