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- PDB-1s2g: Purine 2'deoxyribosyltransferase + 2'-deoxyadenosine -

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Basic information

Entry
Database: PDB / ID: 1s2g
TitlePurine 2'deoxyribosyltransferase + 2'-deoxyadenosine
Componentspurine trans deoxyribosylase
KeywordsTRANSFERASE / PTD / 2'-deoxyadenosine / 2'-purine deoxyribosyltansferase
Function / homology
Function and homology information


nucleoside deoxyribosyltransferase / 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
Chem-3D1 / Nucleoside 2-deoxyribosyltransferase
Similarity search - Component
Biological speciesLactobacillus helveticus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsAnand, R. / Kaminski, P.A. / Ealick, S.E.
CitationJournal: Biochemistry / Year: 2004
Title: Structures of purine 2'-deoxyribosyltransferase, substrate complexes, and the ribosylated enzyme intermediate at 2.0 A resolution.
Authors: Anand, R. / Kaminski, P.A. / Ealick, S.E.
History
DepositionJan 8, 2004Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 30, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Feb 14, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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: purine trans deoxyribosylase
B: purine trans deoxyribosylase
C: purine trans deoxyribosylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)56,9536
Polymers56,2003
Non-polymers7543
Water4,900272
1
A: purine trans deoxyribosylase
B: purine trans deoxyribosylase
C: purine trans deoxyribosylase
hetero molecules

A: purine trans deoxyribosylase
B: purine trans deoxyribosylase
C: purine trans deoxyribosylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)113,90712
Polymers112,3996
Non-polymers1,5076
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_555y,x,-z1
Buried area26230 Å2
ΔGint-109 kcal/mol
Surface area33120 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)79.587, 79.587, 184.973
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212

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Components

#1: Protein purine trans deoxyribosylase


Mass: 18733.189 Da / Num. of mol.: 3 / Fragment: purine 2'-deoxyribosyltansferase
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Lactobacillus helveticus (bacteria) / Production host: Escherichia coli (E. coli)
References: UniProt: Q8RLY5, nucleoside deoxyribosyltransferase
#2: Chemical ChemComp-3D1 / (2R,3S,5R)-5-(6-amino-9H-purin-9-yl)-tetrahydro-2-(hydroxymethyl)furan-3-ol / 2'-DEOXYADENOSINE


Mass: 251.242 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C10H13N5O3
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 272 / 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: 2.71 Å3/Da / Density % sol: 54.18 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 8
Details: 2.0 M ammonium sulfate, 100mM Tris , pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 295K

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Data collection

DiffractionMean temperature: 170 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 8-BM / Wavelength: 0.9791 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Sep 18, 2002
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9791 Å / Relative weight: 1
ReflectionResolution: 2.1→25 Å / Num. all: 40463 / Num. obs: 40463 / % possible obs: 97.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 8 % / Biso Wilson estimate: 19.4 Å2 / Rmerge(I) obs: 0.066 / Rsym value: 0.068 / Net I/σ(I): 20
Reflection shellResolution: 2.1→2.2 Å / Redundancy: 8 % / Rmerge(I) obs: 0.334 / Mean I/σ(I) obs: 10.1 / Rsym value: 0.334 / % possible all: 99.8

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Processing

Software
NameVersionClassification
CNS1.1refinement
DENZOdata reduction
SCALEPACKdata scaling
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.1→19.92 Å / Rfactor Rfree error: 0.005 / Data cutoff high absF: 265301.55 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.298 3396 10 %RANDOM
Rwork0.264 ---
all0.264 40463 --
obs0.264 33912 95.4 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 33.0203 Å2 / ksol: 0.352912 e/Å3
Displacement parametersBiso mean: 32.2 Å2
Baniso -1Baniso -2Baniso -3
1-2.84 Å20 Å20 Å2
2--2.84 Å20 Å2
3----5.67 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.37 Å0.31 Å
Luzzati d res low-5 Å
Luzzati sigma a0.25 Å0.2 Å
Refinement stepCycle: LAST / Resolution: 2.1→19.92 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3813 0 54 272 4139
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.006
X-RAY DIFFRACTIONc_angle_deg1.2
X-RAY DIFFRACTIONc_dihedral_angle_d23.3
X-RAY DIFFRACTIONc_improper_angle_d0.77
LS refinement shellResolution: 2.1→2.23 Å / Rfactor Rfree error: 0.014 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.335 585 10.6 %
Rwork0.296 4956 -
obs--95.3 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAMWATER.TOP
X-RAY DIFFRACTION33DA.PAR3DA.TOP

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