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- PDB-1s2d: Purine 2'-Deoxyribosyl complex with arabinoside: Ribosylated Inte... -

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Basic information

Entry
Database: PDB / ID: 1s2d
TitlePurine 2'-Deoxyribosyl complex with arabinoside: Ribosylated Intermediate (AraA)
ComponentsNucleoside 2-deoxyribosyltransferase
KeywordsTRANSFERASE / ribosylate intermediate / PTD / AraA
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
ADENINE / 2-deoxy-2-fluoro-alpha-D-arabinofuranose / Nucleoside 2-deoxyribosyltransferase
Similarity search - Component
Biological speciesLactobacillus helveticus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MIR / 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 2.0Jul 1, 2020Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Database references / Derived calculations / Non-polymer description / Polymer sequence / Source and taxonomy / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / entity / entity_name_com / entity_poly / entity_poly_seq / entity_src_gen / pdbx_entity_nonpoly / pdbx_nonpoly_scheme / pdbx_poly_seq_scheme / pdbx_struct_assembly_gen / pdbx_struct_mod_residue / pdbx_unobs_or_zero_occ_atoms / struct_asym / struct_conn / struct_ref_seq_dif / struct_site / struct_site_gen
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_asym_id / _atom_site.auth_atom_id / _atom_site.auth_comp_id / _atom_site.auth_seq_id / _atom_site.group_PDB / _atom_site.label_asym_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.label_entity_id / _atom_site.label_seq_id / _atom_site.type_symbol / _chem_comp.formula / _chem_comp.formula_weight / _chem_comp.id / _chem_comp.mon_nstd_flag / _chem_comp.name / _chem_comp.pdbx_synonyms / _chem_comp.type / _entity_poly.nstd_monomer / _entity_poly.pdbx_seq_one_letter_code / _entity_poly_seq.mon_id / _entity_src_gen.pdbx_beg_seq_num / _entity_src_gen.pdbx_end_seq_num / _entity_src_gen.pdbx_gene_src_gene / _entity_src_gen.pdbx_seq_type / _pdbx_poly_seq_scheme.mon_id / _pdbx_poly_seq_scheme.pdb_mon_id / _pdbx_struct_assembly_gen.asym_id_list / _struct_site.pdbx_num_residues
Revision 2.1Jul 29, 2020Group: Derived calculations / Category: struct_site / struct_site_gen / Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.2Nov 6, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature
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: Nucleoside 2-deoxyribosyltransferase
B: Nucleoside 2-deoxyribosyltransferase
C: Nucleoside 2-deoxyribosyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)57,0619
Polymers56,2003
Non-polymers8626
Water5,062281
1
A: Nucleoside 2-deoxyribosyltransferase
B: Nucleoside 2-deoxyribosyltransferase
C: Nucleoside 2-deoxyribosyltransferase
hetero molecules

A: Nucleoside 2-deoxyribosyltransferase
B: Nucleoside 2-deoxyribosyltransferase
C: Nucleoside 2-deoxyribosyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)114,12318
Polymers112,3996
Non-polymers1,72312
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_555y,x,-z1
Buried area25540 Å2
ΔGint-116 kcal/mol
Surface area34100 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 Nucleoside 2-deoxyribosyltransferase / Nucleoside deoxyribosyltransferase / Nucleoside deoxyribosyltransferase-I / Purine trans deoxyribosylase


Mass: 18733.189 Da / Num. of mol.: 3 / Fragment: Purine 2'-deoxyribosyltransferase
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Lactobacillus helveticus (bacteria)
Gene: ptd, ndtA, ntd_1, BC335_1936, BCM45_08885, BDKNPLJD_00991, DM475_00825, GDZ32_10450, LH5_01102
Production host: Escherichia coli (E. coli)
References: UniProt: Q8RLY5, nucleoside deoxyribosyltransferase
#2: Chemical ChemComp-ADE / ADENINE


Mass: 135.127 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C5H5N5
#3: Sugar ChemComp-V3M / 2-deoxy-2-fluoro-alpha-D-arabinofuranose


Type: D-saccharide, alpha linking / Mass: 152.121 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Formula: C5H9FO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 281 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.67 Å3/Da / Density % sol: 53.64 %
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: Jan 1, 2002
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9791 Å / Relative weight: 1
ReflectionResolution: 2.1→50 Å / Num. obs: 35292 / % possible obs: 98.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 8.3 % / Biso Wilson estimate: 20.7 Å2 / Rmerge(I) obs: 0.058 / Rsym value: 0.058 / Net I/σ(I): 22
Reflection shellResolution: 2.1→2.2 Å / Redundancy: 8 % / Rmerge(I) obs: 0.127 / Mean I/σ(I) obs: 10.1 / Rsym value: 0.127 / % possible all: 98.6

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Processing

Software
NameVersionClassification
CNS1.1refinement
DENZOdata reduction
SCALEPACKdata scaling
CNSphasing
RefinementMethod to determine structure: MIR / Resolution: 2.1→48.74 Å / Rfactor Rfree error: 0.004 / Data cutoff high absF: 523494.01 / 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
Rfree0.253 3471 10 %RANDOM
Rwork0.229 ---
obs0.229 34823 97.8 %-
all-34823 --
Solvent computationSolvent model: FLAT MODEL / Bsol: 20.2422 Å2 / ksol: 0.34228 e/Å3
Displacement parametersBiso mean: 34.6 Å2
Baniso -1Baniso -2Baniso -3
1-2.59 Å20 Å20 Å2
2--2.59 Å20 Å2
3----5.17 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.3 Å0.27 Å
Luzzati d res low-5 Å
Luzzati sigma a0.19 Å0.13 Å
Refinement stepCycle: LAST / Resolution: 2.1→48.74 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3882 0 30 281 4193
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.007
X-RAY DIFFRACTIONc_angle_deg1.3
X-RAY DIFFRACTIONc_dihedral_angle_d24
X-RAY DIFFRACTIONc_improper_angle_d1.16
LS refinement shellResolution: 2.1→2.23 Å / Rfactor Rfree error: 0.012 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.285 602 10.6 %
Rwork0.24 5088 -
obs--97.9 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN1.PARAMPROTEIN1.TOP
X-RAY DIFFRACTION2WATER_REP.PARAMWATER.TOP
X-RAY DIFFRACTION3BAS.PARBAS.TOP

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