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- PDB-3df9: Crystal structure of E. coli MTA/SAH nucleosidase in complex with... -

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Basic information

Entry
Database: PDB / ID: 3df9
TitleCrystal structure of E. coli MTA/SAH nucleosidase in complex with BnT-DADMeImmA
ComponentsMTA/SAH nucleosidase
KeywordsHYDROLASE / mixed alpha/beta dimer
Function / homology
Function and homology information


purine deoxyribonucleoside catabolic process / adenosylhomocysteine nucleosidase / adenosylhomocysteine nucleosidase activity / methylthioadenosine nucleosidase activity / L-methionine salvage from S-adenosylmethionine / L-methionine salvage from methylthioadenosine / cytosol
Similarity search - Function
MTA/SAH nucleosidase / Nucleoside phosphorylase domain / Nucleoside phosphorylase domain / Phosphorylase superfamily / Nucleoside phosphorylase superfamily / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Chem-DF9 / 5'-methylthioadenosine/S-adenosylhomocysteine nucleosidase
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.95 Å
AuthorsSiu, K.K.W. / Howell, P.L.
CitationJournal: Acta Crystallogr.,Sect.F / Year: 2008
Title: Structure of Staphylococcus aureus 5'-methylthioadenosine/S-adenosylhomocysteine nucleosidase
Authors: Siu, K.K. / Lee, J.E. / Smith, G.D. / Horvatin-Mrakovcic, C. / Howell, P.L.
History
DepositionJun 11, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 17, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Aug 30, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _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: MTA/SAH nucleosidase
B: MTA/SAH nucleosidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,7154
Polymers50,9762
Non-polymers7392
Water5,386299
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3000 Å2
ΔGint-22.9 kcal/mol
Surface area16790 Å2
MethodPISA
Unit cell
Length a, b, c (Å)51.611, 69.748, 127.868
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein MTA/SAH nucleosidase / P46 / 5'-methylthioadenosine nucleosidase / S-adenosylhomocysteine nucleosidase


Mass: 25488.123 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Strain: O157:H7 / Gene: mtnN, pfs / Plasmid: pPROEX HTA / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: P0AF14, adenosylhomocysteine nucleosidase
#2: Chemical ChemComp-DF9 / (3R,4S)-1-[(4-amino-5H-pyrrolo[3,2-d]pyrimidin-7-yl)methyl]-4-[(benzylsulfanyl)methyl]pyrrolidin-3-ol


Mass: 369.484 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C19H23N5OS
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 299 / 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: 2.26 Å3/Da / Density % sol: 45.51 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 4.5
Details: 35 % (v/v) 2-propanol, 50 mM sodium acetate, pH 4.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU300 / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Jul 20, 2005
RadiationMonochromator: Confocal multilayer / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.95→63.93 Å / Num. all: 34475 / Num. obs: 33372 / % possible obs: 96.8 % / Observed criterion σ(F): 5 / Observed criterion σ(I): 5 / Redundancy: 15.9 % / Rmerge(I) obs: 0.078 / Net I/σ(I): 24.6
Reflection shellResolution: 1.95→2.02 Å / Redundancy: 15.9 % / Rmerge(I) obs: 0.3 / Mean I/σ(I) obs: 9.8 / % possible all: 95.3

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Processing

Software
NameVersionClassification
REFMAC5.4.0066refinement
CrystalCleardata collection
d*TREKdata reduction
d*TREKdata scaling
REFMACphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1Y6Q

1y6q


Resolution: 1.95→63.89 Å / Cor.coef. Fo:Fc: 0.95 / Cor.coef. Fo:Fc free: 0.937 / SU B: 3.384 / SU ML: 0.098 / Cross valid method: THROUGHOUT / ESU R: 0.171 / ESU R Free: 0.145 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.20802 1683 5 %RANDOM
Rwork0.17548 ---
all0.17715 32720 --
obs0.17715 31666 96.78 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 17.654 Å2
Baniso -1Baniso -2Baniso -3
1-0.52 Å20 Å20 Å2
2---0.16 Å20 Å2
3----0.36 Å2
Refinement stepCycle: LAST / Resolution: 1.95→63.89 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3497 0 52 299 3848
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0223616
X-RAY DIFFRACTIONr_angle_refined_deg1.3081.9784922
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.985490
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.99325.347144
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.7815590
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.7721514
X-RAY DIFFRACTIONr_chiral_restr0.0840.2580
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0212725
X-RAY DIFFRACTIONr_mcbond_it0.5761.52350
X-RAY DIFFRACTIONr_mcangle_it1.07123759
X-RAY DIFFRACTIONr_scbond_it1.81231266
X-RAY DIFFRACTIONr_scangle_it2.984.51154
LS refinement shellResolution: 1.95→2.001 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.299 113 -
Rwork0.211 2294 -
obs--95.14 %

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