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- PDB-1y6q: Cyrstal structure of MTA/AdoHcy nucleosidase complexed with MT-DA... -

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Basic information

Entry
Database: PDB / ID: 1y6q
TitleCyrstal structure of MTA/AdoHcy nucleosidase complexed with MT-DADMe-ImmA
ComponentsMTA/SAH nucleosidase
KeywordsHYDROLASE / mixed alpha/beta dimer
Function / homology
Function and homology information


toxic metabolite repair / purine deoxyribonucleoside catabolic process / L-methionine salvage from S-adenosylmethionine / adenosylhomocysteine nucleosidase / adenosylhomocysteine nucleosidase activity / methylthioadenosine nucleosidase activity / L-methionine salvage from methylthioadenosine / protein homodimerization activity / identical protein binding / 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-TDI / 5'-methylthioadenosine/S-adenosylhomocysteine nucleosidase / 5'-methylthioadenosine/S-adenosylhomocysteine nucleosidase
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / FOURIER SYNTHESIS / Resolution: 2.2 Å
AuthorsLee, J.E. / Singh, V. / Evans, G.B. / Tyler, P.C. / Furneaux, R.H. / Cornell, K.A. / Riscoe, M.K. / Schramm, V.L. / Howell, P.L.
Citation
Journal: J.Biol.Chem. / Year: 2005
Title: Structural rationale for the affinity of pico- and femtomolar transition state analogues of Escherichia coli 5'-methylthioadenosine/S-adenosylhomocysteine nucleosidase.
Authors: Lee, J.E. / Singh, V. / Evans, G.B. / Tyler, P.C. / Furneaux, R.H. / Cornell, K.A. / Riscoe, M.K. / Schramm, V.L. / Howell, P.L.
#1: Journal: To be Published
Title: Femtomolar transition state analogue inhibitors of 5'-methylthioadenosine/S-adenosylhomocysteine nucleosidase from Escherichia coli.
Authors: Singh, V. / Evans, G.B. / Lenz, D.H. / Painter, G.F. / Tyler, P.C. / Furneaux, R.H. / Lee, J.E. / Howell, P.L.
History
DepositionDec 6, 2004Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 1, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Aug 23, 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)51,6346
Polymers50,9762
Non-polymers6584
Water3,945219
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4520 Å2
ΔGint-45 kcal/mol
Surface area17010 Å2
MethodPISA
Unit cell
Length a, b, c (Å)51.710, 69.790, 128.340
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) / Gene: mtnN, mtn, pfs / Plasmid: pPROEX HTa / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21 (DE3)
References: UniProt: P24247, UniProt: P0AF12*PLUS, methylthioadenosine nucleosidase, adenosylhomocysteine nucleosidase
#2: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#3: Chemical ChemComp-TDI / (3R,4S)-1-[(4-AMINO-5H-PYRROLO[3,2-D]PYRIMIDIN-7-YL)METHYL]-4-[(METHYLSULFANYL)METHYL]PYRROLIDIN-3-OL / (3R,4S)-1-[9-DEAZAADENIN-9-YL)METHYL]-3-HYDROXY-4-(METHYLTHIOMETHYL)PYRROLIDINE


Mass: 293.388 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C13H19N5OS
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 219 / 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: 2.3 Å3/Da / Density % sol: 45.8 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 4.6
Details: sodium chloride, sodium acetate, pH 4.6, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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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: Nov 4, 2002 / Details: mirrors
RadiationMonochromator: Yale Mirrors / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.2→28.22 Å / Num. obs: 24071 / Observed criterion σ(F): 0 / Biso Wilson estimate: 37.6 Å2 / Limit h max: 23 / Limit h min: 0 / Limit k max: 31 / Limit k min: 0 / Limit l max: 58 / Limit l min: 0 / Observed criterion F max: 906752.43 / Observed criterion F min: 9.426
Reflection shellResolution: 2.2→2.28 Å

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Processing

Software
NameVersionClassificationNB
CNS1.1refinement
CrystalClear(MSC/RIGAKU)data reduction
d*TREKdata scaling
CNS1.1phasing
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: PDB ENTRY 1NC1

1nc1


Resolution: 2.2→28.22 Å / Rfactor Rfree error: 0.007 / Occupancy max: 1 / Occupancy min: 0 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.246 1170 4.9 %RANDOM
Rwork0.198 ---
all-24303 --
obs-24071 99 %-
Solvent computationSolvent model: CNS bulk solvent model used / Bsol: 45.1726 Å2 / ksol: 0.390464 e/Å3
Displacement parametersBiso max: 65.04 Å2 / Biso mean: 29.17 Å2 / Biso min: 7.9 Å2
Baniso -1Baniso -2Baniso -3
1--2.09 Å20 Å20 Å2
2---4.88 Å20 Å2
3---6.97 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.31 Å0.24 Å
Luzzati d res low-5 Å
Luzzati sigma a0.28 Å0.24 Å
Luzzati d res high-2.2
Refinement stepCycle: LAST / Resolution: 2.2→28.22 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3459 0 42 219 3720
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.01
X-RAY DIFFRACTIONx_angle_deg1.5
X-RAY DIFFRACTIONx_torsion_deg24
X-RAY DIFFRACTIONx_torsion_impr_deg0.97
LS refinement shell

Refine-ID: X-RAY DIFFRACTION

Resolution (Å)Rfactor RfreeNum. reflection Rfree% reflection Rfree (%)Rfactor RworkNum. reflection RworkRfactor Rfree errorNum. reflection allNum. reflection obs% reflection obs (%)
2.2-2.30.32714850.30228230.0272989297199.4
2.3-2.420.2981545.10.25428390.0243003299399.7
2.42-2.570.31595.30.22128250.0242993298499.7
2.57-2.770.2891575.30.21628220.0232997297999.4
2.77-3.050.2781354.50.20228900.0243034302599.7
3.05-3.490.2391314.40.19428710.0213028300299.1
3.49-4.390.1921645.40.16128580.0153067302298.5
4.39-28.220.2171223.90.18529730.023214309596.3

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