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- PDB-1y6r: Crystal structure of MTA/AdoHcy nucleosidase complexed with MT-ImmA. -

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Basic information

Entry
Database: PDB / ID: 1y6r
TitleCrystal structure of MTA/AdoHcy nucleosidase complexed with MT-ImmA.
ComponentsMTA/SAH nucleosidase
KeywordsHYDROLASE / mixed alpha/beta
Function / homology
Function and homology information


toxic metabolite repair / purine deoxyribonucleoside catabolic process / adenosylhomocysteine nucleosidase / adenosylhomocysteine nucleosidase activity / methylthioadenosine nucleosidase activity / L-methionine salvage from S-adenosylmethionine / 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-MTM / 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. / Schramm, V.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

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Assembly

Deposited unit
A: MTA/SAH nucleosidase
B: MTA/SAH nucleosidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,5714
Polymers50,9762
Non-polymers5952
Water2,954164
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4150 Å2
ΔGint-31 kcal/mol
Surface area16840 Å2
MethodPISA
Unit cell
Length a, b, c (Å)51.570, 69.600, 127.570
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-MTM / (3S,4R)-2-(4-AMINO-5H-PYRROLO[3,2-D]PYRIMIDIN-7-YL)-5-[(METHYLSULFANYL)METHYL]PYRROLIDINE-3,4-DIOL / (1S)-1-(9-DEAZAADENIN-9-YL)-1,4,5-TRIDEOXY-1,4-IMINO-5-METHYLTHIO-D-RIBITOL


Mass: 297.377 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C12H19N5O2S
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 164 / 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: 2.25 Å3/Da / Density % sol: 45.2 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 4.7
Details: PEG 200, sodium acetate, sodium chloride, cobaltous chloride hexahydrate, pH 4.7, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU300 / Wavelength: 1.51418 Å
DetectorType: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Apr 6, 2001 / Details: mirrors
RadiationMonochromator: Yale mirrors / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.51418 Å / Relative weight: 1
ReflectionResolution: 2.2→47.81 Å / Num. all: 27476 / Num. obs: 27476 / Observed criterion σ(F): 0 / Biso Wilson estimate: 20.4 Å2 / Limit h max: 24 / Limit h min: 0 / Limit k max: 33 / Limit k min: 0 / Limit l max: 60 / Limit l min: 0 / Observed criterion F max: 272471.28 / Observed criterion F min: 0.01
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→34.8 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
Rfree0.244 1159 4.8 %RANDOM
Rwork0.193 ---
all-24035 --
obs-23956 99.7 %-
Solvent computationSolvent model: CNS bulk solvent model used / Bsol: 39.2875 Å2 / ksol: 0.365969 e/Å3
Displacement parametersBiso max: 67.53 Å2 / Biso mean: 27.48 Å2 / Biso min: 7.56 Å2
Baniso -1Baniso -2Baniso -3
1-0.19 Å20 Å20 Å2
2--0.59 Å20 Å2
3----0.78 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.28 Å0.22 Å
Luzzati d res low-5 Å
Luzzati sigma a0.19 Å0.11 Å
Luzzati d res high-2.2
Refinement stepCycle: LAST / Resolution: 2.2→34.8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3435 0 40 164 3639
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.01
X-RAY DIFFRACTIONx_angle_deg1.5
X-RAY DIFFRACTIONx_torsion_deg23.5
X-RAY DIFFRACTIONx_torsion_impr_deg0.93
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 (%)
2.2-2.30.2471615.50.19727780.0192947293999.7
2.3-2.420.2721374.60.228250.0232967296299.8
2.42-2.570.2451274.30.19128400.0222973296799.8
2.57-2.770.2421424.80.18528100.0229532952100
2.77-3.050.2241444.80.18428480.01929932992100
3.05-3.490.2391404.70.20328600.023005300099.8
3.49-4.40.2181464.80.18528730.0183034301999.5
4.4-34.80.2741625.20.20129630.0223184312598.1

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