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- PDB-1nc1: Crystal structure of E. coli MTA/AdoHcy nucleosidase complexed wi... -

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Basic information

Entry
Database: PDB / ID: 1nc1
TitleCrystal structure of E. coli MTA/AdoHcy nucleosidase complexed with 5'-methylthiotubercidin (MTH)
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-MTH / 5'-methylthioadenosine/S-adenosylhomocysteine nucleosidase / 5'-methylthioadenosine/S-adenosylhomocysteine nucleosidase
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsLee, J.E. / Cornell, K.A. / Riscoe, M.K. / Howell, P.L.
CitationJournal: J.Biol.Chem. / Year: 2003
Title: Structure of Escherichia coli 5'-methylthioadenosine/ S-adenosylhomocysteine nucleosidase inhibitor complexes provide insight into the conformational changes required for substrate binding and catalysis.
Authors: Lee, J.E. / Cornell, K.A. / Riscoe, M.K. / Howell, P.L.
History
DepositionDec 4, 2002Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 25, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 28, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Aug 16, 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)51,5694
Polymers50,9762
Non-polymers5932
Water3,639202
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4180 Å2
ΔGint-29 kcal/mol
Surface area16700 Å2
MethodPISA
Unit cell
Length a, b, c (Å)51.300, 69.300, 127.200
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 / MTA/AdoHcy 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: MTN OR PFS OR B0159 OR Z0170 OR ECS0163 / Plasmid: pPROEX HTa / Species (production host): Escherichia coli / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21
References: UniProt: P24247, UniProt: P0AF12*PLUS, adenosylhomocysteine nucleosidase, methylthioadenosine nucleosidase
#2: Chemical ChemComp-MTH / 2-(4-AMINO-PYRROLO[2,3-D]PYRIMIDIN-7-YL)-5-METHYLSULFANYLMETHYL-TETRAHYDRO-FURAN-3,4-DIOL / 5'-DEOXY-5'-(METHYLTHIO)-TUBERCIDIN


Mass: 296.345 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C12H16N4O3S
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 202 / 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: 2.2 Å3/Da / Density % sol: 43.63 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 4.7
Details: PEG 200, sodium acetate, sodium chloride, cobalt chloride, pH 4.7, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X8C / Wavelength: 0.8265 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Apr 30, 2001
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.8265 Å / Relative weight: 1
ReflectionResolution: 2→47.58 Å / Num. obs: 30742 / % possible obs: 97.8 % / Observed criterion σ(I): 5 / Redundancy: 4.8 % / Biso Wilson estimate: 12.4 Å2 / Rmerge(I) obs: 0.062
Reflection shellResolution: 2→2.13 Å / Num. unique all: 4819 / % possible all: 98.9

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Processing

Software
NameClassification
CCDSYSdata collection
d*TREKdata reduction
CNSrefinement
CCDSYSdata reduction
d*TREKdata scaling
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1NC3

1nc3


Resolution: 2→47.58 Å / Isotropic thermal model: Overall / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 5 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.223 1529 -RANDOM
Rwork0.19 ---
obs-30742 97.8 %-
Displacement parametersBiso mean: 25 Å2
Baniso -1Baniso -2Baniso -3
1-2.23 Å20 Å20 Å2
2---1.46 Å20 Å2
3----0.77 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.25 Å0.2 Å
Luzzati d res low-5 Å
Luzzati sigma a0.2 Å0.14 Å
Refinement stepCycle: LAST / Resolution: 2→47.58 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3430 0 40 202 3672
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_angle_deg1.6
X-RAY DIFFRACTIONc_bond_d0.012
X-RAY DIFFRACTIONc_dihedral_angle_d23.6
X-RAY DIFFRACTIONc_improper_angle_d0.94
LS refinement shellResolution: 2→2.13 Å / Rfactor Rfree error: 0.016
RfactorNum. reflection% reflection
Rfree0.262 261 -
Rwork0.218 --
obs-5080 98.9 %

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