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- PDB-2qsu: Structure of Arabidopsis thaliana 5'-Methylthioadenosine nucleosi... -

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Basic information

Entry
Database: PDB / ID: 2qsu
TitleStructure of Arabidopsis thaliana 5'-Methylthioadenosine nucleosidase in apo form
Components5'-methylthioadenosine nucleosidase
KeywordsHYDROLASE / Rossmann fold / 3-layer (a / b / a) sandwich
Function / homology
Function and homology information


methylthioadenosine nucleosidase / phloem or xylem histogenesis / methylthioadenosine nucleosidase activity / nucleoside metabolic process / L-methionine salvage from methylthioadenosine / plasma membrane / cytosol
Similarity search - Function
5'-Methylthioadenosine/S-adenosylhomocysteine nucleosidase / Nucleoside phosphorylase domain / Nucleoside phosphorylase domain / Phosphorylase superfamily / Nucleoside phosphorylase superfamily / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
5'-methylthioadenosine nucleosidase
Similarity search - Component
Biological speciesArabidopsis thaliana (thale cress)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsSiu, K.K.W. / Howell, P.L.
CitationJournal: J.Mol.Biol. / Year: 2008
Title: Molecular determinants of substrate specificity in plant 5'-methylthioadenosine nucleosidases.
Authors: Siu, K.K. / Lee, J.E. / Sufrin, J.R. / Moffatt, B.A. / McMillan, M. / Cornell, K.A. / Isom, C. / Howell, P.L.
History
DepositionJul 31, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 1, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Feb 21, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.3Apr 3, 2024Group: Refinement description / Category: pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: 5'-methylthioadenosine nucleosidase
B: 5'-methylthioadenosine nucleosidase


Theoretical massNumber of molelcules
Total (without water)56,9512
Polymers56,9512
Non-polymers00
Water4,684260
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3900 Å2
MethodPISA
Unit cell
Length a, b, c (Å)40.250, 126.910, 45.340
Angle α, β, γ (deg.)90.00, 106.75, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein 5'-methylthioadenosine nucleosidase


Mass: 28475.695 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Gene: AT4g38800 / Plasmid: pET28A+ / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 C+
References: UniProt: Q9T0I8, methylthioadenosine nucleosidase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 260 / 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: 1.95 Å3/Da / Density % sol: 36.83 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: NH4Cl, PEG3350, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 295K

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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 1, 2004
RadiationMonochromator: Confocal multilayer / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2→63.5 Å / Num. obs: 28189 / % possible obs: 94.6 % / Redundancy: 3.2 % / Biso Wilson estimate: 31.5 Å2 / Rmerge(I) obs: 0.081 / Net I/σ(I): 8.9
Reflection shellResolution: 2→2.06 Å / Redundancy: 3.1 % / Rmerge(I) obs: 0.262 / Mean I/σ(I) obs: 4 / % possible all: 90.7

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Processing

Software
NameVersionClassification
REFMAC5.2.0005refinement
CrystalCleardata collection
d*TREKdata reduction
d*TREKdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: Formycin-A complexed structure of A. thaliana MTAN

Resolution: 2→63.5 Å / Cor.coef. Fo:Fc: 0.953 / Cor.coef. Fo:Fc free: 0.92 / Cross valid method: THROUGHOUT / ESU R: 0.27 / ESU R Free: 0.211 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.25377 2851 10.1 %RANDOM
Rwork0.19759 ---
obs0.20341 25315 94.46 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 27.2 Å2
Baniso -1Baniso -2Baniso -3
1-2.22 Å20 Å22.12 Å2
2---2.33 Å20 Å2
3---1.33 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.27 Å0.27 Å
Luzzati d res low-5 Å
Luzzati sigma a0.4 Å0.37 Å
Refinement stepCycle: LAST / Resolution: 2→63.5 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3715 0 0 260 3975
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0223782
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.4981.9865166
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg10.0175503
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.77625.252139
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.91415637
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.641515
X-RAY DIFFRACTIONr_chiral_restr0.1060.2644
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.022781
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2280.21880
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.310.22662
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1780.2272
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2130.272
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1420.214
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.1211.52466
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.65424009
X-RAY DIFFRACTIONr_scbond_it2.23831316
X-RAY DIFFRACTIONr_scangle_it3.274.51152
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2→2.042 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.382 181 -
Rwork0.311 1803 -
obs--90.06 %

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