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- PDB-2qtg: Crystal Structure of Arabidopsis thaliana 5'-Methylthioadenosine ... -

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Basic information

Entry
Database: PDB / ID: 2qtg
TitleCrystal Structure of Arabidopsis thaliana 5'-Methylthioadenosine nucleosidase in complex with 5'-methylthiotubercidin
Components5'-methylthioadenosine nucleosidase
KeywordsHYDROLASE / nucleosidase / apo / rossmann fold
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
Chem-MTH / 5'-methylthioadenosine nucleosidase
Similarity search - Component
Biological speciesArabidopsis thaliana (thale cress)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.84 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
DepositionAug 2, 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 / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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: 5'-methylthioadenosine nucleosidase
B: 5'-methylthioadenosine nucleosidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)57,6686
Polymers56,9512
Non-polymers7174
Water6,323351
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5490 Å2
MethodPISA
Unit cell
Length a, b, c (Å)40.580, 126.050, 45.540
Angle α, β, γ (deg.)90.00, 109.02, 90.00
Int Tables number4
Space group name H-MP1211
Detailsbiological unit is unknown

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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: 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: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 351 / 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: 1.93 Å3/Da / Density % sol: 36.38 %
Crystal growTemperature: 295 K / pH: 7.5
Details: NH4I, PEG3350, ethylene glycol, pH 7.5, vapor diffusion, hanging drop, temperature 295K, pH 7.50

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU300 / Wavelength: 1.5418 / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Nov 1, 2004 / Details: MIRRORS
RadiationMonochromator: CONFOCAL MULTILAYER / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.84→32.77 Å / Num. obs: 35711 / % possible obs: 95.5 % / Redundancy: 6.36 % / Biso Wilson estimate: 22.8 Å2 / Rmerge(I) obs: 0.06 / Net I/σ(I): 16.2
Reflection shellResolution: 1.84→1.91 Å / Redundancy: 6.81 % / Rmerge(I) obs: 0.299 / Mean I/σ(I) obs: 5.7 / % possible all: 97.3

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Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation2.5 Å32.77 Å
Translation2.5 Å32.77 Å

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Processing

Software
NameVersionClassificationNB
d*TREK9.4Ldata scaling
PHASERphasing
REFMAC5.2.0005refinement
PDB_EXTRACT3data extraction
d*TREKdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.84→32.77 Å / Cor.coef. Fo:Fc: 0.96 / Cor.coef. Fo:Fc free: 0.956 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.169 / ESU R Free: 0.125 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.19 1790 5 %RANDOM
Rwork0.185 ---
obs0.185 35709 95.5 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 22.83 Å2
Baniso -1Baniso -2Baniso -3
1-1.76 Å20 Å21.62 Å2
2---1.07 Å20 Å2
3---0.36 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.22 Å0.21 Å
Luzzati d res low-5 Å
Luzzati sigma a0.16 Å0.17 Å
Refinement stepCycle: LAST / Resolution: 1.84→32.77 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3672 0 48 351 4071
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0180.0223786
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg2.7141.9995172
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg10.1685497
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.78125.259135
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.56915616
X-RAY DIFFRACTIONr_dihedral_angle_4_deg10.561514
X-RAY DIFFRACTIONr_chiral_restr0.1150.2648
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.022770
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2370.22041
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3020.22634
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2350.2322
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2610.281
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1420.228
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.8721.52451
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.41523975
X-RAY DIFFRACTIONr_scbond_it2.31131335
X-RAY DIFFRACTIONr_scangle_it3.3764.51193
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.84→1.89 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.275 150 -
Rwork0.278 2528 -
obs--97.52 %

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