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

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Basic information

Entry
Database: PDB / ID: 2qtt
TitleCrystal Structure of Arabidopsis thaliana 5'-Methylthioadenosine nucleosidase in complex with Formycin A
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
ADENINE / Chem-FMC / 5'-methylthioadenosine nucleosidase
Similarity search - Component
Biological speciesArabidopsis thaliana (thale cress)
MethodX-RAY DIFFRACTION / MAD / Resolution: 1.93 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 4, 2015Group: Data collection
Revision 1.3Feb 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)57,4165
Polymers56,9512
Non-polymers4643
Water7,927440
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5010 Å2
MethodPISA
Unit cell
Length a, b, c (Å)41.300, 127.050, 45.450
Angle α, β, γ (deg.)90.00, 109.63, 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-ADE / ADENINE


Mass: 135.127 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C5H5N5
#3: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#4: Chemical ChemComp-FMC / (1S)-1-(7-amino-1H-pyrazolo[4,3-d]pyrimidin-3-yl)-1,4-anhydro-D-ribitol


Mass: 267.241 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H13N5O4
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 440 / 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: 1.97 Å3/Da / Density % sol: 37.63 %
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

Diffraction
IDMean temperature (K)Crystal-ID
11001
21
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU300 / Wavelength: 1.5418
DetectorType: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Jun 30, 2005 / Details: MIRRORS MIRRORS
Radiation
IDMonochromatorProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1CONFOCAL MULTILAYER ROSENBAUM-ROCK DOUBLE CRYSTAL SAGITTAL FOCUSING MONOCHROMETERSINGLE WAVELENGTHMx-ray1
2Mx-ray1
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.93→23.61 Å / Num. obs: 31340 / % possible obs: 94.8 % / Redundancy: 3.17 % / Rmerge(I) obs: 0.06 / Net I/σ(I): 12.6
Reflection shellResolution: 1.93→2 Å / Redundancy: 2.48 % / Rmerge(I) obs: 0.155 / Mean I/σ(I) obs: 5.2 / % possible all: 90.5

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Processing

Software
NameVersionClassificationNB
d*TREK9.4Ldata scaling
REFMAC5.2.0005refinement
PDB_EXTRACT3data extraction
d*TREKdata reduction
SOLVEphasing
RefinementMethod to determine structure: MAD / Resolution: 1.93→23.61 Å / Cor.coef. Fo:Fc: 0.958 / Cor.coef. Fo:Fc free: 0.928 / Cross valid method: THROUGHOUT / ESU R: 0.212 / ESU R Free: 0.183 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.23275 3131 10 %RANDOM
Rwork0.17158 ---
obs0.17771 28208 94.7 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 19.226 Å2
Baniso -1Baniso -2Baniso -3
1-2.58 Å20 Å20.51 Å2
2---1.2 Å20 Å2
3----1.04 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.2 Å0.2 Å
Luzzati d res low-5 Å
Luzzati sigma a0.1 Å0.11 Å
Refinement stepCycle: LAST / Resolution: 1.93→23.61 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3687 0 33 440 4160
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0223831
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.5091.9975234
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.8185507
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.71225.252139
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.69715639
X-RAY DIFFRACTIONr_dihedral_angle_4_deg7.6231515
X-RAY DIFFRACTIONr_chiral_restr0.1010.2651
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.022810
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2280.21967
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3020.22699
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.140.2359
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1830.268
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1110.222
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.6361.52478
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.11624027
X-RAY DIFFRACTIONr_scbond_it1.90331353
X-RAY DIFFRACTIONr_scangle_it2.8684.51201
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.93→1.98 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.273 211 -
Rwork0.213 1959 -
obs--88.28 %

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