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- PDB-2h8g: 5'-Methylthioadenosine Nucleosidase from Arabidopsis thaliana -

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Basic information

Entry
Database: PDB / ID: 2h8g
Title5'-Methylthioadenosine Nucleosidase from Arabidopsis thaliana
Components5'-Methylthioadenosine Nucleosidase
KeywordsHYDROLASE / Protein-adenine complex
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 / 5'-methylthioadenosine nucleosidase
Similarity search - Component
Biological speciesArabidopsis thaliana (thale cress)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.5 Å
AuthorsPark, E.Y. / Oh, S.I. / Nam, M.J. / Shin, J.S. / Kim, K.N. / Song, H.K.
CitationJournal: Proteins / Year: 2006
Title: Crystal structure of 5'-methylthioadenosine nucleosidase from Arabidopsis thaliana at 1.5-A resolution
Authors: Park, E.Y. / Oh, S.I. / Nam, M.J. / Shin, J.S. / Kim, K.N. / Song, H.K.
History
DepositionJun 7, 2006Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Oct 10, 2006Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Mar 13, 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)57,2224
Polymers56,9512
Non-polymers2702
Water11,854658
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4630 Å2
ΔGint-20 kcal/mol
Surface area18910 Å2
MethodPISA
Unit cell
Length a, b, c (Å)40.543, 126.585, 45.794
Angle α, β, γ (deg.)90.00, 104.38, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein 5'-Methylthioadenosine Nucleosidase / Hypothetical protein AT4g38800


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: pGEX4T3 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) RIL, B834(DE3)
References: UniProt: Q9T0I8, methylthioadenosine nucleosidase
#2: Chemical ChemComp-ADE / ADENINE


Mass: 135.127 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C5H5N5
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 658 / 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: 3

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Sample preparation

CrystalDensity Matthews: 2 Å3/Da / Density % sol: 38.43 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 0.1M Tris-HCl, 0.2M sodium acetate, 30% PEG 4000, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 295K

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21001
31001
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONPhoton Factory AR-NW12A11
SYNCHROTRONPAL/PLS 4A20.95, 0.9795, 0.9797
SYNCHROTRONPAL/PLS 4A30.9918, 1.0064, 1.0084, 1.0087
Detector
TypeIDDetectorDate
ADSC QUANTUM 41CCDDec 3, 2005
ADSC QUANTUM 42CCDOct 27, 2005
ADSC QUANTUM 43CCDOct 27, 2005
Radiation
IDProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1SINGLE WAVELENGTHMx-ray1
2MADMx-ray1
3MADMx-ray1
Radiation wavelength
IDWavelength (Å)Relative weight
111
20.951
30.97951
40.97971
50.99181
61.00641
71.00841
81.00871
ReflectionResolution: 1.5→50 Å / Num. all: 196061 / Num. obs: 67182 / % possible obs: 94 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0
Reflection shellResolution: 1.5→1.55 Å / % possible all: 69

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Processing

Software
NameVersionClassification
ADSCdata collection
HKL-2000data reduction
SOLVEphasing
CNS1.1refinement
HKL-2000data scaling
RefinementMethod to determine structure: MAD / Resolution: 1.5→50 Å / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.224 3307 -random
Rwork0.198 ---
all0.199 71273 --
obs0.199 64982 91.2 %-
Refinement stepCycle: LAST / Resolution: 1.5→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3678 0 20 658 4356
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.004
X-RAY DIFFRACTIONc_angle_deg1.269

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