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- PDB-5dk6: CRYSTAL STRUCTURE OF A 5'-METHYLTHIOADENOSINE/S-ADENOSYLHOMOCYSTE... -

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Basic information

Entry
Database: PDB / ID: 5dk6
TitleCRYSTAL STRUCTURE OF A 5'-METHYLTHIOADENOSINE/S-ADENOSYLHOMOCYSTEINE (MTA/SAH) NUCLEOSIDASE (MTAN) FROM COLWELLIA PSYCHRERYTHRAEA 34H (CPS_4743, TARGET PSI-029300) IN COMPLEX WITH ADENINE AT 2.27 A RESOLUTION
Components5'-methylthioadenosine/S-adenosylhomocysteine nucleosidase
KeywordsHYDROLASE / MTA/SAH NUCLEOSIDASE FAMILY / MTAN / GAMMAPROTEOBACTERIA / Vibrio psychroerythus / ADENINE / PROTEIN-LIGAND COMPLEX / PROTEIN STRUCTURE INITIATIVE / PSI-Biology / Structural Genomics / New York Structural Genomics Research Consortium / NYSGRC
Function / homology
Function and homology information


L-methionine salvage from S-adenosylmethionine / adenosylhomocysteine nucleosidase / adenosylhomocysteine nucleosidase activity / methylthioadenosine nucleosidase activity / nucleoside catabolic process / L-methionine salvage from methylthioadenosine
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
ADENINE / GLYCINE / 5'-methylthioadenosine/S-adenosylhomocysteine nucleosidase
Similarity search - Component
Biological speciesColwellia psychrerythraea (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.27 Å
AuthorsHimmel, D.M. / Bhosle, R. / Toro, R. / Ahmed, M. / Hillerich, B. / Gizzi, A. / Garforth, S. / Kar, A. / Chan, M.K. / Lafluer, J. ...Himmel, D.M. / Bhosle, R. / Toro, R. / Ahmed, M. / Hillerich, B. / Gizzi, A. / Garforth, S. / Kar, A. / Chan, M.K. / Lafluer, J. / Patel, H. / Matikainen, B. / Chamala, S. / Lim, S. / Celikgil, A. / Villegas, G. / Evans, B. / Love, J. / Fiser, A. / Seidel, R.D. / Bonanno, J.B. / Almo, S.C. / New York Structural Genomics Research Consortium (NYSGRC)
Citation
Journal: To be published
Title: CRYSTAL STRUCTURE OF A 5'-METHYLTHIOADENOSINE/S-ADENOSYLHOMOCYSTEINE (MTA/SAH)NUCLEOSIDASE (MTAN) FROM COLWELLIA PSYCHRERYTHRAEA 34H (CPS_4743, TARGET PSI-029300) IN COMPLEX WITH ADENINE AT 2.27 A RESOLUTION
Authors: Himmel, D.M. / Bhosle, R. / Toro, R. / Ahmed, M. / Hillerich, B. / Gizzi, A. / Garforth, S. / Kar, A. / Chan, M.K. / Lafluer, J. / Patel, H. / Matikainen, B. / Chamala, S. / Lim, S. / ...Authors: Himmel, D.M. / Bhosle, R. / Toro, R. / Ahmed, M. / Hillerich, B. / Gizzi, A. / Garforth, S. / Kar, A. / Chan, M.K. / Lafluer, J. / Patel, H. / Matikainen, B. / Chamala, S. / Lim, S. / Celikgil, A. / Villegas, G. / Evans, B. / Love, J. / Fiser, A. / Seidel, R.D. / Bonanno, J.B. / Almo, S.C. / New York Structural Genomics Research Consortium (NYSGRC)
#1: Journal: Biochemistry / Year: 2015
Title: Active site and remote contributions to catalysis in methylthioadenosine nucleosidases.
Authors: Thomas, K. / Cameron, S.A. / Almo, S.C. / Burgos, E.S. / Gulab, S.A. / Schramm, V.L.
#2: Journal: Nat. Chem. Biol. / Year: 2009
Title: Transition state analogs of 5'-methylthioadenosine nucleosidase disrupt quorum sensing.
Authors: Gutierrez, J.A. / Crowder, T. / Rinaldo-Matthis, A. / Ho, M.C. / Almo, S.C. / Schramm, V.L.
History
DepositionSep 3, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 4, 2015Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: 5'-methylthioadenosine/S-adenosylhomocysteine nucleosidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,6963
Polymers28,4861
Non-polymers2102
Water1,820101
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: 5'-methylthioadenosine/S-adenosylhomocysteine nucleosidase
hetero molecules

A: 5'-methylthioadenosine/S-adenosylhomocysteine nucleosidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)57,3926
Polymers56,9722
Non-polymers4204
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation10_666-y+1,-x+1,-z+7/61
Buried area3770 Å2
ΔGint-11 kcal/mol
Surface area19060 Å2
MethodPISA
Unit cell
Length a, b, c (Å)145.427, 145.427, 70.341
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number179
Space group name H-MP6522
Components on special symmetry positions
IDModelComponents
11A-407-

HOH

21A-474-

HOH

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Components

#1: Protein 5'-methylthioadenosine/S-adenosylhomocysteine nucleosidase / MTAN / 5'-methylthioadenosine nucleosidase / MTA nucleosidase / S-adenosylhomocysteine nucleosidase ...MTAN / 5'-methylthioadenosine nucleosidase / MTA nucleosidase / S-adenosylhomocysteine nucleosidase / SRH nucleosidase


Mass: 28485.967 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Colwellia psychrerythraea (bacteria) / Strain: 34H / ATCC BAA-681 / Gene: mtnN, CPS_4743 / Plasmid: pET / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: Q47UY5, adenosylhomocysteine nucleosidase
#2: Chemical ChemComp-GLY / GLYCINE / Glycine


Type: peptide linking / Mass: 75.067 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H5NO2
#3: Chemical ChemComp-ADE / ADENINE / Adenine


Mass: 135.127 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: C5H5N5
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 101 / 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: 3.84 Å3/Da / Density % sol: 68 %
Crystal growTemperature: 292 K / Method: vapor diffusion, sitting drop / pH: 8
Details: Protein (37.95 mg/ml, 20 mM HEPES pH 7.5, 150 mM Sodium Chloride, 5% v/v Glycerol, 5 mM DTT) were combined with an equal volume of Reservoir (100 mM Bicine pH 8.0, 1.98 M Ammonium Sulfate, ...Details: Protein (37.95 mg/ml, 20 mM HEPES pH 7.5, 150 mM Sodium Chloride, 5% v/v Glycerol, 5 mM DTT) were combined with an equal volume of Reservoir (100 mM Bicine pH 8.0, 1.98 M Ammonium Sulfate, 135 mM Sodium Succinate, 4 mM Glycine, 15 mM CYMAL-7); Cryoprotection (75 mM Bicine pH 8.0, 1.49 M Ammonium Sulfate, 101 mM Sodium Succinate, 3 mM Glycine, 11 mM CYMAL-7)

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 31-ID / Wavelength: 0.97931 Å
DetectorType: RAYONIX MX225HE / Detector: CCD / Date: Oct 17, 2013 / Details: MIRRORS
RadiationMonochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97931 Å / Relative weight: 1
ReflectionRedundancy: 3.9 % / Number: 143135 / Rmerge(I) obs: 0.1 / Χ2: 1 / D res high: 2.28 Å / D res low: 26 Å / Num. obs: 37023 / % possible obs: 96.4
Diffraction reflection shell
Highest resolution (Å)Lowest resolution (Å)IDRmerge(I) obsChi squaredRedundancy
4.92610.0691.0245.3
3.94.910.10.985.2
3.43.910.0721.0054.9
3.093.410.1061.0094.4
2.873.0910.1610.9983.9
2.72.8710.2141.0053.6
2.572.710.2670.9863.3
2.462.5710.3141.0053.1
2.362.4610.350.9852.6
2.282.3610.3371.0062
ReflectionResolution: 2.268→26 Å / Num. obs: 37023 / % possible obs: 96.4 % / Observed criterion σ(I): -0.3 / Redundancy: 3.9 % / Biso Wilson estimate: 33.16 Å2 / Rmerge(I) obs: 0.1 / Net I/σ(I): 11.5
Reflection shellResolution: 2.27→2.36 Å / Redundancy: 2 % / Rmerge(I) obs: 0.337 / Mean I/σ(I) obs: 2.148 / % possible all: 82.8

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
HKL-2000data collection
SCALEPACK1.99.2data scaling
PDB_EXTRACT3.15data extraction
PHENIX1.9-1692phasing
HKL-2000data reduction
RefinementMethod to determine structure: SAD / Resolution: 2.27→25.28 Å / SU ML: 0.23 / Cross valid method: FREE R-VALUE / σ(F): 1.45 / Phase error: 22.27 / Stereochemistry target values: MLHL
RfactorNum. reflection% reflectionSelection details
Rfree0.2371 1002 4.9 %Random
Rwork0.2082 ---
obs0.21 20433 98.2 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 31.6 Å2 / ksol: 0.34 e/Å3
Displacement parametersBiso mean: 43.6 Å2
Refinement stepCycle: LAST / Resolution: 2.27→25.28 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1802 0 14 101 1917
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.011843
X-RAY DIFFRACTIONf_angle_d1.2012493
X-RAY DIFFRACTIONf_dihedral_angle_d18.474657
X-RAY DIFFRACTIONf_chiral_restr0.043295
X-RAY DIFFRACTIONf_plane_restr0.005321
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.2676-2.3870.32451250.29872506X-RAY DIFFRACTION91
2.387-2.53650.29281240.27682768X-RAY DIFFRACTION99
2.5365-2.73210.27381450.24392766X-RAY DIFFRACTION100
2.7321-3.00660.25571250.22862795X-RAY DIFFRACTION99
3.0066-3.44080.24161640.20612783X-RAY DIFFRACTION99
3.4408-4.33150.21041490.17962835X-RAY DIFFRACTION100
4.3315-25.27980.20641700.1792978X-RAY DIFFRACTION99

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