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- PDB-4kn5: Crystal structure of a putative methylthioadenosine nucleosidase ... -

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Basic information

Entry
Database: PDB / ID: 4kn5
TitleCrystal structure of a putative methylthioadenosine nucleosidase from Weissella paramesenteroides ATCC 33313 (Target NYSGRC-029342 )
ComponentsMethylthioadenosine nucleosidase
KeywordsHYDROLASE / 5'-methylthioadenosine nucleosidase / Structural genomics / NYSGRC / New York Structural Genomics Research Consortium / PSI-Biology
Function / homology
Function and homology information


adenosylhomocysteine nucleosidase / adenosylhomocysteine nucleosidase activity / methylthioadenosine nucleosidase activity / nucleoside catabolic process / L-methionine salvage from methylthioadenosine / purine-nucleoside phosphorylase activity
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
5'-methylthioadenosine/S-adenosylhomocysteine nucleosidase
Similarity search - Component
Biological speciesWeissella paramesenteroides (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.7 Å
AuthorsSampathkumar, P. / Almo, S.C. / New York Structural Genomics Research Consortium (NYSGRC)
CitationJournal: to be published
Title: Crystal structure of a putative methylthioadenosine nucleosidase from Weissella paramesenteroides ATCC 33313 (Target NYSGRC-029342)
Authors: Sampathkumar, P. / Ahmed, M. / Attonito, J. / Bhosle, R. / Bonanno, J. / Chamala, S. / Chowdhury, S. / Eromenok, G. / Fiser, A. / Glenn, A.S. / Hammonds, J. / Hillerich, B. / Himmel, D.M. / ...Authors: Sampathkumar, P. / Ahmed, M. / Attonito, J. / Bhosle, R. / Bonanno, J. / Chamala, S. / Chowdhury, S. / Eromenok, G. / Fiser, A. / Glenn, A.S. / Hammonds, J. / Hillerich, B. / Himmel, D.M. / Khafizov, K. / Lafleur, J. / Love, J.D. / Stead, M. / Seidel, R. / Toro, R. / Morisco, L.L. / Sojitra, S.S. / Wasserman, S.R. / Haapalainen, A. / Suarez, J. / Schramm, V.L. / Almo, S.C.
History
DepositionMay 8, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 29, 2013Provider: repository / Type: Initial release
Revision 1.1Nov 27, 2013Group: Structure summary
Revision 1.2Nov 15, 2017Group: Refinement description / Category: software / Item: _software.classification / _software.name

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Methylthioadenosine nucleosidase
B: Methylthioadenosine nucleosidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)55,2147
Polymers54,8732
Non-polymers3405
Water4,306239
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3880 Å2
ΔGint-6 kcal/mol
Surface area18300 Å2
MethodPISA
Unit cell
Length a, b, c (Å)89.252, 89.252, 127.545
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number96
Space group name H-MP43212
DetailsDIMERIC

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Components

#1: Protein Methylthioadenosine nucleosidase


Mass: 27436.584 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Weissella paramesenteroides (bacteria) / Strain: ATCC 33313 / Gene: HMPREF0877_0999 / Plasmid: pSGC-His / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) RIL
References: UniProt: C5RAK4, methylthioadenosine nucleosidase
#2: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C2H6O2
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 239 / 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: 2.31 Å3/Da / Density % sol: 46.86 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: Protein (20mM HEPES pH7.5, 150mM NaCl, 5% glycerol, and 5mM DTT); Reservoir (MCSG3 #47: 0.1 M HEPES:NaOH pH 7.5, 0.8 M NaH2PO4, 0.8 M KH2PO4 ); Cryoprotection (33% Ethylene glycol), VAPOR ...Details: Protein (20mM HEPES pH7.5, 150mM NaCl, 5% glycerol, and 5mM DTT); Reservoir (MCSG3 #47: 0.1 M HEPES:NaOH pH 7.5, 0.8 M NaH2PO4, 0.8 M KH2PO4 ); Cryoprotection (33% Ethylene glycol), VAPOR DIFFUSION, SITTING DROP, temperature 298K

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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: Mar 29, 2013 / Details: MIRRORS
RadiationMonochromator: Diamond(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97931 Å / Relative weight: 1
ReflectionResolution: 1.7→38.38 Å / Num. obs: 57368 / % possible obs: 100 % / Observed criterion σ(F): 0 / Redundancy: 29.2 % / Biso Wilson estimate: 19.7 Å2 / Rmerge(I) obs: 0.113 / Net I/σ(I): 27.8
Reflection shellResolution: 1.7→1.73 Å / Redundancy: 27.7 % / Rmerge(I) obs: 1.986 / Mean I/σ(I) obs: 2.3 / Num. unique all: 3003 / % possible all: 99.8

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Processing

Software
NameVersionClassificationNB
REFMAC5.7.0029refinement
PDB_EXTRACT3.11data extraction
CBASSdata collection
XDSdata reduction
Aimlessdata scaling
SHELXCphasing
SHELXDphasing
SHELXEmodel building
RefinementMethod to determine structure: SAD / Resolution: 1.7→38.12 Å / Cor.coef. Fo:Fc: 0.963 / Cor.coef. Fo:Fc free: 0.947 / Occupancy max: 1 / Occupancy min: 0.5 / SU B: 1.975 / SU ML: 0.065 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.097 / ESU R Free: 0.097 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2114 2906 5.1 %RANDOM
Rwork0.1792 ---
obs0.1808 57283 99.97 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso max: 83.35 Å2 / Biso mean: 27.668 Å2 / Biso min: 11.71 Å2
Baniso -1Baniso -2Baniso -3
1--0.61 Å2-0 Å2-0 Å2
2---0.61 Å20 Å2
3---1.21 Å2
Refinement stepCycle: LAST / Resolution: 1.7→38.12 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3467 0 22 239 3728
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0193686
X-RAY DIFFRACTIONr_bond_other_d0.0010.023491
X-RAY DIFFRACTIONr_angle_refined_deg1.5021.9575025
X-RAY DIFFRACTIONr_angle_other_deg0.79238033
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.2555505
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.30125.398176
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.59515561
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.5531516
X-RAY DIFFRACTIONr_chiral_restr0.0920.2584
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.024347
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02843
LS refinement shellResolution: 1.7→1.744 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.314 230 -
Rwork0.276 3935 -
all-4165 -
obs-3935 99.78 %

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