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- PDB-4jwt: Crystal structure of a putative 5'-methylthioadenosine/S-adenosyl... -

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Basic information

Entry
Database: PDB / ID: 4jwt
TitleCrystal structure of a putative 5'-methylthioadenosine/S-adenosylhomocysteine nucleosidase from Sulfurimonas denitrificans DSM 1251 (Target NYSGRC-029304 )
ComponentsMethylthioadenosine nucleosidase
KeywordsHYDROLASE / Sulfurimonas denitrificans / 5'-methylthioadenosine/S-adenosylhomocysteine nucleosidase / adenine / 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 / L-methionine salvage from S-adenosylmethionine / nucleoside catabolic process / L-methionine salvage from methylthioadenosine / cytosol
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 / adenosylhomocysteine nucleosidase
Similarity search - Component
Biological speciesSulfurimonas denitrificans (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.05 Å
AuthorsSampathkumar, P. / Almo, S.C. / New York Structural Genomics Research Consortium (NYSGRC)
CitationJournal: To be Published
Title: Crystal structure of a putative 5'-methylthioadenosine/S-adenosylhomocysteine nucleosidase from Sulfurimonas denitrificans DSM 1251
Authors: Sampathkumar, P. / Gizzi, A. / Ahmed, M. / Banu, N. / Bhosle, R. / Bonanno, J. / Chamala, S. / Chowdhury, S. / Fiser, A. / Glenn, A.S. / Hammonds, J. / Hillerich, B. / Khafizov, K. / ...Authors: Sampathkumar, P. / Gizzi, A. / Ahmed, M. / Banu, N. / Bhosle, R. / Bonanno, J. / Chamala, S. / Chowdhury, S. / Fiser, A. / Glenn, A.S. / Hammonds, J. / Hillerich, B. / Khafizov, K. / Lafleur, J. / Suarez, J. / Haapalainen, A. / Love, J.D. / Stead, M. / Seidel, R. / Toro, R. / Schramm, V.L. / Almo, S.C.
History
DepositionMar 27, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 8, 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
Revision 1.3Oct 30, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details / _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

Downloads & links

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Assembly

Deposited unit
A: Methylthioadenosine nucleosidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,0216
Polymers28,6381
Non-polymers3835
Water2,504139
1
A: Methylthioadenosine nucleosidase
hetero molecules

A: Methylthioadenosine nucleosidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)58,04212
Polymers57,2762
Non-polymers76710
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation10_665-y+1,-x+1,-z+1/61
Buried area5210 Å2
ΔGint0 kcal/mol
Surface area19920 Å2
MethodPISA
Unit cell
Length a, b, c (Å)77.598, 77.598, 228.425
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-457-

HOH

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Components

#1: Protein Methylthioadenosine nucleosidase


Mass: 28637.805 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Sulfurimonas denitrificans (bacteria) / Strain: DSM 1251 / Gene: Suden_1392 / Plasmid: pSGC-His / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) CodonPlus RIL
References: UniProt: Q30QR2, 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-ADE / ADENINE


Mass: 135.127 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C5H5N5
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 139 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 3.54 Å3/Da / Density % sol: 65.26 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 4.6
Details: Protein (20mM HEPES pH7.5, 150mM NaCl, 5% glycerol, and 5mM DTT); Reservoir (MCSG3 #84; 0.1 M Sodium Acetate:HCl pH 4.6, 2.0 M Sodium Formate ); Cryoprotection (33% Ethylene glycol), VAPOR ...Details: Protein (20mM HEPES pH7.5, 150mM NaCl, 5% glycerol, and 5mM DTT); Reservoir (MCSG3 #84; 0.1 M Sodium Acetate:HCl pH 4.6, 2.0 M Sodium Formate ); Cryoprotection (33% Ethylene glycol), VAPOR DIFFUSION, SITTING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X29A / Wavelength: 0.9791 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Feb 15, 2013 / Details: MIRRORS
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9791 Å / Relative weight: 1
ReflectionResolution: 2.05→50 Å / Num. obs: 26487 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 22.8 % / Biso Wilson estimate: 33 Å2 / Rmerge(I) obs: 0.109 / Net I/σ(I): 26.75
Reflection shellResolution: 2.05→2.09 Å / Redundancy: 23.1 % / Rmerge(I) obs: 0.738 / Mean I/σ(I) obs: 5.42 / Num. unique all: 1283 / % possible all: 100

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Processing

Software
NameVersionClassificationNB
REFMAC5.7.0029refinement
PDB_EXTRACT3.11data extraction
CBASSdata collection
HKL-3000data reduction
SCALEPACKdata scaling
SHELXCphasing
SHELXDphasing
SHELXEmodel building
RefinementMethod to determine structure: SAD / Resolution: 2.05→43.55 Å / Cor.coef. Fo:Fc: 0.96 / Cor.coef. Fo:Fc free: 0.957 / Occupancy max: 1 / Occupancy min: 0.5 / SU B: 2.987 / SU ML: 0.081 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.129 / ESU R Free: 0.115 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY. AUTHORS NOTE AN ELECTRON DENSITY FEATURE JUST BELOW ADENINE, WHICH COULD NOT BE SATISFACTORILY EXPLAINED ...Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY. AUTHORS NOTE AN ELECTRON DENSITY FEATURE JUST BELOW ADENINE, WHICH COULD NOT BE SATISFACTORILY EXPLAINED WITH BUFFER OR CRYSTALLIZATION COMPONENTS.
RfactorNum. reflection% reflectionSelection details
Rfree0.1929 1314 5 %RANDOM
Rwork0.1775 ---
obs0.1783 26403 99.86 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso max: 113.73 Å2 / Biso mean: 38.1574 Å2 / Biso min: 20.88 Å2
Baniso -1Baniso -2Baniso -3
1-0.26 Å20.26 Å20 Å2
2--0.26 Å20 Å2
3----0.83 Å2
Refinement stepCycle: LAST / Resolution: 2.05→43.55 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1851 0 26 139 2016
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0191941
X-RAY DIFFRACTIONr_bond_other_d0.0010.021860
X-RAY DIFFRACTIONr_angle_refined_deg1.2851.9982620
X-RAY DIFFRACTIONr_angle_other_deg0.71834311
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.9125256
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.04525.92176
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.81615307
X-RAY DIFFRACTIONr_dihedral_angle_4_deg12.282152
X-RAY DIFFRACTIONr_chiral_restr0.0740.2297
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.022188
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02407
LS refinement shellResolution: 2.052→2.105 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.257 85 -
Rwork0.225 1797 -
all-1882 -
obs-1797 98.9 %

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