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- PDB-3bl6: Crystal structure of Staphylococcus aureus 5'-methylthioadenosine... -

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Basic information

Entry
Database: PDB / ID: 3bl6
TitleCrystal structure of Staphylococcus aureus 5'-methylthioadenosine/S-adenosylhomocysteine nucleosidase in complex with formycin A
Components5'-methylthioadenosine nucleosidase/S-adenosylhomocysteine nucleosidase
KeywordsHYDROLASE / nucleosidase / MTAN / alpha and beta proteins
Function / homology
Function and homology information


nucleoside catabolic process / adenosylhomocysteine nucleosidase / adenosylhomocysteine nucleosidase activity / methylthioadenosine nucleosidase activity / L-methionine salvage from S-adenosylmethionine / 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
Chem-FMC / 5'-methylthioadenosine/S-adenosylhomocysteine nucleosidase
Similarity search - Component
Biological speciesStaphylococcus aureus (bacteria)
MethodX-RAY DIFFRACTION / Resolution: 1.7 Å
AuthorsSiu, K.K.W. / Lee, J.E. / Smith, G.D. / Horvatin, C. / Howell, P.L.
CitationJournal: Acta Crystallogr.,Sect.F / Year: 2008
Title: Structure of Staphylococcus aureus 5'-methylthioadenosine/S-adenosylhomocysteine nucleosidase
Authors: Siu, K.K. / Lee, J.E. / Smith, G.D. / Horvatin-Mrakovcic, C. / Howell, P.L.
History
DepositionDec 10, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 10, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Feb 21, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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_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: 5'-methylthioadenosine nucleosidase/S-adenosylhomocysteine nucleosidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,0242
Polymers24,7561
Non-polymers2671
Water3,423190
1
A: 5'-methylthioadenosine nucleosidase/S-adenosylhomocysteine nucleosidase
hetero molecules

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


Theoretical massNumber of molelcules
Total (without water)50,0474
Polymers49,5132
Non-polymers5342
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_655-x+1,-y,z1
Buried area4210 Å2
MethodPISA
Unit cell
Length a, b, c (Å)58.250, 81.670, 45.460
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21212

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Components

#1: Protein 5'-methylthioadenosine nucleosidase/S-adenosylhomocysteine nucleosidase


Mass: 24756.336 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Staphylococcus aureus (bacteria) / Strain: MRSA 703 / Gene: pfs / Plasmid: pET28a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: Q99TQ0, adenosylhomocysteine nucleosidase, methylthioadenosine nucleosidase
#2: 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
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 190 / 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: 2.18 Å3/Da / Density % sol: 43.68 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: PEG 8000, Potassium phosphate monobasic, pH 7.5, vapour diffusion, hanging drop, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU300 / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Details: MIRRORS
RadiationMonochromator: CONFOCAL MULTILAYER / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionRedundancy: 5.68 % / Av σ(I) over netI: 50.7 / Number: 144276 / Rmerge(I) obs: 0.025 / Χ2: 0.92 / D res high: 1.65 Å / D res low: 32.81 Å / Num. obs: 24119 / % possible obs: 90
Diffraction reflection shell

ID: 1

Highest resolution (Å)Lowest resolution (Å)% possible obs (%)Rmerge(I) obsChi squaredRedundancyRejects
3.5532.8195.50.0141.365.082181
2.823.5596.20.0171.095.6898
2.462.8294.70.0230.915.77516
2.242.4693.60.0320.985.69831
2.082.2493.80.0350.95.95344
1.962.0892.20.0410.816.07248
1.861.9691.80.0530.816.12218
1.781.8689.80.0650.756.12487
1.711.7885.40.0880.795.471340
1.651.7166.40.0980.824.77151
ReflectionResolution: 1.7→32.8 Å / Num. obs: 24529 / % possible obs: 93.1 % / Redundancy: 5.5 % / Rmerge(I) obs: 0.028 / Net I/σ(I): 19.9
Reflection shellResolution: 1.7→1.76 Å / Rmerge(I) obs: 0.11 / Mean I/σ(I) obs: 5.8 / % possible all: 88.1

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Processing

Software
NameVersionClassificationNB
d*TREKdata scaling
CNSrefinement
PDB_EXTRACT3.004data extraction
CrystalCleardata collection
d*TREKdata reduction
CNSphasing
RefinementResolution: 1.7→32.8 Å / FOM work R set: 0.915 / σ(F): 0
RfactorNum. reflection% reflection
Rfree0.187 1110 4.5 %
Rwork0.181 --
obs-22806 92.9 %
Solvent computationBsol: 67.135 Å2
Displacement parametersBiso mean: 13.588 Å2
Baniso -1Baniso -2Baniso -3
1-2.326 Å20 Å20 Å2
2---3.472 Å20 Å2
3---1.146 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.19 Å0.18 Å
Luzzati d res low-5 Å
Luzzati sigma a0.14 Å0.12 Å
Refinement stepCycle: LAST / Resolution: 1.7→32.8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1718 0 19 192 1929
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_mcbond_it1.2561.5
X-RAY DIFFRACTIONc_scbond_it2.4122
X-RAY DIFFRACTIONc_mcangle_it1.7092
X-RAY DIFFRACTIONc_scangle_it3.4232.5
Xplor file
Refine-IDSerial noParam file
X-RAY DIFFRACTION1protein_rep.param
X-RAY DIFFRACTION2water_rep.param
X-RAY DIFFRACTION3formycin.param

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