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- PDB-4gmh: Crystal structure of staphylococcus aureus 5'-methylthioadenosine... -

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Basic information

Entry
Database: PDB / ID: 4gmh
TitleCrystal structure of staphylococcus aureus 5'-methylthioadenosine/s-adenosylhomocysteine nucleosidase
Components5'-methylthioadenosine/S-adenosylhomocysteine nucleosidase
KeywordsHYDROLASE / NUCLEOSIDASE / MTAN / ALPHA/BETA PROTEINS / S-ADENOSYLHOMOCYSTEINE / CLEAVAGE
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
ACETATE ION / 5'-methylthioadenosine/S-adenosylhomocysteine nucleosidase
Similarity search - Component
Biological speciesStaphylococcus aureus subsp. aureus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsBrown, R.L. / Anderson, B.F. / Norris, G.E. / Tyler, P.C. / Evans, G.B. / Sutherland-Smith, A.J.
CitationJournal: To be Published
Title: Crystal structure of staphylococcus aureus 5'-methylthioadenosine/s-adenosylhomocysteine nucleosidase
Authors: Brown, R.L. / Anderson, B.F. / Norris, G.E. / Tyler, P.C. / Evans, G.B. / Sutherland-Smith, A.J.
History
DepositionAug 15, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 28, 2012Provider: repository / Type: Initial release
Revision 1.1Sep 13, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / 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

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)24,8754
Polymers24,6981
Non-polymers1773
Water2,486138
1
A: 5'-methylthioadenosine/S-adenosylhomocysteine nucleosidase
hetero molecules

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


Theoretical massNumber of molelcules
Total (without water)49,7518
Polymers49,3962
Non-polymers3546
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555x,-y,-z1
Buried area4220 Å2
ΔGint-30 kcal/mol
Surface area18420 Å2
MethodPISA
Unit cell
Length a, b, c (Å)47.423, 55.852, 97.022
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP22121
Components on special symmetry positions
IDModelComponents
11A-429-

HOH

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Components

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


Mass: 24698.191 Da / Num. of mol.: 1 / Fragment: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Staphylococcus aureus subsp. aureus (bacteria)
Strain: MU50 / Gene: mtnN, SAV1599 / Plasmid: PPROEX HTB / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: Q99TQ0, adenosylhomocysteine nucleosidase
#2: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H3O2
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 138 / 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: 2.63 Å3/Da / Density % sol: 53.93 %
Crystal growpH: 8.5
Details: 4.2M FORMATE, 0.1M TRIS HCL, CRYOPROTECTANT 20% GLYCEROL, pH 8.50, VAPOR DIFFUSION, HANGING DROP, temperature 110K

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Data collection

DiffractionMean temperature: 110 K
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX1 / Wavelength: 1.5418
DetectorType: ADSC QUANTUM 210r / Detector: CCD / Date: Jul 17, 2007
RadiationMonochromator: DOUBLE MIRRORS / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.75→27.93 Å / Num. obs: 18068 / % possible obs: 100 % / Observed criterion σ(I): 0 / Redundancy: 6.91 % / Rmerge(I) obs: 0.15 / Net I/σ(I): 3.49
Reflection shellResolution: 2→2.11 Å / Redundancy: 6.87 % / Rmerge(I) obs: 0.66 / Mean I/σ(I) obs: 1.23 / % possible all: 100

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Processing

Software
NameVersionClassification
MOLREPphasing
REFMAC5.1.24refinement
MOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: S AUREUS MTAN 3BL6

3bl6


Resolution: 2→26.72 Å / Cor.coef. Fo:Fc: 0.954 / Cor.coef. Fo:Fc free: 0.928 / SU B: 4.132 / SU ML: 0.115 / Isotropic thermal model: ISOTROPIC / Cross valid method: THROUGHOUT / ESU R: 0.169 / ESU R Free: 0.159 / Stereochemistry target values: ENGH & HUBER
Details: HYDROGENS HAVE BEEN ADDED IN THEIR RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.23305 919 5.1 %RANDOM
Rwork0.18343 ---
obs0.18591 17111 99.92 %-
all-17111 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 25.331 Å2
Baniso -1Baniso -2Baniso -3
1--0 Å2-0 Å2-0 Å2
2--0.04 Å20 Å2
3----0.04 Å2
Refinement stepCycle: LAST / Resolution: 2→26.72 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1727 0 12 138 1877
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0320.0191815
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg2.1171.9672463
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.9875241
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.46826.66772
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.17215321
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.48153
X-RAY DIFFRACTIONr_chiral_restr0.1650.2295
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.0211352
X-RAY DIFFRACTIONr_gen_planes_other0.001
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it
X-RAY DIFFRACTIONr_scbond_it
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2→2.052 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.366 65 -
Rwork0.264 1225 -
obs--100 %

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