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- PDB-1wta: Crystal Structure of 5'-Deoxy-5'-methylthioadenosine from Aeropyr... -

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Basic information

Entry
Database: PDB / ID: 1wta
TitleCrystal Structure of 5'-Deoxy-5'-methylthioadenosine from Aeropyrum pernix (R32 form)
Components5'-methylthioadenosine phosphorylase
KeywordsTRANSFERASE / A/B STRUCTURE
Function / homology
Function and homology information


S-methyl-5'-thioadenosine phosphorylase / S-methyl-5-thioadenosine phosphorylase activity / L-methionine salvage from methylthioadenosine / purine ribonucleoside salvage / cytosol
Similarity search - Function
Methylthioadenosine phosphorylase (MTAP) / Purine phosphorylase, family 2, conserved site / Purine and other phosphorylases family 2 signature. / Nucleoside phosphorylase domain / Nucleoside phosphorylase domain / Phosphorylase superfamily / Nucleoside phosphorylase superfamily / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
ADENINE / PHOSPHATE ION / : / S-methyl-5'-thioadenosine phosphorylase
Similarity search - Component
Biological speciesAeropyrum pernix (archaea)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.78 Å
AuthorsTsunoda, M. / Murakami, Y. / Nakamura, K.T.
CitationJournal: To be Published
Title: Crystal Structure of 5'-Deoxy-5'-methylthioadenosine from Aeropyrum pernix (R32 form)
Authors: Tsunoda, M. / Murakami, Y. / Nakamura, K.T.
History
DepositionNov 18, 2004Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Feb 7, 2006Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Source and taxonomy / Version format compliance
Revision 1.3Oct 11, 2017Group: Advisory / Refinement description / Category: pdbx_unobs_or_zero_occ_atoms / software
Revision 1.4Nov 1, 2017Group: Derived calculations / Category: pdbx_struct_assembly / Item: _pdbx_struct_assembly.method_details
Revision 1.5Nov 20, 2024Group: Advisory / Data collection ...Advisory / 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 / pdbx_unobs_or_zero_occ_atoms / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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 phosphorylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,0073
Polymers30,7771
Non-polymers2302
Water6,449358
1
A: 5'-methylthioadenosine phosphorylase
hetero molecules

A: 5'-methylthioadenosine phosphorylase
hetero molecules

A: 5'-methylthioadenosine phosphorylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)93,0229
Polymers92,3323
Non-polymers6906
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_655-y+1,x-y,z1
crystal symmetry operation3_665-x+y+1,-x+1,z1
2
A: 5'-methylthioadenosine phosphorylase
hetero molecules
x 6


Theoretical massNumber of molelcules
Total (without water)186,04518
Polymers184,6646
Non-polymers1,38112
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-y,x-y,z1
crystal symmetry operation3_555-x+y,-x,z1
crystal symmetry operation4_555y,x,-z1
crystal symmetry operation5_555x-y,-y,-z1
crystal symmetry operation6_555-x,-x+y,-z1
Buried area27890 Å2
ΔGint-121 kcal/mol
Surface area48810 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)78.150, 78.150, 230.430
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number155
Space group name H-MH32
Components on special symmetry positions
IDModelComponents
11A-1301-

HOH

21A-1410-

HOH

31A-1451-

HOH

41A-1486-

HOH

51A-1569-

HOH

61A-1613-

HOH

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Components

#1: Protein 5'-methylthioadenosine phosphorylase / 5'-DEOXY-5'-METHYLTHIOADENOSINE PHOSPHORYLASE


Mass: 30777.336 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Aeropyrum pernix (archaea) / Strain: K1 / Plasmid: pET-11a / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta-gami(DE3)
References: GenBank: 14601697, UniProt: Q9YAQ8*PLUS, S-methyl-5'-thioadenosine phosphorylase
#2: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4
#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.: 358 / 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: 2.2 Å3/Da / Density % sol: 44.16 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 4.5
Details: MPD, glycerol, pH 4.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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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 / Date: Jul 6, 2004 / Details: mirrors
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.78→76.7 Å / Num. obs: 26274 / % possible obs: 99.4 % / Redundancy: 3.8 % / Rmerge(I) obs: 0.058 / Net I/σ(I): 9
Reflection shellResolution: 1.78→1.84 Å / Redundancy: 3.72 % / Rmerge(I) obs: 0.282 / Mean I/σ(I) obs: 2.6 / Num. unique all: 2594 / % possible all: 99

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Processing

Software
NameVersionClassification
REFMAC5.1.24refinement
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.78→58.36 Å / Cor.coef. Fo:Fc: 0.959 / Cor.coef. Fo:Fc free: 0.935 / SU B: 2.531 / SU ML: 0.077 / Cross valid method: THROUGHOUT / ESU R: 0.121 / ESU R Free: 0.112 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.1955 1327 5.1 %RANDOM
Rwork0.16392 ---
obs0.16555 24941 99.35 %-
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 mean: 15.474 Å2
Baniso -1Baniso -2Baniso -3
1-0.03 Å20.02 Å20 Å2
2--0.03 Å20 Å2
3----0.05 Å2
Refinement stepCycle: LAST / Resolution: 1.78→58.36 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2133 0 15 358 2506
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0212182
X-RAY DIFFRACTIONr_bond_other_d0.0020.021994
X-RAY DIFFRACTIONr_angle_refined_deg1.231.962974
X-RAY DIFFRACTIONr_angle_other_deg1.07834603
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.35272
X-RAY DIFFRACTIONr_dihedral_angle_2_deg
X-RAY DIFFRACTIONr_dihedral_angle_3_deg
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.0710.2329
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.022433
X-RAY DIFFRACTIONr_gen_planes_other0.0050.02450
X-RAY DIFFRACTIONr_nbd_refined0.1890.2594
X-RAY DIFFRACTIONr_nbd_other0.2450.22444
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other0.1310.21523
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1440.2209
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1660.264
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2520.2139
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.210.240
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_mcbond_it0.4391.51361
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it0.83822209
X-RAY DIFFRACTIONr_scbond_it1.4693819
X-RAY DIFFRACTIONr_scangle_it2.4234.5760
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.78→1.826 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.343 85
Rwork0.311 1796

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