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- PDB-1v4n: Structure of 5'-deoxy-5'-methylthioadenosine phosphorylase homolo... -

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Basic information

Entry
Database: PDB / ID: 1v4n
TitleStructure of 5'-deoxy-5'-methylthioadenosine phosphorylase homologue from Sulfolobus tokodaii
Components271aa long hypothetical 5'-methylthioadenosine phosphorylase
KeywordsTRANSFERASE / STRUCTURAL GENOMICS
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
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
: / S-methyl-5'-thioadenosine phosphorylase
Similarity search - Component
Biological speciesSulfolobus tokodaii (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.45 Å
AuthorsKitago, Y. / Yasutake, Y. / Sakai, N. / Tsujimura, M. / Yao, M. / Watanabe, N. / Kawarabayasi, Y. / Tanaka, I.
CitationJournal: To be Published
Title: Crystal structure of Sulfolobus tokodaii MTAP
Authors: Kitago, Y. / Yasutake, Y. / Sakai, N. / Tsujimura, M. / Yao, M. / Watanabe, N. / Kawarabayasi, Y. / Tanaka, I.
History
DepositionNov 14, 2003Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jan 4, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 25, 2023Group: Data collection / Database references / 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
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: 271aa long hypothetical 5'-methylthioadenosine phosphorylase
B: 271aa long hypothetical 5'-methylthioadenosine phosphorylase
C: 271aa long hypothetical 5'-methylthioadenosine phosphorylase


Theoretical massNumber of molelcules
Total (without water)94,7483
Polymers94,7483
Non-polymers00
Water4,954275
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7440 Å2
ΔGint-41 kcal/mol
Surface area29490 Å2
MethodPISA
Unit cell
Length a, b, c (Å)79.869, 142.888, 169.564
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221
DetailsThe biological assembly is homotrimer in the asymmetric unit.

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Components

#1: Protein 271aa long hypothetical 5'-methylthioadenosine phosphorylase / MTAP


Mass: 31582.643 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Sulfolobus tokodaii (archaea) / Gene: ST0485 / Plasmid: pET-23a / Production host: Escherichia coli (E. coli) / Strain (production host): B834(DE3)
References: GenBank: 15920700, UniProt: F9VN03*PLUS, S-methyl-5'-thioadenosine phosphorylase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 275 / 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: 2.64 Å3/Da / Density % sol: 53.08 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7
Details: Tris buffer, PEG1000, pH 7.0, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-18B / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: May 27, 2003 / Details: a mirror and monochrometer
RadiationMonochromator: Si 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.45→50 Å / Num. all: 36084 / Num. obs: 36084 / % possible obs: 100 % / Observed criterion σ(I): -3 / Redundancy: 6.93 % / Biso Wilson estimate: 33.59 Å2 / Rsym value: 0.101 / Net I/σ(I): 13.7
Reflection shellResolution: 2.45→2.54 Å / Redundancy: 6.81 % / Rmerge(I) obs: 0.229 / Num. unique all: 3576 / Rsym value: 0.229 / % possible all: 100

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Processing

Software
NameClassification
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
CNSrefinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB code 1cg6

1cg6


Resolution: 2.45→50 Å / Isotropic thermal model: isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.2409 1806 5 %RANDOM
Rwork0.1903 ---
all-36061 --
obs-36061 100 %-
Displacement parametersBiso mean: 34.228 Å2
Baniso -1Baniso -2Baniso -3
1--8.066 Å20 Å20 Å2
2---2.035 Å20 Å2
3---10.101 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.33 Å0.25 Å
Luzzati d res low-5 Å
Luzzati sigma a0.27 Å0.16 Å
Refinement stepCycle: LAST / Resolution: 2.45→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6264 0 0 275 6539
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.021457
X-RAY DIFFRACTIONc_angle_deg2.12317
X-RAY DIFFRACTIONc_improper_angle_d1.33247
X-RAY DIFFRACTIONc_dihedral_angle_d25.49259
X-RAY DIFFRACTIONc_mcbond_it1.4
X-RAY DIFFRACTIONc_mcangle_it2.34
X-RAY DIFFRACTIONc_scbond_it2.14
X-RAY DIFFRACTIONc_scangle_it3.041
LS refinement shellResolution: 2.45→2.54 Å / Total num. of bins used: 10
RfactorNum. reflection% reflection
Rfree0.2885 196 -
Rwork0.2135 1806 -
obs-3572 100 %

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