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- PDB-1odi: Purine nucleoside phosphorylase from Thermus Thermophilus -

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Basic information

Entry
Database: PDB / ID: 1odi
TitlePurine nucleoside phosphorylase from Thermus Thermophilus
ComponentsPURINE NUCLEOSIDE PHOSPHORYLASE
KeywordsTRANSFERASE / NUCLEOSIDE PHOSPHORYLASE / ALPHA-BETA PROTEIN / ADENOSINE / RIKEN STRUCTURAL GENOMICS/PROTEOMICS INITIATIVE / RSGI / STRUCTURAL GENOMICS
Function / homology
Function and homology information


pentosyltransferase activity / uridine phosphorylase / nucleoside catabolic process / cytosol
Similarity search - Function
Nucleoside phosphorylase, conserved site / Purine and other phosphorylases family 1 signature. / Nucleoside phosphorylase domain / Nucleoside phosphorylase domain / Phosphorylase superfamily / Nucleoside phosphorylase superfamily / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
ADENOSINE / Uridine phosphorylase
Similarity search - Component
Biological speciesTHERMUS THERMOPHILUS (bacteria)
MethodX-RAY DIFFRACTION / OTHER / Resolution: 2.4 Å
AuthorsTahirov, T.H. / Inagaki, E. / Miyano, M.
CitationJournal: J.Mol.Biol. / Year: 2004
Title: Crystal Structure of Purine Nucleoside Phosphorylase from Thermus Thermophilus
Authors: Tahirov, T.H. / Inagaki, E. / Ohshima, N. / Kitao, T. / Kuroishi, C. / Ukita, Y. / Takio, K. / Kobayashi, M. / Kuramitsu, S. / Yokoyama, S. / Miyano, M.
History
DepositionFeb 19, 2003Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 27, 2003Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3May 8, 2019Group: Data collection / Experimental preparation / Other
Category: exptl_crystal_grow / pdbx_database_proc ...exptl_crystal_grow / pdbx_database_proc / pdbx_database_status / struct_biol
Item: _exptl_crystal_grow.method / _exptl_crystal_grow.temp / _pdbx_database_status.recvd_author_approval
Revision 1.4May 8, 2024Group: Data collection / Database references / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf
Remark 700 SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "AA","BA" IN EACH CHAIN ON SHEET RECORDS ... SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "AA","BA" IN EACH CHAIN ON SHEET RECORDS BELOW ARE ACTUALLY 10-STRANDED BARRELS THIS IS REPRESENTED BY A 11-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL. SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "CA", "DA", "EA", "FA" IN EACH CHAIN ON SHEET RECORDS BELOW ARE ACTUALLY AN 8-STRANDED BARRELS THIS IS REPRESENTED BY A 9-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: PURINE NUCLEOSIDE PHOSPHORYLASE
B: PURINE NUCLEOSIDE PHOSPHORYLASE
C: PURINE NUCLEOSIDE PHOSPHORYLASE
D: PURINE NUCLEOSIDE PHOSPHORYLASE
E: PURINE NUCLEOSIDE PHOSPHORYLASE
F: PURINE NUCLEOSIDE PHOSPHORYLASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)155,03720
Polymers152,6656
Non-polymers2,37214
Water7,044391
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)132.365, 132.365, 171.009
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212

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Components

#1: Protein
PURINE NUCLEOSIDE PHOSPHORYLASE


Mass: 25444.100 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) THERMUS THERMOPHILUS (bacteria) / Strain: HB8 / Production host: ESCHERICHIA COLI BL21(DE3) (bacteria)
References: UniProt: Q5SID9*PLUS, S-methyl-5'-thioadenosine phosphorylase
#2: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: SO4
#3: Chemical
ChemComp-ADN / ADENOSINE


Mass: 267.241 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C10H13N5O4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 391 / 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: 2.5 Å3/Da / Density % sol: 49.9 %
Description: THE REFINED STRUCTURE OF PURINE NUCLEOSIDE PEPTIDASE FROM THERMUS THERMOPHILUS WAS USED AS STARTING MODEL FOR REFINEMENT
Crystal growTemperature: 291 K / Method: microbatch / pH: 6.3
Details: MICROBATCH METHOD UNDER OIL WAS USED. 15.1 MG/ML OF PROTEIN SOLUTION CONTAINING 0.02M DTT WAS MIXED WITH 1.65M SODIUM ACETATE AND 0.1M MES PH 6.3. THE CRYSTALLIZATION TEMPERATURE WAS 291 K. ...Details: MICROBATCH METHOD UNDER OIL WAS USED. 15.1 MG/ML OF PROTEIN SOLUTION CONTAINING 0.02M DTT WAS MIXED WITH 1.65M SODIUM ACETATE AND 0.1M MES PH 6.3. THE CRYSTALLIZATION TEMPERATURE WAS 291 K. PARATONE-N OIL MIXED WITH 10% W/W OF GLYCEROL WAS USED FOR CRYOPROTECTION. LIGAND BOUND CRYSTALS WERE OBTAINED BY 7 H SOAKING OF NATIVE CRYSTALS IN SOLUTION CONTAINING 1.2M SODIUM ACETATE PH 6.3, 20MM AMMONIUM SULFATE, 2MM MAGNESIUM SULFATE AND 5MM ADENOSINE
Crystal grow
*PLUS
Temperature: 291 K / Method: microseeding
Components of the solutions
*PLUS
IDConc.UnitCommon nameCrystal-IDSol-ID
115 mg/mlprotein1drop
20.02 Mdithiothreitol1drop
31.65 Msodium acetate1reservoir
4MMES1reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU FR-D / Wavelength: 1.5418
DetectorType: RIGAKU IMAGE PLATE, RAXIS-VII / Detector: IMAGE PLATE / Date: Jan 15, 2003 / Details: MIRRORS
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.4→30 Å / Num. obs: 56385 / % possible obs: 94.4 % / Observed criterion σ(I): -0.5 / Redundancy: 4.1 % / Biso Wilson estimate: 14.8 Å2 / Rmerge(I) obs: 0.088 / Net I/σ(I): 13.2
Reflection shellResolution: 2.4→2.49 Å / Rmerge(I) obs: 0.335 / Mean I/σ(I) obs: 2.9 / % possible all: 88.8
Reflection shell
*PLUS
% possible obs: 88.8 %

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Processing

Software
NameVersionClassification
CNS1.1refinement
HKL-2000data reduction
HKL-2000data scaling
CNSphasing
RefinementMethod to determine structure: OTHER / Resolution: 2.4→19.96 Å / Rfactor Rfree error: 0.004 / Data cutoff high absF: 247589.73 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.234 2837 5.1 %RANDOM
Rwork0.176 ---
obs0.176 56004 93.9 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 31.0905 Å2 / ksol: 0.350542 e/Å3
Displacement parametersBiso mean: 27.8 Å2
Baniso -1Baniso -2Baniso -3
1--1.08 Å20 Å20 Å2
2---1.08 Å20 Å2
3---2.17 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.33 Å0.24 Å
Luzzati d res low-5 Å
Luzzati sigma a0.43 Å0.31 Å
Refinement stepCycle: LAST / Resolution: 2.4→19.96 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10716 0 154 391 11261
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.006
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.3
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d22.9
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.88
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it2.551.5
X-RAY DIFFRACTIONc_mcangle_it3.72
X-RAY DIFFRACTIONc_scbond_it4.122
X-RAY DIFFRACTIONc_scangle_it5.462.5
LS refinement shellResolution: 2.4→2.55 Å / Rfactor Rfree error: 0.015 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.312 427 5 %
Rwork0.25 8039 -
obs--86.1 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAMWATER.TOP
X-RAY DIFFRACTION3ION.PARAMION.TOP
X-RAY DIFFRACTION4ADN.PARADN.TOP
Software
*PLUS
Name: CNS / Version: 1.1 / Classification: refinement
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg22.9
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.88

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