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- PDB-1odk: PURINE NUCLEOSIDE PHOSPHORYLASE FROM THERMUS THERMOPHILUS -

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Basic information

Entry
Database: PDB / ID: 1odk
TitlePURINE NUCLEOSIDE PHOSPHORYLASE FROM THERMUS THERMOPHILUS
ComponentsPURINE NUCLEOSIDE PHOSPHORYLASE
KeywordsTRANSFERASE / NUCLEOSIDE PHOSPHORYLASE / ALPHA-BETA PROTEIN / 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
Uridine phosphorylase
Similarity search - Component
Biological speciesTHERMUS THERMOPHILUS (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.9 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 1.4Dec 13, 2023Group: Data collection / Database references ...Data collection / Database references / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model
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. THE SHEETS PRESENTED AS "CA" "DA" "EA" "FA" IN EACH CHAIN ON SHEET RECORDS BELOW ARE ACTUALLY 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)153,21712
Polymers152,6656
Non-polymers5536
Water13,799766
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)131.919, 131.919, 169.906
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 / Plasmid: PET11A / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): B834(DE3)PLYSS
References: UniProt: Q5SID9*PLUS, S-methyl-5'-thioadenosine phosphorylase
#2: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C3H8O3
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 766 / 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 %
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
Crystal grow
*PLUS
Temperature: 291 K / Method: microseeding
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
115 mg/mlprotein1drop
20.02 Mdithiothreitol1drop
31.65 Msodium acetate1reservoir
40.1 MMES1reservoir

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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: 1.9→20 Å / Num. obs: 116626 / % possible obs: 98.8 % / Observed criterion σ(I): -0.5 / Redundancy: 7.2 % / Biso Wilson estimate: 9.1 Å2 / Rmerge(I) obs: 0.058 / Net I/σ(I): 26
Reflection shellResolution: 1.9→1.97 Å / Rmerge(I) obs: 0.267 / Mean I/σ(I) obs: 4 / % possible all: 97.2
Reflection shell
*PLUS
% possible obs: 97.2 %

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Processing

Software
NameVersionClassification
CNS1.1refinement
HKL-2000data reduction
HKL-2000data scaling
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1JE1

1je1


Resolution: 1.9→19.98 Å / Rfactor Rfree error: 0.003 / Data cutoff high absF: 424717.4 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Details: DISORDERED REGIONS WERE MODELED STEREOCHEMICALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.208 5879 5 %RANDOM
Rwork0.18 ---
obs0.18 116505 98.8 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 59.5162 Å2 / ksol: 0.410759 e/Å3
Displacement parametersBiso mean: 22.5 Å2
Baniso -1Baniso -2Baniso -3
1-0.24 Å20 Å20 Å2
2--0.24 Å20 Å2
3----0.47 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.22 Å0.19 Å
Luzzati d res low-5 Å
Luzzati sigma a0.21 Å0.18 Å
Refinement stepCycle: LAST / Resolution: 1.9→19.98 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10567 0 36 766 11369
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.005
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_d22.8
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.82
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it1.791.5
X-RAY DIFFRACTIONc_mcangle_it2.472
X-RAY DIFFRACTIONc_scbond_it2.882
X-RAY DIFFRACTIONc_scangle_it4.042.5
LS refinement shellResolution: 1.9→2.02 Å / Rfactor Rfree error: 0.008 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.261 947 5 %
Rwork0.236 17962 -
obs--97.5 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAMWATER.TOP
X-RAY DIFFRACTION3ION.PARAMION.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_deg22.8
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.82

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