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- PDB-6tk9: Purine-nucleoside phosphorylase from Thermus thermophilus -

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Basic information

Entry
Database: PDB / ID: 6tk9
TitlePurine-nucleoside phosphorylase from Thermus thermophilus
ComponentsPurine nucleoside phosphorylase
KeywordsTRANSFERASE / phosphorylase
Function / homology
Function and homology information


nucleoside metabolic process / purine-nucleoside phosphorylase / purine-nucleoside phosphorylase activity
Similarity search - Function
Purine nucleoside phosphorylase I, inosine/guanosine-specific / Purine nucleoside phosphorylase / Nucleoside phosphorylase domain / Phosphorylase superfamily / Nucleoside phosphorylase superfamily
Similarity search - Domain/homology
PHOSPHATE ION / Purine nucleoside phosphorylase
Similarity search - Component
Biological speciesThermus thermophilus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å
AuthorsTimofeev, V.I. / Abramchik, Y.A. / Kostromina, M.A. / Tuzova, E.S. / Esipov, R.S. / Kuranova, I.P.
CitationJournal: To Be Published
Title: Purine-nucleoside phosphorylase from Thermus thermophilus
Authors: Timofeev, V.I. / Abramchik, Y.A. / Kostromina, M.A. / Tuzova, E.S. / Esipov, R.S. / Kuranova, I.P.
History
DepositionNov 28, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 16, 2020Provider: repository / Type: Initial release
Revision 1.1Jan 24, 2024Group: 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
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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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)180,16412
Polymers179,5946
Non-polymers5706
Water1,02757
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area20250 Å2
ΔGint-135 kcal/mol
Surface area51880 Å2
MethodPISA
Unit cell
Length a, b, c (Å)89.850, 120.950, 215.470
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein
Purine nucleoside phosphorylase / / Inosine-guanosine phosphorylase


Mass: 29932.400 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermus thermophilus (bacteria) / Gene: TthHC11_05990 / Production host: Thermus thermophilus (bacteria)
References: UniProt: A0A510IGW9, purine-nucleoside phosphorylase
#2: Chemical
ChemComp-PO4 / PHOSPHATE ION / Phosphate


Mass: 94.971 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: PO4
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 57 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 3.26 Å3/Da / Density % sol: 62.26 %
Crystal growTemperature: 297 K / Method: counter-diffusion / Details: SA

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.979 / Wavelength: 0.979 Å
DetectorType: DECTRIS EIGER R 1M / Detector: PIXEL / Date: Oct 12, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2.5→20 Å / Num. obs: 80416 / % possible obs: 98.1 % / Redundancy: 4.35 % / CC1/2: 0.998 / Rmerge(I) obs: 0.085 / Net I/σ(I): 13.32
Reflection shellResolution: 2.5→3 Å / Rmerge(I) obs: 0.435 / Num. unique obs: 33938 / CC1/2: 0.922 / Rrim(I) all: 0.491

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Processing

Software
NameVersionClassification
SCALAdata scaling
REFMAC5.8.0257refinement
PDB_EXTRACT3.25data extraction
iMOSFLMdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4UC0

4uc0


Resolution: 2.5→19.98 Å / Cor.coef. Fo:Fc: 0.94 / Cor.coef. Fo:Fc free: 0.911 / SU B: 10.587 / SU ML: 0.225 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.395 / ESU R Free: 0.278
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2661 4021 5 %RANDOM
Rwork0.2172 ---
obs0.2197 76395 98.11 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 147.19 Å2 / Biso mean: 47.895 Å2 / Biso min: 21.22 Å2
Baniso -1Baniso -2Baniso -3
1-0.02 Å2-0 Å20 Å2
2---0.02 Å2-0 Å2
3----0 Å2
Refinement stepCycle: final / Resolution: 2.5→19.98 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms12690 0 30 57 12777
Biso mean--45.78 34.8 -
Num. residues----1626
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.01313026
X-RAY DIFFRACTIONr_bond_other_d0.0010.01712444
X-RAY DIFFRACTIONr_angle_refined_deg1.5831.64717682
X-RAY DIFFRACTIONr_angle_other_deg1.2121.56728578
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.1851620
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.04419.431738
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.542152058
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.7815144
X-RAY DIFFRACTIONr_chiral_restr0.0690.21572
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0214808
X-RAY DIFFRACTIONr_gen_planes_other0.0010.023048
LS refinement shellResolution: 2.5→2.564 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.459 292 -
Rwork0.393 5558 -
all-5850 -
obs--99.2 %

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