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- PDB-4ts9: Crystal structure of wild type E. Coli purine nucleoside phosphor... -

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Basic information

Entry
Database: PDB / ID: 4ts9
TitleCrystal structure of wild type E. Coli purine nucleoside phosphorylase with 6 FMC molecules
ComponentsPurine nucleoside phosphorylase DeoD-type
KeywordsTRANSFERASE / Purine nucleoside phosphorylase / formicyn A
Function / homology
Function and homology information


purine nucleoside interconversion / guanosine phosphorylase activity / purine nucleoside catabolic process / purine-nucleoside phosphorylase / purine-nucleoside phosphorylase activity / DNA damage response / membrane / identical protein binding / cytosol
Similarity search - Function
Purine nucleoside phosphorylase DeoD-type / 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
Chem-FMC / PHOSPHATE ION / Purine nucleoside phosphorylase DeoD-type / :
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.77 Å
AuthorsStefanic, Z. / Bzowska, A.
CitationJournal: Sci Rep / Year: 2018
Title: Crystallographic snapshots of ligand binding to hexameric purine nucleoside phosphorylase and kinetic studies give insight into the mechanism of catalysis.
Authors: Stefanic, Z. / Narczyk, M. / Mikleusevic, G. / Kazazic, S. / Bzowska, A. / Luic, M.
History
DepositionJun 18, 2014Deposition site: RCSB / Processing site: PDBE
Revision 1.0Jul 8, 2015Provider: repository / Type: Initial release
Revision 1.1Mar 16, 2016Group: Database references / Structure summary
Revision 1.2Oct 31, 2018Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.3Dec 20, 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
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 DeoD-type
B: Purine nucleoside phosphorylase DeoD-type
C: Purine nucleoside phosphorylase DeoD-type
hetero molecules


Theoretical massNumber of molelcules
Total (without water)78,2949
Polymers77,2073
Non-polymers1,0876
Water12,935718
1
A: Purine nucleoside phosphorylase DeoD-type
B: Purine nucleoside phosphorylase DeoD-type
C: Purine nucleoside phosphorylase DeoD-type
hetero molecules

A: Purine nucleoside phosphorylase DeoD-type
B: Purine nucleoside phosphorylase DeoD-type
C: Purine nucleoside phosphorylase DeoD-type
hetero molecules


Theoretical massNumber of molelcules
Total (without water)156,58718
Polymers154,4146
Non-polymers2,17312
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation11_555-x+y,y,-z+1/21
Buried area26380 Å2
ΔGint-167 kcal/mol
Surface area44530 Å2
MethodPISA
Unit cell
Length a, b, c (Å)120.625, 120.625, 240.006
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number178
Space group name H-MP6122
Components on special symmetry positions
IDModelComponents
11A-452-

HOH

21A-476-

HOH

31B-411-

HOH

41B-412-

HOH

51B-462-

HOH

61C-423-

HOH

71C-432-

HOH

DetailsThe biological assembly is a hexamer generated from the trimer in the asymmetric unit by the operation: -X+Y, Y, -Z+1/2

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Components

#1: Protein Purine nucleoside phosphorylase DeoD-type / PNP


Mass: 25735.658 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli)
References: UniProt: U0SVH6, UniProt: P0ABP8*PLUS, purine-nucleoside phosphorylase
#2: Chemical ChemComp-FMC / (1S)-1-(7-amino-1H-pyrazolo[4,3-d]pyrimidin-3-yl)-1,4-anhydro-D-ribitol


Mass: 267.241 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C10H13N5O4
#3: Chemical ChemComp-PO4 / PHOSPHATE ION / Phosphate


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


Mass: 18.015 Da / Num. of mol.: 718 / 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: 3.3 Å3/Da / Density % sol: 62.1 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 5.2 / Details: 50 mM citric buffer, 32 % ammonium sulphate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 0.97977 Å
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: Jul 3, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97977 Å / Relative weight: 1
ReflectionResolution: 1.77→48.17 Å / Num. obs: 98266 / % possible obs: 97.3 % / Observed criterion σ(I): -3 / Redundancy: 39 % / Biso Wilson estimate: 24.012 Å2 / Rmerge F obs: 1 / Rmerge(I) obs: 0.085 / Rrim(I) all: 0.087 / Net I/σ(I): 42.19 / Num. measured all: 3871879
Reflection shell
Resolution (Å)Highest resolution (Å)Rmerge F obsRmerge(I) obsMean I/σ(I) obsNum. measured obsNum. possibleNum. unique obsRrim(I) allDiffraction-ID% possible all
1.77-1.870.9770.4589.647889616040138650.464186.4
1.87-20.9950.31416.362609715147149370.31898.6
2-2.160.9970.19724.155731714120139780.19999
2.16-2.370.9990.1433.554093313033129320.14299.2
2.37-2.650.9990.10242.846568211858117920.10399.4
2.65-3.0610.07658.243328110533104950.07799.6
3.06-3.7410.05281.5350035899789860.05299.9
3.74-5.2710.042102.6268029709170890.042100
5.2710.041101.1151609420241920.04199.8

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Processing

Software
NameVersionClassification
XDSdata reduction
PDB_EXTRACT3.1data extraction
PHENIX(phenix.refine: 1.8.2_1309)refinement
XSCALEdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1K9S

1k9s


Resolution: 1.77→48.16 Å / Occupancy max: 1 / Occupancy min: 0.18 / FOM work R set: 0.9016 / SU ML: 0.12 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 16.05 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.177 4914 5 %random
Rwork0.156 93346 --
obs0.1571 98260 97.28 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 109.57 Å2 / Biso mean: 21.4381 Å2 / Biso min: 6.21 Å2
Refinement stepCycle: LAST / Resolution: 1.77→48.16 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5385 0 72 718 6175
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0075662
X-RAY DIFFRACTIONf_angle_d1.2247662
X-RAY DIFFRACTIONf_chiral_restr0.082872
X-RAY DIFFRACTIONf_plane_restr0.005987
X-RAY DIFFRACTIONf_dihedral_angle_d13.9112094
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 30

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.7676-1.78770.22421190.19132264238372
1.7877-1.80880.20991330.17752524265781
1.8088-1.83080.20161460.17192773291987
1.8308-1.8540.19091590.16183024318396
1.854-1.87840.18581610.14773051321298
1.8784-1.90410.17031640.15173107327198
1.9041-1.93130.17941630.15093100326399
1.9313-1.96010.18541630.15383097326099
1.9601-1.99080.16781640.15243119328399
1.9908-2.02340.1751650.15273131329699
2.0234-2.05830.17491640.15453122328699
2.0583-2.09570.17691650.15093131329699
2.0957-2.1360.17171650.15623135330099
2.136-2.17960.19191660.15333154332099
2.1796-2.2270.18891650.15383134329999
2.227-2.27880.18881660.15693161332799
2.2788-2.33580.19131660.14993147331399
2.3358-2.3990.18831660.15293159332599
2.399-2.46960.16571670.15363175334299
2.4696-2.54930.1661660.15523157332399
2.5493-2.64040.19351670.15533178334599
2.6404-2.74610.18011690.155732083377100
2.7461-2.87110.19381690.160331953364100
2.8711-3.02240.18121680.163732053373100
3.0224-3.21170.1821700.154232193389100
3.2117-3.45970.15671700.150532313401100
3.4597-3.80770.16331720.142632653437100
3.8077-4.35840.15051730.133432993472100
4.3584-5.48980.16111760.152233473523100
5.4898-48.17780.20081870.202535343721100

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