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- PDB-4tta: Crystal structure of double mutant E. Coli purine nucleoside phos... -

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Basic information

Entry
Database: PDB / ID: 4tta
TitleCrystal structure of double mutant E. Coli purine nucleoside phosphorylase with 2 FMC molecules
ComponentsPurine nucleoside phosphorylase DeoD-type
KeywordsTRANSFERASE / formicyn A
Function / homology
Function and homology information


purine nucleoside interconversion / guanosine phosphorylase activity / purine-nucleoside phosphorylase / purine-nucleoside phosphorylase activity / purine nucleoside catabolic process / DNA damage response / identical protein binding / membrane / 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: 2 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 20, 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: Advisory / Data collection / Database references
Category: citation / citation_author / pdbx_unobs_or_zero_occ_residues
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: Advisory / Data collection ...Advisory / 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 / pdbx_unobs_or_zero_occ_residues
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
D: Purine nucleoside phosphorylase DeoD-type
E: Purine nucleoside phosphorylase DeoD-type
F: Purine nucleoside phosphorylase DeoD-type
hetero molecules


Theoretical massNumber of molelcules
Total (without water)155,23020
Polymers153,5496
Non-polymers1,68114
Water23,7981321
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area24870 Å2
ΔGint-233 kcal/mol
Surface area44680 Å2
MethodPISA
Unit cell
Length a, b, c (Å)62.686, 123.862, 188.656
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
DetailsThe biological assembly is a hexamer. One hexamer is found in asymmetric unit.

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Components

#1: Protein
Purine nucleoside phosphorylase DeoD-type / PNP / Purine nucleoside phosphorylase wild type from E. coli


Mass: 25591.508 Da / Num. of mol.: 6 / 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-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: PO4
#3: 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.: 2 / Source method: obtained synthetically / Formula: C10H13N5O4
#4: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: SO4
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1321 / 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: 2.4 Å3/Da / Density % sol: 48.1 %
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: DECTRIS 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: 1.99→48 Å / Num. obs: 100218 / % possible obs: 99 % / Observed criterion σ(I): -3 / Redundancy: 12.8 % / Biso Wilson estimate: 21.695 Å2 / Rmerge F obs: 0.997 / Rmerge(I) obs: 0.142 / Rrim(I) all: 0.148 / Net I/σ(I): 16.49 / Num. measured all: 1280788
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
1.99-2.110.9450.5335.519621916176155620.556196.2
2.11-2.260.9660.3987.519556015209150720.41499.1
2.26-2.440.9810.2910.218549114175140840.30199.4
2.44-2.670.9860.2212.416149013075130160.22999.5
2.67-2.990.9930.16216.515737511906118610.16899.6
2.99-3.450.9960.12313136910530105180.10499.9
3.45-4.210.9980.06532.7117778897089500.06799.8
4.21-5.940.9990.05237.186675704870380.05499.9
5.940.9990.0538.648831413541170.05399.6

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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: 2→48 Å / Occupancy max: 1 / Occupancy min: 0 / SU ML: 0.17 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 18.68 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.1953 1999 2.01 %random
Rwork0.151 97459 --
obs0.1519 99458 99.44 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 89.22 Å2 / Biso mean: 16.7794 Å2 / Biso min: 2.35 Å2
Refinement stepCycle: LAST / Resolution: 2→48 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10624 0 98 1321 12043
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00710993
X-RAY DIFFRACTIONf_angle_d1.11614850
X-RAY DIFFRACTIONf_chiral_restr0.0741694
X-RAY DIFFRACTIONf_plane_restr0.0041906
X-RAY DIFFRACTIONf_dihedral_angle_d13.3214016
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 14

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2-2.050.23971390.17636814695399
2.05-2.10540.25761410.16786825696699
2.1054-2.16740.21651410.16136854699599
2.1674-2.23740.22121400.1616867700799
2.2374-2.31730.21941410.15856905704699
2.3173-2.41010.23241420.15846889703199
2.4101-2.51980.2321410.1616917705899
2.5198-2.65260.21431420.154669127054100
2.6526-2.81880.17891430.157869717114100
2.8188-3.03640.2161430.1669537096100
3.0364-3.34190.2071440.148170137157100
3.3419-3.82530.14981440.131770547198100
3.8253-4.81880.15091470.118471227269100
4.8188-48.12350.17831510.166373637514100

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