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

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Basic information

Entry
Database: PDB / ID: 4ttj
TitleCrystal structure of double mutant 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 activity / purine-nucleoside phosphorylase / 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: 1.874 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 21, 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_atoms
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 1.3Nov 14, 2018Group: Data collection / Database references ...Data collection / Database references / Source and taxonomy / Structure summary
Category: entity / entity_name_com ...entity / entity_name_com / entity_src_gen / entity_src_nat / struct_ref / struct_ref_seq / struct_ref_seq_dif
Item: _entity.src_method / _entity_name_com.name ..._entity.src_method / _entity_name_com.name / _struct_ref.db_code / _struct_ref.pdbx_db_accession / _struct_ref_seq.pdbx_db_accession / _struct_ref_seq_dif.pdbx_seq_db_accession_code
Revision 1.4Dec 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_atoms
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Purine nucleoside phosphorylase DeoD-type
B: Purine nucleoside phosphorylase DeoD-type
D: Purine nucleoside phosphorylase DeoD-type
hetero molecules


Theoretical massNumber of molelcules
Total (without water)78,14912
Polymers76,7753
Non-polymers1,3759
Water15,223845
1
A: Purine nucleoside phosphorylase DeoD-type
B: Purine nucleoside phosphorylase DeoD-type
D: Purine nucleoside phosphorylase DeoD-type
hetero molecules

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


Theoretical massNumber of molelcules
Total (without water)156,29924
Polymers153,5496
Non-polymers2,75018
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation12_545x,x-y-1,-z+1/61
Buried area27230 Å2
ΔGint-235 kcal/mol
Surface area44140 Å2
MethodPISA
Unit cell
Length a, b, c (Å)120.696, 120.696, 239.538
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-454-

HOH

21B-413-

HOH

31B-414-

HOH

41B-461-

HOH

51B-470-

HOH

61D-423-

HOH

71D-437-

HOH

DetailsBiological 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 / Inosine phosphorylase


Mass: 25591.508 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: deoD, pup, b4384, JW4347 / Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: P0ABP8, purine-nucleoside phosphorylase
#2: Chemical ChemComp-PO4 / PHOSPHATE ION


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


Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO4
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 845 / 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: 62.3 %
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: ESRF / Beamline: BM14 / Wavelength: 0.95373 Å
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: Mar 12, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.95373 Å / Relative weight: 1
ReflectionResolution: 1.82→48.14 Å / Num. all: 1745845 / Num. obs: 93755 / % possible obs: 98.9 % / Observed criterion σ(I): -3 / Redundancy: 18.6 % / Biso Wilson estimate: 23.152 Å2 / Rmerge F obs: 0.145 / Rmerge(I) obs: 0.352 / Rrim(I) all: 0.363 / Net I/σ(I): 7.61 / Num. measured all: 1745809
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
1.82-1.930.5871.0762.623813715075141911.109194.1
1.93-2.060.2610.7444.530282314190141300.76299.6
2.06-2.230.1850.5486.226996213187131490.56299.7
2.23-2.440.1510.4437.423958312268122410.45599.8
2.44-2.730.1210.3598.820676211108110940.3799.9
2.73-3.150.0930.30210.3175664989398840.31199.9
3.15-3.850.0610.2712.2142207843284320.279100
3.85-5.430.0480.26613.4109747666566630.275100
5.430.0490.26312.960924399139710.27299.5

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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: PDB entry 1k9s

1k9s


Resolution: 1.874→48.14 Å / Occupancy max: 1 / Occupancy min: 0 / SU ML: 0.15 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 18.59 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.1937 2000 2.36 %random
Rwork0.1566 82796 --
obs0.1575 84796 99.71 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 91.23 Å2 / Biso mean: 23.5468 Å2 / Biso min: 6.22 Å2
Refinement stepCycle: LAST / Resolution: 1.874→48.14 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5358 0 87 845 6290
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0075715
X-RAY DIFFRACTIONf_angle_d1.1387760
X-RAY DIFFRACTIONf_chiral_restr0.083883
X-RAY DIFFRACTIONf_plane_restr0.004989
X-RAY DIFFRACTIONf_dihedral_angle_d13.5372155
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 (%)
1.8738-1.92060.30511380.25495704584298
1.9206-1.97260.231410.201858115952100
1.9726-2.03060.20631400.180757955935100
2.0306-2.09610.20971400.165558465986100
2.0961-2.17110.20621410.155858375978100
2.1711-2.2580.21441420.162858646006100
2.258-2.36070.1811420.152958586000100
2.3607-2.48520.20361410.153458756016100
2.4852-2.64090.21681440.152459176061100
2.6409-2.84480.21181420.15359066048100
2.8448-3.1310.18691440.151459446088100
3.131-3.5840.18081440.14260016145100
3.584-4.51490.13371470.127260546201100
4.5149-48.15980.20491540.173263846538100

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