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- PDB-6gfm: Crystal structure of the Escherichia coli nucleosidase PpnN (pppG... -

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Basic information

Entry
Database: PDB / ID: 6gfm
TitleCrystal structure of the Escherichia coli nucleosidase PpnN (pppGpp-form)
ComponentsPyrimidine/purine nucleotide 5'-monophosphate nucleosidase
KeywordsHYDROLASE / YgdH / PpnN / allosteric enzyme / nucleotide metabolism / stringent response / antibiotic tolerance / persistence / fluoroquinolone
Function / homology
Function and homology information


inosinate nucleosidase activity / pyrimidine-5'-nucleotide nucleosidase / pyrimidine-5'-nucleotide nucleosidase activity / AMP nucleosidase / AMP nucleosidase activity / Hydrolases; Glycosylases; Hydrolysing N-glycosyl compounds / guanosine tetraphosphate binding / protein-containing complex / cytosol
Similarity search - Function
MCP/YpsA-like / MoCo carrier protein-like / Pyrimidine/purine nucleotide 5'-monophosphate nucleosidase, C-terminal domain / Pyrimidine/purine nucleotide 5'-monophosphate nucleosidase, N-terminal / Pyrimidine/purine nucleotide 5'-monophosphate nucleosidase PpnN-like superfamily / Pyrimidine/purine nucleotide monophosphate nucleosidase, C-terminal / Pyrimidine/purine nucleotide 5'-monophosphate nucleosidases / LOG family / Possible lysine decarboxylase / Rossmann fold - #450 ...MCP/YpsA-like / MoCo carrier protein-like / Pyrimidine/purine nucleotide 5'-monophosphate nucleosidase, C-terminal domain / Pyrimidine/purine nucleotide 5'-monophosphate nucleosidase, N-terminal / Pyrimidine/purine nucleotide 5'-monophosphate nucleosidase PpnN-like superfamily / Pyrimidine/purine nucleotide monophosphate nucleosidase, C-terminal / Pyrimidine/purine nucleotide 5'-monophosphate nucleosidases / LOG family / Possible lysine decarboxylase / Rossmann fold - #450 / Rossmann fold / 2-Layer Sandwich / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Chem-0O2 / Pyrimidine/purine nucleotide 5'-monophosphate nucleosidase
Similarity search - Component
Biological speciesEscherichia coli K-12 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.77 Å
AuthorsZhang, Y. / Baerentsen, R.L. / Gerdes, K. / Brodersen, D.E.
Funding support Denmark, 1items
OrganizationGrant numberCountry
Danish National Research FoundationDNRF120 Denmark
CitationJournal: Mol.Cell / Year: 2019
Title: (p)ppGpp Regulates a Bacterial Nucleosidase by an Allosteric Two-Domain Switch.
Authors: Zhang, Y.E. / Baerentsen, R.L. / Fuhrer, T. / Sauer, U. / Gerdes, K. / Brodersen, D.E.
History
DepositionMay 1, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 24, 2019Provider: repository / Type: Initial release
Revision 2.0May 1, 2019Group: Atomic model / Data collection / Database references
Category: atom_site / citation ...atom_site / citation / citation_author / database_PDB_rev / database_PDB_rev_record / diffrn_source / pdbx_data_processing_status / pdbx_database_proc
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_atom_id / _atom_site.label_atom_id / _atom_site.pdbx_auth_atom_name / _citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.title / _citation.year / _diffrn_source.pdbx_synchrotron_site
Revision 2.1May 8, 2019Group: Data collection / Database references / Category: citation / citation_author / pdbx_database_proc
Item: _citation.pdbx_database_id_PubMed / _citation.title ..._citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID / _citation_author.name
Revision 2.2Jul 3, 2019Group: Data collection / Database references
Category: citation / database_PDB_rev ...citation / database_PDB_rev / database_PDB_rev_record / pdbx_database_proc
Item: _citation.journal_volume / _citation.page_first
Revision 2.3Jul 31, 2019Group: Data collection / Database references / Category: citation_author / diffrn_source
Item: _citation_author.name / _diffrn_source.pdbx_synchrotron_site
Revision 2.4Sep 27, 2023Group: Data collection / Database references / Source and taxonomy
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / entity_src_gen
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _entity_src_gen.pdbx_gene_src_scientific_name
Revision 2.5Jan 17, 2024Group: Refinement description / Category: pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Pyrimidine/purine nucleotide 5'-monophosphate nucleosidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)53,9272
Polymers53,2441
Non-polymers6831
Water1,78399
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area21010 Å2
MethodPISA
Unit cell
Length a, b, c (Å)176.920, 176.920, 94.480
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number98
Space group name H-MI4122
Space group name HallI4bw2bw
Symmetry operation#1: x,y,z
#2: -y+1/2,x,z+3/4
#3: y+1/2,-x,z+3/4
#4: x+1/2,-y,-z+3/4
#5: -x+1/2,y,-z+3/4
#6: -x,-y,z
#7: y,x,-z
#8: -y,-x,-z
#9: x+1/2,y+1/2,z+1/2
#10: -y+1,x+1/2,z+5/4
#11: y+1,-x+1/2,z+5/4
#12: x+1,-y+1/2,-z+5/4
#13: -x+1,y+1/2,-z+5/4
#14: -x+1/2,-y+1/2,z+1/2
#15: y+1/2,x+1/2,-z+1/2
#16: -y+1/2,-x+1/2,-z+1/2
Components on special symmetry positions
IDModelComponents
11A-658-

HOH

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Components

#1: Protein Pyrimidine/purine nucleotide 5'-monophosphate nucleosidase / AMP nucleosidase / CMP nucleosidase / GMP nucleosidase / IMP nucleosidase / UMP nucleosidase / dTMP ...AMP nucleosidase / CMP nucleosidase / GMP nucleosidase / IMP nucleosidase / UMP nucleosidase / dTMP nucleosidase


Mass: 53244.168 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli K-12 (bacteria) / Strain: K12 / Gene: ppnN, ygdH, b2795, JW2766 / Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: P0ADR8, Hydrolases; Glycosylases; Hydrolysing N-glycosyl compounds, pyrimidine-5'-nucleotide nucleosidase, AMP nucleosidase
#2: Chemical ChemComp-0O2 / guanosine 5'-(tetrahydrogen triphosphate) 3'-(trihydrogen diphosphate)


Mass: 683.140 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H18N5O20P5
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 99 / 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: 3.48 Å3/Da / Density % sol: 64.64 %
Crystal growTemperature: 277.15 K / Method: vapor diffusion, sitting drop / pH: 7 / Details: 0.4M KNa tartrate hydrate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: PETRA III, EMBL c/o DESY / Beamline: P13 (MX1) / Wavelength: 0.97623 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Oct 20, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97623 Å / Relative weight: 1
ReflectionResolution: 2.77→34.7 Å / Num. obs: 19332 / % possible obs: 99.77 % / Redundancy: 24.8 % / Biso Wilson estimate: 84.07 Å2 / CC1/2: 0.99 / Rmerge(I) obs: 0.1421 / Rpim(I) all: 0.029 / Rrim(I) all: 0.1451 / Net I/σ(I): 17.45
Reflection shellResolution: 2.77→2.869 Å / Redundancy: 18.2 % / Rmerge(I) obs: 2.704 / Mean I/σ(I) obs: 1.35 / Num. unique obs: 1907 / CC1/2: 0.58 / Rpim(I) all: 0.6416 / Rrim(I) all: 2.781 / % possible all: 99.74

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Processing

Software
NameClassification
PHENIXrefinement
XDSdata reduction
XSCALEdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6GFL

6gfl


Resolution: 2.77→34.7 Å / Cross valid method: FREE R-VALUE
RfactorNum. reflection% reflection
Rfree0.2319 --
Rwork0.1813 --
obs-19329 99.74 %
Refinement stepCycle: LAST / Resolution: 2.77→34.7 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3471 0 40 99 3610

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