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- PDB-6gfl: Crystal structure of the Escherichia coli nucleosidase PpnN (apo form) -

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Basic information

Entry
Database: PDB / ID: 6gfl
TitleCrystal structure of the Escherichia coli nucleosidase PpnN (apo 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 activity / pyrimidine-5'-nucleotide nucleosidase / AMP nucleosidase / AMP nucleosidase activity / Hydrolases; Glycosylases; Hydrolysing N-glycosyl compounds / guanosine tetraphosphate binding / protein homotetramerization / protein-containing complex / identical protein binding / 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 ...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
Pyrimidine/purine nucleotide 5'-monophosphate nucleosidase
Similarity search - Component
Biological speciesEscherichia coli K-12 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.48 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 1.1May 1, 2019Group: Data collection / Database references / Category: citation / citation_author / pdbx_database_proc
Item: _citation.country / _citation.journal_abbrev ..._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
Revision 1.2May 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 1.3Jul 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 1.4Jul 31, 2019Group: Data collection / Database references / Category: citation_author / Item: _citation_author.name
Revision 1.5Jan 17, 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
Revision 1.6Oct 9, 2024Group: Derived calculations / Source and taxonomy / Structure summary
Category: entity_src_gen / pdbx_entry_details ...entity_src_gen / pdbx_entry_details / pdbx_struct_assembly / pdbx_struct_assembly_gen / pdbx_struct_assembly_prop / pdbx_struct_oper_list
Item: _entity_src_gen.pdbx_gene_src_scientific_name / _pdbx_struct_assembly.oligomeric_count ..._entity_src_gen.pdbx_gene_src_scientific_name / _pdbx_struct_assembly.oligomeric_count / _pdbx_struct_assembly.oligomeric_details / _pdbx_struct_assembly_gen.oper_expression / _pdbx_struct_assembly_prop.value

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)106,4882
Polymers106,4882
Non-polymers00
Water2,900161
1
A: Pyrimidine/purine nucleotide 5'-monophosphate nucleosidase
B: Pyrimidine/purine nucleotide 5'-monophosphate nucleosidase

A: Pyrimidine/purine nucleotide 5'-monophosphate nucleosidase
B: Pyrimidine/purine nucleotide 5'-monophosphate nucleosidase


Theoretical massNumber of molelcules
Total (without water)212,9774
Polymers212,9774
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,-y,z1
Buried area9380 Å2
ΔGint-30 kcal/mol
Surface area67360 Å2
MethodPISA
Unit cell
Length a, b, c (Å)94.170, 101.080, 112.290
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21212
Space group name HallP22ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x+1/2,y+1/2,-z
#4: -x,-y,z

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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.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli K-12 (bacteria) / Strain: K12 / Gene: ppnN, ygdH, b2795, JW2766 / Plasmid: pCA24N / Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: P0ADR8, Hydrolases; Glycosylases; Hydrolysing N-glycosyl compounds, pyrimidine-5'-nucleotide nucleosidase, AMP nucleosidase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 161 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationN

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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: 2.86 Å3/Da / Density % sol: 57.08 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 0.1M HEPES pH 7.5 36% v/v PEG200 5 mg/ml protein concentration

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I24 / Wavelength: 0.9686 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Oct 30, 2017
Details: Oxford Danfysik/SESO Two stage demagnification using two K-B pairs of bimorph type mirrors
RadiationMonochromator: ACCEL Fixed exit Double Crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9686 Å / Relative weight: 1
ReflectionResolution: 2.48→49.08 Å / Num. obs: 38638 / % possible obs: 99.92 % / Redundancy: 13.4 % / Biso Wilson estimate: 65.26 Å2 / CC1/2: 0.99 / Rmerge(I) obs: 0.13 / Rpim(I) all: 0.03 / Rrim(I) all: 0.13 / Net I/σ(I): 12.97
Reflection shellResolution: 2.48→2.57 Å / Redundancy: 7.4 % / Rmerge(I) obs: 1.74 / Mean I/σ(I) obs: 1.15 / Num. unique obs: 3781 / CC1/2: 0.56 / Rpim(I) all: 0.68 / Rrim(I) all: 1.87 / % possible all: 99.95

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Processing

Software
NameClassification
PHENIXrefinement
XDSdata reduction
XSCALEdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2PMB

2pmb


Resolution: 2.48→49.08 Å / Cross valid method: FREE R-VALUE
RfactorNum. reflection% reflection
Rfree0.269 --
Rwork0.2117 --
obs-38638 99.95 %
Refinement stepCycle: LAST / Resolution: 2.48→49.08 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6771 0 0 161 6932

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