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- PDB-8j3n: Solution NMR structure of purS subunit of phosphoribosylformylgly... -

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Basic information

Entry
Database: PDB / ID: 8j3n
TitleSolution NMR structure of purS subunit of phosphoribosylformylglycinamidine synthase enzyme from Staphylococcus aureus
ComponentsPhosphoribosylformylglycinamidine synthase subunit PurS
KeywordsLYASE / Phosphoribosylformylglycinamidine synthase / subunit PurS / Staphylococcus aureus
Function / homologyPhosphoribosylformylglycinamidine synthase subunit PurS / Phosphoribosylformylglycinamidine (FGAM) synthase / Phosphoribosylformylglycinamidine synthase subunit PurS-like superfamily / phosphoribosylformylglycinamidine synthase / phosphoribosylformylglycinamidine synthase activity / 'de novo' IMP biosynthetic process / ATP binding / cytoplasm / Phosphoribosylformylglycinamidine synthase subunit PurS
Function and homology information
Biological speciesStaphylococcus aureus subsp. aureus Mu50 (bacteria)
MethodSOLUTION NMR / na
AuthorsWahab, A. / Ashraf, F. / Choudhary, M.I.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: To Be Published
Title: Solution NMR structure of purS subunit of phosphoribosylformylglycinamidine synthase enzyme from Staphylococcus aureus
Authors: Wahab, A. / Ashraf, F. / Choudhary, M.I.
History
DepositionApr 17, 2023Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0May 17, 2023Provider: repository / Type: Initial release
Revision 1.1May 15, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2 / Item: _database_2.pdbx_DOI

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Phosphoribosylformylglycinamidine synthase subunit PurS


Theoretical massNumber of molelcules
Total (without water)10,0601
Polymers10,0601
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_5551
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)18 / 100structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

#1: Protein Phosphoribosylformylglycinamidine synthase subunit PurS / FGAM synthase / Formylglycinamide ribonucleotide amidotransferase subunit III / FGAR ...FGAM synthase / Formylglycinamide ribonucleotide amidotransferase subunit III / FGAR amidotransferase III / FGAR-AT III / Phosphoribosylformylglycinamidine synthase subunit III


Mass: 10060.316 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: ATCC
Source: (gene. exp.) Staphylococcus aureus subsp. aureus Mu50 (bacteria)
Gene: purS, SAV1067 / Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: A0A0H3JUS1, phosphoribosylformylglycinamidine synthase

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDSample stateSpectrometer-IDType
111isotropic12D 1H-15N HSQC
121isotropic12D 1H-13C HSQC aliphatic
131isotropic12D 1H-13C HSQC aromatic
141isotropic13D HNCA
151isotropic13D HN(CA)CB
161isotropic13D HNCO
171isotropic13D HNHA
181isotropic13D 1H-13C NOESY aliphatic
191isotropic13D 1H-13C NOESY aromatic
1101isotropic13D 1H-15N NOESY

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Sample preparation

DetailsType: solution
Contents: 1.2 mM 15N,13C Uniformly labeled Subunit PurS of phosphoribosylformylglycinamidine synthase, 20 mM sodium phosphate, 20 mM sodium chloride, 1 mM DTT, 0.03 % sodium azide, 0.15 mM DSS, 95% H2O/5% D2O
Details: 1.2 mM protein in 20 mM sodium phosphate buffer pH 6.0, 20 mM sodium chloride, 1 mM DTT.
Label: 15N,13C / Solvent system: 95% H2O/5% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
1.2 mMSubunit PurS of phosphoribosylformylglycinamidine synthase15N,13C Uniformly labeled1
20 mMsodium phosphatenatural abundance1
20 mMsodium chloridenatural abundance1
1 mMDTTnatural abundance1
0.03 %sodium azidenatural abundance1
0.15 mMDSSnatural abundance1
Sample conditionsDetails: 1.2 mM protein in 20 mM sodium phosphate buffer pH 6.0, 20 mM sodium chloride, 1 mM DTT, NaN3 0.03%, DSS 0.15 mM
Ionic strength: 20 mM / Label: 15N,13C Uniformly Labeled / pH: 6.0 / Pressure: 1 atm / Temperature: 298 K

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NMR measurement

NMR spectrometerType: Bruker AVANCE III HD / Manufacturer: Bruker / Model: AVANCE III HD / Field strength: 800 MHz

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Processing

NMR software
NameVersionDeveloperClassification
CARA1.8.4.2Keller and Wuthrichchemical shift assignment
Sparky3.114T. D. Goddard and D. G. Knellerchemical shift assignment
Sparky3.114T. D. Goddard and D. G. Knellerpeak picking
TopSpin3.5pl7Bruker Biospincollection
TopSpin3.5pl7Bruker Biospinprocessing
CYANA3.98.15Guntert, Mumenthaler and Wuthrichstructure calculation
TALOS-N4.12Yang Shen, and Ad Baxdata analysis
MOLMOLKoradi, Billeter and Wuthrichdata analysis
PyMOLSchrodinger, and DeLanodata analysis
RefinementMethod: na / Software ordinal: 6
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 100 / Conformers submitted total number: 18

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