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- PDB-2lrj: NMR solution structure of staphyloxanthin biosynthesis protein -

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Basic information

Entry
Database: PDB / ID: 2lrj
TitleNMR solution structure of staphyloxanthin biosynthesis protein
ComponentsStaphyloxanthin biosynthesis protein, putative
KeywordsBIOSYNTHETIC PROTEIN / Structural Genomics / Center for Structural Genomics of Infectious Diseases / CSGID
Function / homology
Function and homology information


CHAP domain profile. / CHAP domain / CHAP domain / endopeptidase domain like (from Nostoc punctiforme) / endopeptidase fold (from Nostoc punctiforme) / Papain-like cysteine peptidase superfamily / Alpha-Beta Complex / Alpha Beta
Similarity search - Domain/homology
Staphyloxanthin biosynthesis protein, putative / Staphyloxanthin biosynthesis protein, putative
Similarity search - Component
Biological speciesStaphylococcus aureus (bacteria)
MethodSOLUTION NMR / simulated annealing
Model detailsclosest to the average, model 1
AuthorsZhang, Y. / Winsor, J. / Anderson, W. / Radhakrishnan, I. / Center for Structural Genomics of Infectious Diseases (CSGID)
CitationJournal: To be Published
Title: Solution structure of a putative S. aureus enzyme involved in the biosynthesis of staphyloxanthin
Authors: Zhang, Y. / Winsor, J. / Anderson, W. / Radhakrishnan, I.
History
DepositionApr 3, 2012Deposition site: BMRB / Processing site: RCSB
Revision 1.0Apr 18, 2012Provider: repository / Type: Initial release
Revision 1.1Apr 25, 2012Group: Structure summary
Revision 1.2Jun 14, 2023Group: Data collection / Database references / Other
Category: database_2 / pdbx_database_status ...database_2 / pdbx_database_status / pdbx_nmr_software / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_nmr_data / _pdbx_nmr_software.name / _struct_ref_seq_dif.details
Revision 1.3May 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: Staphyloxanthin biosynthesis protein, putative


Theoretical massNumber of molelcules
Total (without water)11,7231
Polymers11,7231
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 80structures with the lowest energy
RepresentativeModel #1closest to the average

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Components

#1: Protein Staphyloxanthin biosynthesis protein, putative


Mass: 11722.541 Da / Num. of mol.: 1 / Fragment: UNP residues 55-166
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Staphylococcus aureus (bacteria) / Strain: subsp. aureus COL / Gene: SACOL2295 / Production host: Escherichia coli (E. coli) / References: UniProt: Q5HDQ5, UniProt: A0A0H2X0D9*PLUS

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR / Details: CSGID target number: IDP00632
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D 1H-15N HSQC
1212D 1H-13C HSQC
1313D CBCA(CO)NH
1413D C(CO)NH
1513D HNCO
1613D HN(CA)CB
1713D HBHA(CO)NH
1813D 1H-15N NOESY
1923D 1H-13C NOESY aliphatic
11023D (H)CCH-COSY
11123D (H)CCH-TOCSY
11223D 1H-13C NOESY aromatic

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Sample preparation

Details
Solution-IDContentsSolvent system
1137 mM sodium chloride, 5 mM beta-mercaptoethanol, 2 mM potassium phosphate, 10 mM sodium phosphate, 90% H2O/10% D2O90% H2O/10% D2O
2137 mM sodium chloride, 5 mM beta-mercaptoethanol, 10 mM sodium phosphate, 2 mM potassium phosphate, 100% D2O100% D2O
Sample
Conc. (mg/ml)ComponentSolution-ID
137 mMsodium chloride-11
5 mMbeta-mercaptoethanol-21
2 mMpotassium phosphate-31
10 mMsodium phosphate-41
137 mMsodium chloride-52
5 mMbeta-mercaptoethanol-62
10 mMsodium phosphate-72
2 mMpotassium phosphate-82
Sample conditionsIonic strength: 0.137 / pH: 6.8 / Pressure: ambient / Temperature: 298 K

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NMR measurement

NMR spectrometerType: Varian INOVA / Manufacturer: Varian / Model: INOVA / Field strength: 600 MHz

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Processing

NMR software
NameVersionDeveloperClassification
ARIA1.2Linge, O'Donoghue and Nilgeschemical shift assignment
ARIA1.2Linge, O'Donoghue and Nilgesdata analysis
ARIA1.2Linge, O'Donoghue and Nilgesrefinement
CNS1.2Brunger, Adams, Clore, Gros, Nilges and Readchemical shift assignment
CNS1.2Brunger, Adams, Clore, Gros, Nilges and Readdata analysis
CNS1.2Brunger, Adams, Clore, Gros, Nilges and Readrefinement
SparkyGoddardchemical shift assignment
SparkyGoddarddata analysis
SparkyGoddardrefinement
AutoAssignZimmerman, Moseley, Kulikowski and Montelionechemical shift assignment
AutoAssignZimmerman, Moseley, Kulikowski and Montelionedata analysis
AutoAssignZimmerman, Moseley, Kulikowski and Montelionerefinement
RefinementMethod: simulated annealing / Software ordinal: 1
NMR representativeSelection criteria: closest to the average
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 80 / Conformers submitted total number: 20

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