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- PDB-2m8w: Restrained CS-Rosetta Solution NMR Structure of Staphylococcus au... -

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Basic information

Entry
Database: PDB / ID: 2m8w
TitleRestrained CS-Rosetta Solution NMR Structure of Staphylococcus aureus protein SAV1430. Northeast Structural Genomics Target ZR18. Structure determination
ComponentsUncharacterized protein
KeywordsUNKNOWN FUNCTION / Structural Genomics / NORTHEAST STRUCTURAL GENOMICS CONSORTIUM / NESG / PSI-Biology / Protein Structure Initiative
Function / homology
Function and homology information


Scaffold protein Nfu/NifU, N-terminal domain / Scaffold protein Nfu/NifU, N-terminal / Scaffold protein Nfu/NifU, N-terminal domain superfamily / Scaffold protein Nfu/NifU N terminal / Scaffold protein Nfu/NifU N terminal / Ribosomal Protein S8; Chain: A, domain 1 / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Scaffold protein Nfu/NifU N-terminal domain-containing protein / Nfu_N domain-containing protein
Similarity search - Component
Biological speciesStaphylococcus aureus subsp. aureus (bacteria)
MethodSOLUTION NMR
Model detailslowest energy, model1
AuthorsMao, B. / Tejero, R.T. / Aramini, J.M. / Snyder, D.A. / Montelione, G.T. / Northeast Structural Genomics Consortium (NESG)
CitationJournal: J.Biomol.Nmr / Year: 2013
Title: PDBStat: a universal restraint converter and restraint analysis software package for protein NMR.
Authors: Tejero, R. / Snyder, D. / Mao, B. / Aramini, J.M. / Montelione, G.T.
History
DepositionMay 29, 2013Deposition site: BMRB / Processing site: RCSB
Revision 1.0Aug 21, 2013Provider: repository / Type: Initial release
Revision 1.1Feb 5, 2014Group: Database references
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: Uncharacterized protein


Theoretical massNumber of molelcules
Total (without water)10,4881
Polymers10,4881
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 / 10000structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

#1: Protein Uncharacterized protein / SAV1430


Mass: 10487.755 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Staphylococcus aureus subsp. aureus (bacteria)
Strain: Mu50 / Gene: SAV1430 / Plasmid: ZR18-21 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21MGK / References: UniProt: Q99U58, UniProt: A0A0H3JRL4*PLUS

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR / Details: Structure refined using Restrained CS-Rosetta
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
112NH HSQC
122HNCO
132HN(CA)CB
142HN(CO)CACB
172HCC(CO)NH-TOCSY
182H(CCCO)NH-TOCSY
192(HA)CA(CO)NH
1102HACANH
1112CH HSQC
1122(H)CCH-COSY
113213C EDITED NOESY
1142(HB)CB(CGCD)HD RD
1152AROMATICTOCSY RD
1161hetNOE
1171HNHA
118215N EDITED NOESY
1191CH HSQC high res.
NMR detailsText: THE FIRST REPRESENTATIVE STRUCTURE IN THE ENSEMBLE IS THE MEDOID STRUCTURE.

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Sample preparation

Details
Solution-IDContentsSolvent system
11.3 mM [U-100% 15N; U-5% 13C] ZR18, 20 mM MES, 100 mM NaCl, 5 mM CaCl2, 10 mM DTT, 0.02 % NaN3, 5 % D2O, 95% H2O/5% D2O95% H2O/5% D2O
21.15 mM [U-100% 15N; U-100% 13C] ZR18, 20 mM MES, 100 mM NaCl, 5 mM CaCl2, 10 mM DTT, 0.02 % NaN3, 5 % D2O, 95% H2O/5% D2O95% H2O/5% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
1.3 mMZR18-1[U-100% 15N; U-5% 13C]1
20 mMMES-21
100 mMNaCl-31
5 mMCaCl2-41
10 mMDTT-51
0.02 %NaN3-61
5 %D2O-71
1.15 mMZR18-8[U-100% 15N; U-100% 13C]2
20 mMMES-92
100 mMNaCl-102
5 mMCaCl2-112
10 mMDTT-122
0.02 %NaN3-132
5 %D2O-142
Sample conditionsIonic strength: 0.1 / pH: 6.5 / Temperature: 298 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Varian UNITY InovaVarianUNITY Inova5001
Varian UNITY InovaVarianUNITY Inova6002

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Processing

NMR software
NameVersionDeveloperClassification
HYPER3.2Tejero, Monleon, Celda, Powers and Montelionedata analysis
TALOS2.1Cornilescu, Delaglio and Baxdata analysis
VNMR6.1CVariandata collection
NMRPipeDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxraw spectral data processing
SparkyGoddardspectral visualization
AutoAssignZimmerman, Moseley, Kulikowski and Montelioneautomated backbone assignments
SPINSBaran, Montelioneintegrated spectral analysus software
SPINSBaran, Montelioneintegrated spectral analysus software
Rosettarefinement
RefinementSoftware ordinal: 1
Details: Structures were calculated by Restrained CS-Rosetta method using NOE-based distance, dihedral angle, and hydrogen bond restraints from the original AutoStructure structure calculations
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 10000 / Conformers submitted total number: 20

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