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- PDB-2m6q: Refined Solution NMR Structure of Staphylococcus aureus protein S... -

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Basic information

Entry
Database: PDB / ID: 2m6q
TitleRefined Solution NMR Structure of Staphylococcus aureus protein SAV1430. Northeast Strucutral Genomics Consortium Target ZR18
ComponentsSAV1430
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 / simulated annealing
Model detailslowest energy, model1
AuthorsBaran, M.C. / Aramini, J.M. / Huang, Y.J. / Xiao, R. / Acton, T.B. / Shih, L. / Montelione, G.T. / Northeast Structural Genomics Consortium (NESG)
Citation
Journal: 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.
#1: Journal: J.Am.Chem.Soc. / Year: 2006
Title: FAST-NMR: functional annotation screening technology using NMR spectroscopy.
Authors: Mercier, K.A. / Baran, M. / Ramanathan, V. / Revesz, P. / Xiao, R. / Montelione, G.T. / Powers, R.
History
DepositionApr 8, 2013Deposition site: BMRB / Processing site: RCSB
Revision 1.0May 1, 2013Provider: repository / Type: Initial release
Revision 1.1Aug 21, 2013Group: Database references
Revision 1.2Feb 5, 2014Group: Database references
Revision 1.3Jun 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 1.4May 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: SAV1430


Theoretical massNumber of molelcules
Total (without water)10,4881
Polymers10,4881
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)10 / 56structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

#1: 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: Refinement of PDB 1PQX
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
112NH HSQC
122HNCO
132HN(CA)CB
142HN(CO)CACB
152HNCA
162HN(CO)CA
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.

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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, 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, 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
1.15 mMZR18-7[U-100% 15N; U-100% 13C]2
20 mMMES-82
100 mMNaCl-92
5 mMCaCl2-102
10 mMDTT-112
0.02 %NaN3-122
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
AutoStructure1.1.2Huang, Tejero, Powers and Montelioneautomated structural determination
SPINSBaran, Montelioneintegrated spectral analysus software
SPINSBaran, Montelioneintegrated spectral analysus software
CNSrefinement
RefinementMethod: simulated annealing / Software ordinal: 1
Details: Refinement of PDB 1PQX coordinates (10 models) using CNS in explicit water. The original 1PQX models were generated by AutoStructure.
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 56 / Conformers submitted total number: 10

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