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- PDB-1pqx: Solution NMR Structure of Staphylococcus aureus protein SAV1430. ... -

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Basic information

Entry
Database: PDB / ID: 1pqx
TitleSolution NMR Structure of Staphylococcus aureus protein SAV1430. Northeast Structural Genomics Consortium Target ZR18.
Componentsconserved hypothetical protein
KeywordsStructural genomics / unknown function / ZR18 / AUTOSTRUCTURE / SPINS / AUTOASSIGN / Northeast Structural Genomics Consortium / Protein Structure Initiative / PSI / NESG
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 Mu50 (bacteria)
MethodSOLUTION NMR / torsion angle dynamics
AuthorsBaran, M.C. / Aramini, J.M. / Xiao, R. / Huang, Y.J. / Acton, T.B. / Shih, L. / Montelione, G.T. / Northeast Structural Genomics Consortium (NESG)
CitationJournal: To be Published
Title: Solution Strucutre of the Hypothetical Staphylococcus Aureus protein SAV1430. Northest Strucutral Genomics Consortium target ZR18
Authors: Baran, M.C. / Aramini, J.M. / Xiao, R. / Huang, Y.J. / Acton, T.B. / Shih, L. / Montelione, G.T.
History
DepositionJun 19, 2003Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 7, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jun 6, 2018Group: Data collection / Derived calculations / Experimental preparation
Category: pdbx_nmr_exptl_sample_conditions / pdbx_struct_assembly ...pdbx_nmr_exptl_sample_conditions / pdbx_struct_assembly / pdbx_struct_assembly_prop / pdbx_struct_oper_list
Item: _pdbx_nmr_exptl_sample_conditions.temperature
Revision 1.4Sep 9, 2020Group: Data collection / Database references / Structure summary
Category: pdbx_nmr_software / struct / struct_ref_seq_dif
Item: _pdbx_nmr_software.name / _struct.title / _struct_ref_seq_dif.details
Revision 1.5Aug 24, 2022Group: Database references / Other / Category: database_2 / pdbx_database_status
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_nmr_data
Revision 1.6May 22, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: conserved hypothetical 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_5551
Buried area0 Å2
ΔGint0 kcal/mol
Surface area6810 Å2
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)10 / 56overall energy
RepresentativeModel #1lowest target function

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Components

#1: Protein conserved hypothetical protein / Hypothetical protein MW1320


Mass: 10487.755 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: ZR18
Source: (gene. exp.) Staphylococcus aureus subsp. aureus Mu50 (bacteria)
Species: Staphylococcus aureus / Strain: subsp. aureus Mu50 / Gene: SAV1430 / Variant: subsp. aureus Mu50 / 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
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1123D 15N-NOESY, 3D 13C-NOESY (aliphatic and aromatic)
123HNHA
132high resolution 13C, 1H-HSQC
143H/D exchange
152backbone TR experiments and 3D TOCSY's
162(H)CCH-COSY
NMR detailsText: The structure was determined using triple-resonance nmr spectroscopy. All Automatic analysis software was run out of the SPINS software. Automatic backbone resonance assignments were made using ...Text: The structure was determined using triple-resonance nmr spectroscopy. All Automatic analysis software was run out of the SPINS software. Automatic backbone resonance assignments were made using autoassign. automatic noesy assignments as well as distance and hydrogen bond restraints were determined using hyper and talos.

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Sample preparation

Details
Solution-IDContentsSolvent system
11.15 mM ZR18, 20mM MES, 100mM NaCl, 5mM CaCl2, 10mM DTT, 0.02% NaN3, 5% D20 ph 6.55% D20, 95% H20
21.3 mM ZR18, 20mM MES, 100mM NaCl, 5mM CaCl2, 10mM DTT, 0.02% NaN3, 5% D20 ph 6.55% D20, 95% H20
30.88 mM ZR18, 20mM MES, 100mM NaCl, 5mM CaCl2, 10mM DTT, 0.02% NaN3, 5% D20 ph 6.55% D20, 95% H20
40.88 mM ZR18, 20mM MES, 100mM NaCl, 5mM CaCl2, 10mM DTT, 0.02% NaN3, 5% D20 ph 6.5D20
Sample conditionsIonic strength: 100 mM NaCl / pH: 6.5 / Pressure: ambient / Temperature: 274 K

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NMR measurement

RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M
Radiation wavelengthRelative weight: 1
NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Varian INOVAVarianINOVA5001
Varian UNITYVarianUNITY6002

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Processing

NMR software
NameVersionDeveloperClassification
VNMR6.1BVariancollection
NMRPipe2.1Delaglioprocessing
AutoProc1Bayro, Montelioneprocessing
Sparky3.106Goddarddata analysis
AutoAssign1.9Zimmerman, Moseley, Montelionedata analysis
AutoStructure1.1.2Huang, Montelionedata analysis
X-PLORstructure solution
X-PLORrefinement
RefinementMethod: torsion angle dynamics / Software ordinal: 1
Details: The structures are based on a total of 1100 conformationally-restricting NOE-derived distance restraints, 185 dihedral angle restraints, and 28 hydrogen bond restraints.(14.8 constraints per ...Details: The structures are based on a total of 1100 conformationally-restricting NOE-derived distance restraints, 185 dihedral angle restraints, and 28 hydrogen bond restraints.(14.8 constraints per residue; 4.4 long-range constraints per residue). Structure Determination was performed iterativly using AutoStructure (XPLOR). The constrain file for this entry was updated to correspond to the XPLOR format on September 28, 2004.
NMR representativeSelection criteria: lowest target function
NMR ensembleConformer selection criteria: overall energy / Conformers calculated total number: 56 / Conformers submitted total number: 10

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