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- PDB-1xhj: Solution Structure Of The Staphylococcus Epidermidis Protein SE06... -

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Basic information

Entry
Database: PDB / ID: 1xhj
TitleSolution Structure Of The Staphylococcus Epidermidis Protein SE0630. Northest Structural Genomics Consortium Target SeR8.
ComponentsNitrogen Fixation Protein NifU
KeywordsMETAL BINDING PROTEIN / Alpha-beta / NifU-like / Structural Genomics / Protein Structure Initiative / NESG / PSI / Northeast Structural Genomics Consortium
Function / homology
Function and homology information


iron-sulfur cluster assembly / iron-sulfur cluster binding / iron ion binding / structural molecule activity
Similarity search - Function
NIF system FeS cluster assembly, NifU, C-terminal / NifU-like domain / Fe-S cluster assembly (FSCA) / Fe-S cluster assembly domain superfamily / GMP Synthetase; Chain A, domain 3 / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Nitrogen fixation protein NifU / Nitrogen fixation protein NifU
Similarity search - Component
Biological speciesStaphylococcus epidermidis (bacteria)
MethodSOLUTION NMR / simulated annealing
AuthorsBaran, M.C. / Huang, Y.P. / Acton, T. / Xiao, R. / Montelione, G.T. / Northeast Structural Genomics Consortium (NESG)
CitationJournal: To be Published
Title: Solution Structure Of The Staphylococcus Epidermidis Protein SE0630. Northest Strucutral Genomics Consortium Target SeR8.
Authors: Baran, M.C. / Huang, Y.P. / Acton, T. / Xiao, R. / Montelione, G.T.
History
DepositionSep 20, 2004Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 7, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Source and taxonomy / Version format compliance
Revision 1.3May 1, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_nmr_software / pdbx_nmr_spectrometer / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_nmr_software.name / _pdbx_nmr_spectrometer.model / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Nitrogen Fixation Protein NifU


Theoretical massNumber of molelcules
Total (without water)9,8151
Polymers9,8151
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)10 / 100structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

#1: Protein Nitrogen Fixation Protein NifU


Mass: 9815.145 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Staphylococcus epidermidis (bacteria) / Strain: ATCC 12228 / Gene: SE0936 / Plasmid: SER8-21 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21MGK / References: UniProt: Q8CPV7, UniProt: A0A0H2VHU6*PLUS

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
111C13-HSQC
122NH-HSQC
132HNCO
142HNCAB
152N15-NOESY
162C13-NOESY
NMR detailsText: The structure was determined using triple resonance nmr spectroscopy. Automatic backbone assignments were made using AutoAssign. Automatic NOESY assignments were made using AutoStructure. ...Text: The structure was determined using triple resonance nmr spectroscopy. Automatic backbone assignments were made using AutoAssign. Automatic NOESY assignments were made using AutoStructure. Dihedral angle restraints were made using HYPER and Talos. The SPINS database software was used as an integrating agent.

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Sample preparation

Details
Solution-IDContentsSolvent system
10.02% NaN3, 10mM DTT, 5mM CaCl2, 100mM NaCl, 20mM MES, pH 6.5, 5% C13, 100% N15, 5% D2O, 95% H205% D2O, 95% H20
20.02% NaN3, 10mM DTT, 5mM CaCl2, 100mM NaCl, 20mM MES, pH 6.5, 100% C13, 100% N15, 5% D2O, 95% H205% D2O, 95% H20
Sample conditionsIonic strength: 100 mM NaCl / pH: 6.5 / Pressure: 1 atm / Temperature: 293 K

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NMR measurement

RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthRelative weight: 1
NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Varian INOVAVarianINOVA6001
Bruker AVANCEBrukerAVANCE5002
Bruker8003

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Processing

NMR software
NameVersionDeveloperClassification
X-PLOR2.9.7Brungerstructure solution
NMRPipe2.1Delaglioprocessing
AutoAssign1.14Zimmerman, Moseley, Montelionedata analysis
AutoStructure2Huang, Montelionedata analysis
SPINS5Baran, Montelionedata analysis
HYPER3.2Tejero, Montelionedata analysis
Sparky3.106Goddarddata analysis
VNMR6.1variancollection
xwin-nmrBrukercollection
X-PLOR2.9.7Brungerrefinement
RefinementMethod: simulated annealing / Software ordinal: 1
Details: The structure is based on a total of 1311 conformationally restricting non-derived distance restraints. The structure contains 14.9 restraints per residue, with 3.5 long range restraints per ...Details: The structure is based on a total of 1311 conformationally restricting non-derived distance restraints. The structure contains 14.9 restraints per residue, with 3.5 long range restraints per residue. Structure determination was performed iteratively using AutoStructure.
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 100 / Conformers submitted total number: 10

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