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- PDB-1xjs: Solution structure of Iron-Sulfur cluster assembly protein IscU f... -

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Basic information

Entry
Database: PDB / ID: 1xjs
TitleSolution structure of Iron-Sulfur cluster assembly protein IscU from Bacillus subtilis, with Zinc bound at the active site. Northeast Structural Genomics Consortium Target SR17
ComponentsNifU-like protein
KeywordsSTRUCTURAL GENOMICS / UNKNOWN FUNCTION / SR17 / Autostructure / Iron-Sulfur / Zinc / Northeast Structural Genomics Consortium / NESG / NIFU-LIKE / Protein Structure Initiative / PSI
Function / homology
Function and homology information


Transferases / iron-sulfur cluster assembly / ferrous iron binding / 2 iron, 2 sulfur cluster binding / transferase activity / intracellular iron ion homeostasis / cytoplasm
Similarity search - Function
Sufe protein. Chain: A - #10 / Sufe protein. Chain: A / NIF system FeS cluster assembly, NifU, N-terminal / NifU-like N terminal domain / Alpha-Beta Complex / Alpha Beta
Similarity search - Domain/homology
Zinc-dependent sulfurtransferase SufU
Similarity search - Component
Biological speciesBacillus subtilis (bacteria)
MethodSOLUTION NMR / Minimal constraint structure contained 492 conformationally restricting NOE-derived distance constraints, 108 hydrogen bond constraints, and 197 dihedral angle constraints. This resulted in 5.9 constraints per residue, 1.2 long range constraints per residue. Structure determination was performed with the following steps: AutoStructure-Dyana was used to identify distance constraints. These distance constraints were used as input into a Simulated Annealing with Xplor-NIH. The top ten structures were energy minimized with water using CNS.
AuthorsKornhaber, G.J. / Swapna, G.V.T. / Ramelot, T.A. / Cort, J.R. / Kennedy, M.A. / Montelione, G.T. / Northeast Structural Genomics Consortium (NESG)
CitationJournal: To be Published
Title: Solution structure of Iron-Sulfur cluster assembly protein IscU from Bacillus subtilis, with Zinc bound at the active site. Northeast Structural Genomics Consortium Target SR17.
Authors: Kornhaber, G.J. / Swapna, G.V.T. / Ramelot, T.A. / Cort, J.R. / Kennedy, M.A. / Montelione, G.T.
History
DepositionSep 24, 2004Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 4, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Mar 2, 2022Group: Data collection / Database references / Derived calculations
Category: database_2 / pdbx_nmr_software ...database_2 / pdbx_nmr_software / pdbx_struct_assembly / pdbx_struct_conn_angle / pdbx_struct_oper_list / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_nmr_software.name / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4May 22, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: NifU-like protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,2512
Polymers16,1851
Non-polymers651
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 / 60structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

#1: Protein NifU-like protein / Iron-Sulfur cluster assembly protein IscU


Mass: 16185.479 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus subtilis (bacteria) / Gene: nifU / Plasmid: pET21d / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)pMGK / References: UniProt: O32163
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1123D-TOCSYS
12213C,1H-HSQC
13215N,1H-HSQC
14113C,1H-HSQC
15115N,1H-HSQC, 2D Homonuclear NOESY
1614D 13C-separated NOESY
1713D 13C-separated NOESY
1813D 15N-separated NOESY
192H/D exchange
NMR detailsText: This structure was determined using a selective isotopic labeling strategy involving the protonation of specific residues in a perdeuterated background. Protonated atoms include: ile HD1, val ...Text: This structure was determined using a selective isotopic labeling strategy involving the protonation of specific residues in a perdeuterated background. Protonated atoms include: ile HD1, val HG*, leu HD*. All tyr and phe side-chains are protonated. In addition to the atoms mentioned above, exchangeable atoms were protonated.

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Sample preparation

Details
Solution-IDContentsSolvent system
1100mM Potassium Phosphate, 200mM Glycerol, 1mM DTT, 0.02% NaN3, 5% D2O, 95% H2O5% D2O, 95% H2O
220mM Sodium Phosphate, 50mM Sodium Chloride, 10mM DTT, 0.02% NaN3, 95% H2O, 5% D2O95% H2O/5% D2O
Sample conditionsIonic strength: 100mM / pH: 6.5 / Pressure: ambient / Temperature: 293 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 INOVAVarianINOVA7501
Varian INOVAVarianINOVA8002
Varian INOVAVarianINOVA6003

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Processing

NMR software
NameVersionDeveloperClassification
AutoAssign1.9Zimmerman, Moseley and Montelionedata analysis
AutoStructure2.0.0Huang and Montelionestructure solution
TALOS2.1Cornilescu, Delaglio and Baxstructure solution
Hyper, PDBstat3.2 and 3.32Tejero and Montelionestructure solution
NMRPipe2.1Delaglio et al.processing
X-PLOR2.0.6Schwieters, et al.refinement
CNS1Brunger, et al.refinement
Sparky3.106Goddarddata analysis
RefinementMethod: Minimal constraint structure contained 492 conformationally restricting NOE-derived distance constraints, 108 hydrogen bond constraints, and 197 dihedral angle constraints. This resulted in 5. ...Method: Minimal constraint structure contained 492 conformationally restricting NOE-derived distance constraints, 108 hydrogen bond constraints, and 197 dihedral angle constraints. This resulted in 5.9 constraints per residue, 1.2 long range constraints per residue. Structure determination was performed with the following steps: AutoStructure-Dyana was used to identify distance constraints. These distance constraints were used as input into a Simulated Annealing with Xplor-NIH. The top ten structures were energy minimized with water using CNS.
Software ordinal: 1
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 60 / Conformers submitted total number: 10

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