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- PDB-1r9p: Solution NMR Structure Of The Haemophilus Influenzae Iron-Sulfur ... -

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Basic information

Entry
Database: PDB / ID: 1r9p
TitleSolution NMR Structure Of The Haemophilus Influenzae Iron-Sulfur Cluster Assembly Protein U (IscU) with Zinc Bound at the Active Site. Northeast Structural Genomics Consortium Target IR24.
ComponentsNifU-like protein
KeywordsSTRUCTURAL GENOMICS / UNKNOWN FUNCTION / iron-sulfur cluster binding / zinc binding / three conserved Cys / 3beta strands / 4 alpha helixes / NESG / PSI-2 / Protein Structure Initiative / Northeast Structural Genomics Consortium
Function / homology
Function and homology information


iron-sulfur cluster assembly / ferrous iron binding / 2 iron, 2 sulfur cluster binding / intracellular iron ion homeostasis / cytoplasm
Similarity search - Function
Sufe protein. Chain: A - #10 / Sufe protein. Chain: A / ISC system FeS cluster assembly, IscU scaffold / NIF system FeS cluster assembly, NifU, N-terminal / NifU-like N terminal domain / Alpha-Beta Complex / Alpha Beta
Similarity search - Domain/homology
Iron-sulfur cluster assembly scaffold protein IscU
Similarity search - Component
Biological speciesHaemophilus influenzae (bacteria)
MethodSOLUTION NMR / SIMULATED ANNEALING, TORSION ANGLE DYNAMICS, AUTOMATED ANALYSIS OF NOESY DATA, 3D STRUCTURES
AuthorsRamelot, T.A. / Cort, J.R. / Xiao, R. / Shastry, R. / Acton, T.B. / Montelione, G.T. / Kennedy, M.A. / Northeast Structural Genomics Consortium (NESG)
CitationJournal: J.Mol.Biol. / Year: 2004
Title: Solution NMR structure of the iron-sulfur cluster assembly protein U (IscU) with zinc bound at the active site.
Authors: Ramelot, T.A. / Cort, J.R. / Goldsmith-Fischman, S. / Kornhaber, G.J. / Xiao, R. / Shastry, R. / Acton, T.B. / Honig, B. / Montelione, G.T. / Kennedy, M.A.
History
DepositionOct 30, 2003Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 9, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Sep 24, 2014Group: Database references
Revision 1.4May 1, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_nmr_software / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / 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_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Remark 400COMPOUND THIS PROTEIN HAS STOICHIOMETRIC ZINC BOUND. THIS PDB ENTRY IS A MODEL CALCULATED WITH THE ...COMPOUND THIS PROTEIN HAS STOICHIOMETRIC ZINC BOUND. THIS PDB ENTRY IS A MODEL CALCULATED WITH THE ZINC-BINDING CONSTRAINTS OBTAINED BY INDIRECT METHODS. PDB ENTRY 1Q48 IS THE SAME PROTEIN MODELED WITHOUT ZINC-BINDING CONSTRAINTS.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: NifU-like protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,5522
Polymers14,4861
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)20 / 25structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

#1: Protein NifU-like protein / IscU


Mass: 14486.342 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Haemophilus influenzae (bacteria) / Gene: HI0377 / Plasmid: pET21d / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (lamda DE3) pMGK / References: UniProt: Q57074
#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
1113D 15N-separated NOESY
1213D 13C-separated NOESY
131HNHA
1424D 13C-separated NOESY
15313C HSQC
NMR detailsText: THE STRUCTURE WAS DETERMINED USING TRIPLE-RESONANCE NMR SPECTROSCOPY, AUTOMATED ANALYSIS OF 3D STRUCTURE.

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Sample preparation

Details
Solution-IDContentsSolvent system
11 mM U-15N, U-13C IscU in 20 mM MES, 100mM NaCl, 5 mM CaCl2, 10 mM DTT, 0.02% NaN395% H2O/5% D2O
21 mM U-15N, U-13C IscU in 20 mM MES, 100mM NaCl, 5 mM CaCl2, 10 mM DTT, 0.02% NaN3100% D2O
31 mM U-15N, U-5%-13C IscU in 20 mM MES, 100mM NaCl, 5 mM CaCl2, 10 mM DTT, 0.02% NaN395% H2O/5% D2O
Sample conditionsIonic strength: 20 mM MES, 100 mM NaCl, 5 mM CaCl2 / pH: 6.5 / Pressure: ambient / 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 INOVAVarianINOVA8001
Varian INOVAVarianINOVA7502
Varian INOVAVarianINOVA6003
Varian UNITYVarianUNITY6004

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Processing

NMR software
NameVersionDeveloperClassification
Felix98MSI (Accelrys)processing
X-PLORXplor-NIH-2.0.6Schwieters, C.D., Kuszewski, J.J., Tjandra, N., Core, G.M.structure solution
Sparky3.98Goddard, T.D., Kneller, D.G.data analysis
XPLORXplor-NIH-2.0.6SCHWIETERS, C.D., KUSZEWSKI, J.J. TJANDRA, N., CLORE, G.M.refinement
AutoStructure1.1.2Huang, Y.J., Montelione, G.T.refinement
TALOS1999.019.15.47data analysis
RefinementMethod: SIMULATED ANNEALING, TORSION ANGLE DYNAMICS, AUTOMATED ANALYSIS OF NOESY DATA, 3D STRUCTURES
Software ordinal: 1
Details: THE STRUCTURES ARE BASED ON A TOTAL OF 933 RESTRAINTS. SUMMARY OF EXPERIMENTAL CONSTRAINTS: DISTANCE RESTRAINTS: TOTAL = 800; INTRA-RESIDUE [I=J] = 12; SEQUENTIAL [(I-J)=1] = 260; MEDIUM ...Details: THE STRUCTURES ARE BASED ON A TOTAL OF 933 RESTRAINTS. SUMMARY OF EXPERIMENTAL CONSTRAINTS: DISTANCE RESTRAINTS: TOTAL = 800; INTRA-RESIDUE [I=J] = 12; SEQUENTIAL [(I-J)=1] = 260; MEDIUM RANGE [1<(I-J)<5] = 185; LONG RANGE [(I-J)>=5] = 255; HYDROGEN BOND RESTRAINTS = 78 (2 PER H-BOND); ZN RESTRAINTS 10; NUMBER OF DISTANCE RESTRAINTS PER RESIDUE = 8.2; DIHEDRAL-ANGLE RESTRAINTS = 133 (66 PHI, 67 PSI); TOTAL NUMBER OF RESTRAINTS PER RESIDUE = 9.5 (RESIDES 26-123); NUMBER OF LONG RANGE RESTRAINTS PER RESIDUE = 2.6; NUMBER OF STRUCTURES COMPUTED = 25; NUMBER OF STRUCTURES USED = 20. AVERAGE DISTANCE VIOLATIONS >0.0001 ANG = 27.4; AVERAGE R.M.S. DISTANCE VIOLATION = 0.003 ANG; MAXIMUM NUMBER OF DISTANCE VIOLATIONS 33. AVERAGE DIHEDRAL ANGLE VIOLATIONS: >0.0001 DEG = 1.0; MAX NUMBER OF DIHEDRAL ANGLE VIOLATIONS = 3; AVERAGE R.M.S. ANGLE VIOLATION = 0.01 DEG. RMSD VALUES: BACKBONE ATOMS (N,C,C',O, RESIDUES 26-123) = 0.76 ANG; ALL HEAVY ATOMS = 1.19 ANG; PROCHECK (RESDIUES 26-123): MOST FAVORED REGIONS = 78%; ADDITIONAL ALLOWED REGIONS = 18%; GENEROUSLY ALLOWED REGIONS = 3%; DISALLOWED REGIONS = 0%.
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 25 / Conformers submitted total number: 20

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