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- PDB-1q48: Solution NMR Structure of The Haemophilus Influenzae Iron-Sulfur ... -

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Basic information

Entry
Database: PDB / ID: 1q48
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. This protein is not apo, it is a model without zinc binding constraints.
ComponentsNifU-like protein
KeywordsSTRUCTURAL GENOMICS / UNKNOWN FUNCTION / Iron-Sulfur cluster binding / Three conserved Cys / 3 beta strands / 4 alpha helixes / NESG / PSI / 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
ISC system FeS cluster assembly, IscU scaffold / 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
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
DepositionAug 1, 2003Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 18, 2003Provider: 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
Remark 400COMPOUND THIS PROTEIN HAS STOICHIOMETRIC ZINC BOUND. THIS PDB ENTRY IS A MODEL CALCULATED WITHOUT ...COMPOUND THIS PROTEIN HAS STOICHIOMETRIC ZINC BOUND. THIS PDB ENTRY IS A MODEL CALCULATED WITHOUT THE ZINC-BINDING CONSTRIANTS. PDB ENTRY 1R9P IS THE SAME PROTEIN MODELED WITH ZINC-BINDING CONSTRAINTS OBTAINED BY INDIRECT METHODS.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: NifU-like protein


Theoretical massNumber of molelcules
Total (without water)14,4861
Polymers14,4861
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)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

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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, 100 mM NaCl, 5 mM CaCl2, 10 mM DTT, 0.02% NaN395% H2O/5% D2O
21 mM U-15N, U-13C IscU in 20 mM MES, 100 mM NaCl, 5 mM CaCl2, 10 mM DTT, 0.02% NaN3100% D2O
31 mM U-15N, U-5%-13C IscU in 20 mM MES, 100 mM 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
Crystal grow
*PLUS
Method: other / Details: NMR

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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., Clore, 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
AutoStructureHuang, 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 923 RESTRAINTS. SUMMARY OF EXPERIMENTAL CONSTRAINTS: DISTANCE CONSTRAINTS: TOTAL = 790; INTRA-RESIDUE [I=J] = 12; SEQUENTIAL [(I-J)=1] = 260; MEDIUM ...Details: THE STRUCTURES ARE BASED ON A TOTAL OF 923 RESTRAINTS. SUMMARY OF EXPERIMENTAL CONSTRAINTS: DISTANCE CONSTRAINTS: TOTAL = 790; 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 CONSTRAINTS = 58 (2 PER H-BOND); NUMBER OF DISTANCE CONSTRAINTS PER RESIDUE = 8.0; DIHEDRAL-ANGLE CONSTRAINTS = 133 (66 PHI, 67 PSI); TOTAL NUMBER OF CONSTRAINTS PER RESIDUE = 9.4 (RESIDES 26-123); NUMBER OF LONG RANGE CONSTRAINTS PER RESIDUE = 2.6; NUMBER OF STRUCTURES COMPUTED = 25; NUMBER OF STRUCTURES USED = 20. AVERAGE DISTANCE VIOLATIONS >0.0001 ANG = 24.3; AVERAGE R.M.S. DISTANCE VIOLATION = 0.003 ANG; MAXIMUM NUMBER OF DISTANCE VIOLATIONS 31. AVERAGE DIHEDRAL ANGLE VIOLATIONS: >0.0001 DEG = 1.0; MAX NUMBER OF DIHEDRAL ANGLE VIOLATIONS = 4; AVERAGE R.M.S. ANGLE VIOLATION = 0.01 DEG. RMSD VALUES: BACKBONE ATOMS (N,C,C',O) = 0.80 ANG; ALL HEAVY ATOMS = 1.17 ANG; PROCHECK: MOST FAVORED REGIONS = 77%; ADDITIONAL ALLOWED REGIONS = 20%; 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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