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- PDB-2z7e: Crystal structure of Aquifex aeolicus IscU with bound [2Fe-2S] cluster -

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Basic information

Entry
Database: PDB / ID: 2z7e
TitleCrystal structure of Aquifex aeolicus IscU with bound [2Fe-2S] cluster
ComponentsNifU-like protein
KeywordsBIOSYNTHETIC PROTEIN / iron-sulfur cluster / iron / biosynthesis / [2Fe-2S] / ISC / IscU / NifU / asymmetric trimer / three conserved Cys
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 / NIF system FeS cluster assembly, NifU, N-terminal / NifU-like N terminal domain / Alpha-Beta Complex / Alpha Beta
Similarity search - Domain/homology
FE2/S2 (INORGANIC) CLUSTER / Iron-sulfur cluster assembly scaffold protein IscU
Similarity search - Component
Biological speciesAquifex aeolicus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.3 Å
AuthorsShimomura, Y. / Wada, K. / Takahashi, Y. / Fukuyama, K.
CitationJournal: J.Mol.Biol. / Year: 2008
Title: The asymmetric trimeric architecture of [2Fe-2S] IscU: implications for its scaffolding during iron-sulfur cluster biosynthesis
Authors: Shimomura, Y. / Wada, K. / Fukuyama, K. / Takahashi, Y.
History
DepositionAug 20, 2007Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Aug 19, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 10, 2021Group: Database references / Derived calculations / Category: database_2 / 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 / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.3Oct 30, 2024Group: Data collection / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: NifU-like protein
B: NifU-like protein
C: NifU-like protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)53,0718
Polymers52,5113
Non-polymers5605
Water2,918162
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4800 Å2
ΔGint-104 kcal/mol
Surface area17750 Å2
MethodPISA
2
A: NifU-like protein
B: NifU-like protein
C: NifU-like protein
hetero molecules

A: NifU-like protein
B: NifU-like protein
C: NifU-like protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)106,14316
Polymers105,0236
Non-polymers1,12010
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_665-x+1,-y+1,z1
Buried area13550 Å2
ΔGint-252 kcal/mol
Surface area31560 Å2
MethodPISA
Unit cell
Length a, b, c (Å)72.903, 122.136, 62.051
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212
Components on special symmetry positions
IDModelComponents
11A-160-

SO4

DetailsThe biological assembly is a trimer which consists of the three protomers in the asymmetric unit.

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Components

#1: Protein NifU-like protein / IscU protein


Mass: 17503.795 Da / Num. of mol.: 3 / Mutation: D38A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Aquifex aeolicus (bacteria) / Strain: VF5 / Gene: AQ_896 / Plasmid: pET21a(+) / Production host: Escherichia coli (E. coli) / Strain (production host): C41(DE3) / References: UniProt: O67045
#2: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-FES / FE2/S2 (INORGANIC) CLUSTER


Mass: 175.820 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Fe2S2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 162 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.63 Å3/Da / Density % sol: 53.24 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 1.6M ammonium sulfate, 0.5M lithium chloride, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL41XU / Wavelength: 1.7407, 1.7423, 1.6947, 1.5000
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Mar 26, 2006
RadiationProtocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
11.74071
21.74231
31.69471
41.51
ReflectionResolution: 2.3→47.25 Å / Num. obs: 24440 / % possible obs: 96.5 % / Biso Wilson estimate: 28 Å2

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Processing

Software
NameVersionClassification
CNS1.1refinement
HKL-2000data reduction
HKL-2000data scaling
CNSphasing
RefinementMethod to determine structure: MAD / Resolution: 2.3→47.25 Å / Rfactor Rfree error: 0.007 / Data cutoff high absF: 1635058.45 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.252 1226 5 %RANDOM
Rwork0.225 ---
obs0.225 24440 96.5 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 74.561 Å2 / ksol: 0.38913 e/Å3
Displacement parametersBiso mean: 49.9 Å2
Baniso -1Baniso -2Baniso -3
1--5.37 Å20 Å20 Å2
2---12.5 Å20 Å2
3---17.86 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.35 Å0.31 Å
Luzzati d res low-5 Å
Luzzati sigma a0.34 Å0.27 Å
Refinement stepCycle: LAST / Resolution: 2.3→47.25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3087 0 24 162 3273
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.007
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.3
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d22.6
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.84
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it1.431.5
X-RAY DIFFRACTIONc_mcangle_it2.462
X-RAY DIFFRACTIONc_scbond_it2.052
X-RAY DIFFRACTIONc_scangle_it3.012.5
LS refinement shellResolution: 2.3→2.44 Å / Rfactor Rfree error: 0.022 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.297 181 5.4 %
Rwork0.277 3189 -
obs--81.3 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2water_rep.paramwater_rep.top
X-RAY DIFFRACTION3fes_xplor_param.txtfes_xplor_top.txt
X-RAY DIFFRACTION4so4_xplor_param.txtso4_xplor_top.txt

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