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- PDB-1s98: E.coli IscA crystal structure to 2.3 A -

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Basic information

Entry
Database: PDB / ID: 1s98
TitleE.coli IscA crystal structure to 2.3 A
ComponentsProtein yfhF
KeywordsMETAL TRANSPORT / IscA / Fe-S cluster / iron / sulfur / Isc
Function / homology
Function and homology information


iron-sulfur cluster transfer complex / protein maturation by iron-sulfur cluster transfer / iron chaperone activity / iron-sulfur cluster assembly / ferrous iron binding / 2 iron, 2 sulfur cluster binding / cytosol / cytoplasm
Similarity search - Function
Iron-binding protein IscA, proteobacteria / FeS cluster insertion, C-terminal, conserved site / Hypothetical hesB/yadR/yfhF family signature. / FeS cluster insertion protein / Hypothetical Protein Aq_1857; Chain: A; / HesB-like domain / FeS cluster biogenesis / HesB-like domain superfamily / Iron-sulphur cluster biosynthesis / Sandwich / Mainly Beta
Similarity search - Domain/homology
Iron-binding protein IscA
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.3 Å
AuthorsCupp-Vickery, J.R. / Silberg, J.J. / Ta, D.T. / Vickery, L.E.
CitationJournal: J.Mol.Biol. / Year: 2004
Title: Crystal structure of IscA, an iron-sulfur cluster assembly protein from Escherichia coli.
Authors: Cupp-Vickery, J.R. / Silberg, J.J. / Ta, D.T. / Vickery, L.E.
History
DepositionFeb 3, 2004Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 1, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jan 31, 2018Group: Experimental preparation / Category: exptl_crystal_grow / Item: _exptl_crystal_grow.temp
Revision 1.4Oct 27, 2021Group: Database references / Category: database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details
Revision 1.5Feb 14, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Protein yfhF
B: Protein yfhF


Theoretical massNumber of molelcules
Total (without water)23,1722
Polymers23,1722
Non-polymers00
Water68538
1
A: Protein yfhF
B: Protein yfhF

A: Protein yfhF
B: Protein yfhF


Theoretical massNumber of molelcules
Total (without water)46,3444
Polymers46,3444
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_555y,x,-z1
Unit cell
Length a, b, c (Å)66.252, 66.252, 150.850
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221
DetailsThe biological assembly is a tetramer generated from the dimer in the asymmetric uni by the operations: Rotation 0 180 60 Trans 0 0 0

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Components

#1: Protein Protein yfhF


Mass: 11586.058 Da / Num. of mol.: 2 / Mutation: L69M
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: YFHF, B2528, C3053, Z3795, ECS3394, SF2575, S2747 / Plasmid: pTrc / Production host: Escherichia coli (E. coli) / Strain (production host): DL41 / References: UniProt: P0AAC8
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 38 / Source method: isolated from a natural source / Formula: H2O

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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: 4.74 Å3/Da / Density % sol: 73.83 %
Crystal growTemperature: 296 K / Method: vapor diffusion, hanging drop / pH: 4.6
Details: NaPhosphate, pH 4.6, VAPOR DIFFUSION, HANGING DROP, temperature 23K

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Data collection

DiffractionMean temperature: 93 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL9-2 / Wavelength: 0.97
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Dec 20, 2002
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97 Å / Relative weight: 1
ReflectionResolution: 2.3→20 Å / Num. obs: 20165 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 8.2 % / Biso Wilson estimate: 47.3 Å2 / Rsym value: 0.069 / Net I/σ(I): 7.2
Reflection shellResolution: 2.3→2.35 Å / Redundancy: 6.2 % / Mean I/σ(I) obs: 2 / Num. unique all: 1148 / Rsym value: 0.436 / % possible all: 99.6

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Processing

Software
NameVersionClassification
REFMAC5.1.24refinement
MOSFLMdata reduction
CCP4(SCALA)data scaling
CNSphasing
RefinementMethod to determine structure: SAD / Resolution: 2.3→19.92 Å / Cor.coef. Fo:Fc: 0.945 / Cor.coef. Fo:Fc free: 0.929 / SU B: 5.242 / SU ML: 0.123 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.376 / ESU R Free: 0.182
Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.24967 1785 10.1 %RANDOM
Rwork0.212 ---
all0.215 ---
obs0.215 15810 99.54 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 53.454 Å2
Baniso -1Baniso -2Baniso -3
1-0.18 Å20.09 Å20 Å2
2--0.18 Å20 Å2
3----0.27 Å2
Refinement stepCycle: LAST / Resolution: 2.3→19.92 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1441 0 0 38 1479
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0380.0221464
X-RAY DIFFRACTIONr_bond_other_d0.0050.021329
X-RAY DIFFRACTIONr_angle_refined_deg2.5071.9581977
X-RAY DIFFRACTIONr_angle_other_deg1.22833082
X-RAY DIFFRACTIONr_dihedral_angle_1_deg9.0285192
X-RAY DIFFRACTIONr_chiral_restr0.1850.2225
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.021682
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02306
X-RAY DIFFRACTIONr_nbd_refined0.2670.2267
X-RAY DIFFRACTIONr_nbd_other0.2920.21493
X-RAY DIFFRACTIONr_nbtor_other0.1060.2954
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2070.233
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2780.28
X-RAY DIFFRACTIONr_symmetry_vdw_other0.3460.235
X-RAY DIFFRACTIONr_symmetry_hbond_refined1.3960.21
X-RAY DIFFRACTIONr_mcbond_it2.9491.5953
X-RAY DIFFRACTIONr_mcangle_it4.46821514
X-RAY DIFFRACTIONr_scbond_it6.4393511
X-RAY DIFFRACTIONr_scangle_it8.7744.5463
LS refinement shellResolution: 2.3→2.359 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.37 120
Rwork0.281 1148

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