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- PDB-1ew4: CRYSTAL STRUCTURE OF ESCHERICHIA COLI CYAY PROTEIN REVEALS A NOVE... -

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Basic information

Entry
Database: PDB / ID: 1ew4
TitleCRYSTAL STRUCTURE OF ESCHERICHIA COLI CYAY PROTEIN REVEALS A NOVEL FOLD FOR THE FRATAXIN FAMILY
ComponentsCYAY PROTEIN
KeywordsUNKNOWN FUNCTION / Friedreich ataxia / frataxin family / CyaY / iron homeostasis
Function / homology
Function and homology information


iron-sulfur cluster assembly / ferric iron binding / ferrous iron binding / cytoplasm / cytosol
Similarity search - Function
: / Frataxin/CyaY / Metal Transport, Frataxin; Chain A / Frataxin/CyaY / Frataxin conserved site / Frataxin-like domain / Frataxin family signature. / Frataxin family profile. / Frataxin-like domain / Frataxin/CyaY superfamily ...: / Frataxin/CyaY / Metal Transport, Frataxin; Chain A / Frataxin/CyaY / Frataxin conserved site / Frataxin-like domain / Frataxin family signature. / Frataxin family profile. / Frataxin-like domain / Frataxin/CyaY superfamily / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Iron-sulfur cluster assembly protein CyaY
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 1.4 Å
AuthorsSuh, S.W. / Cho, S. / Lee, M.G. / Yang, J.K. / Lee, J.Y. / Song, H.K.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2000
Title: Crystal structure of Escherichia coli CyaY protein reveals a previously unidentified fold for the evolutionarily conserved frataxin family.
Authors: Cho, S.J. / Lee, M.G. / Yang, J.K. / Lee, J.Y. / Song, H.K. / Suh, S.W.
History
DepositionApr 22, 2000Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 9, 2000Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 7, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: CYAY PROTEIN


Theoretical massNumber of molelcules
Total (without water)12,2421
Polymers12,2421
Non-polymers00
Water2,198122
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)44.178, 44.178, 98.286
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221

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Components

#1: Protein CYAY PROTEIN


Mass: 12242.358 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Plasmid: PET22B-CYAY / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P27838
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 122 / 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: 2.26 Å3/Da / Density % sol: 45.61 %
Crystal growTemperature: 296 K / Method: vapor diffusion, hanging drop / pH: 5.12
Details: 0.1 M sodium acetate, 34% PEG 4000, pH 5.12, VAPOR DIFFUSION, HANGING DROP, temperature 296K
Crystal grow
*PLUS
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
117 mg/mlprotein1drop
22.0 Mmagnesium chloride1drop
3100 mMsodium acetate1reservoir
434 %(w/v)PEG40001reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-6A / Wavelength: 1
DetectorType: FUJI / Detector: IMAGE PLATE / Date: Feb 25, 2000
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.4→50 Å / Num. all: 22616 / Num. obs: 204695 / % possible obs: 99.9 % / Redundancy: 9 % / Biso Wilson estimate: 16.5 Å2 / Rmerge(I) obs: 0.041 / Net I/σ(I): 46
Reflection shellResolution: 1.4→1.45 Å / Redundancy: 6.5 % / Rmerge(I) obs: 0.399 / Num. unique all: 2190 / % possible all: 99.4
Reflection
*PLUS
Num. obs: 22616 / Num. measured all: 204695
Reflection shell
*PLUS
% possible obs: 99.4 %

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Processing

Software
NameVersionClassification
SHARPphasing
CNS0.9refinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementResolution: 1.4→19.13 Å / Rfactor Rfree error: 0.005 / Data cutoff high absF: 1533641.61 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 2
Stereochemistry target values: maximum likelihood target using amplitudes
RfactorNum. reflection% reflectionSelection details
Rfree0.213 1944 10 %RANDOM
Rwork0.188 ---
obs0.188 19479 86.1 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 33.32 Å2 / ksol: 0.312 e/Å3
Displacement parametersBiso mean: 20.9 Å2
Baniso -1Baniso -2Baniso -3
1--0.22 Å20 Å20 Å2
2---0.22 Å20 Å2
3---0.44 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.17 Å0.15 Å
Luzzati d res low-5 Å
Luzzati sigma a0.04 Å0.02 Å
Refinement stepCycle: LAST / Resolution: 1.4→19.13 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms863 0 0 122 985
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.011
X-RAY DIFFRACTIONc_angle_deg1.48
X-RAY DIFFRACTIONc_dihedral_angle_d24.1
X-RAY DIFFRACTIONc_improper_angle_d0.66
X-RAY DIFFRACTIONc_mcbond_it2.071.5
X-RAY DIFFRACTIONc_mcangle_it3.192
X-RAY DIFFRACTIONc_scbond_it4.022
X-RAY DIFFRACTIONc_scangle_it5.862.5
LS refinement shellResolution: 1.4→1.49 Å / Rfactor Rfree error: 0.015 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.216 217 10.6 %
Rwork0.187 1829 -
obs--55.2 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAMWATER.TOP
Software
*PLUS
Name: CNS / Version: 0.9 / Classification: refinement
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg24.1
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.66

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