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- PDB-2eff: Crystal structure analysis of the complex between CyaY and Co(II) -

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Basic information

Entry
Database: PDB / ID: 2eff
TitleCrystal structure analysis of the complex between CyaY and Co(II)
ComponentsProtein cyaY
KeywordsUNKNOWN FUNCTION / FRATAXIN / FRIEDREICH'S ATAXIA IRON BINDING / IRON-SULFUR CLUSTER ASSEMBLY / DETOXIFYING REDOX-ACTIVE IRON
Function / homology
Function and homology information


iron-sulfur cluster assembly / ferric iron binding / ferrous iron binding / cytosol / cytoplasm
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 / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsSica, F. / Franzese, M.
Citation
Journal: Febs J. / Year: 2007
Title: Understanding the binding properties of an unusual metal-binding protein - a study of bacterial frataxin
Authors: Pastore, C. / Franzese, M. / Sica, F. / Temussi, P. / Pastore, A.
#1: Journal: Structure / Year: 2004
Title: Solution structure of the bacterial frataxin ortholog, CyaY: mapping the iron binding sites
Authors: Nair, M. / Adinolfi, S. / Pastore, C. / Kelly, G. / Temussi, P. / Pastore, A.
#2: Journal: 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
DepositionFeb 22, 2007Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Oct 2, 2007Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Oct 25, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Protein cyaY
hetero molecules


Theoretical massNumber of molelcules
Total (without water)12,3603
Polymers12,2421
Non-polymers1182
Water2,432135
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)43.828, 43.828, 98.596
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 Protein cyaY


Mass: 12242.358 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: CYAY, B3807 / Plasmid: pET22b-CyaY / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P27838
#2: Chemical ChemComp-CO / COBALT (II) ION


Mass: 58.933 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Co
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 135 / 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: 2.23 Å3/Da / Density % sol: 44.91 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 4.7
Details: 30% w/v PEG 4000, 200mM CoCl2, 2mM beta-mercaptoethanol, 100 mM sodium acetate, pH 4.7, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ELETTRA / Beamline: 5.2R / Wavelength: 1.2 Å
DetectorType: MAR CCD 130 mm / Detector: CCD / Date: Nov 8, 2005
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.2 Å / Relative weight: 1
ReflectionResolution: 1.75→30 Å / Num. obs: 20336 / % possible obs: 99.2 % / Redundancy: 5 % / Rmerge(I) obs: 0.057 / Net I/σ(I): 29.7
Reflection shellResolution: 1.75→1.78 Å / Redundancy: 5 % / Rmerge(I) obs: 0.212 / Mean I/σ(I) obs: 6.9 / % possible all: 99.6

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Processing

Software
NameClassification
HKL-2000data collection
AMoREphasing
SHELXL-97refinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB Entry 1EW4

1ew4


Resolution: 1.8→18.6 Å / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / σ(F): 4 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.228 1873 -RANDOM
Rwork0.177 ---
all0.189 18541 --
obs0.182 18541 10 %-
Refinement stepCycle: LAST / Resolution: 1.8→18.6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms860 0 2 135 997
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONs_bond_d0.004
X-RAY DIFFRACTIONs_angle_d1.3

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