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- PDB-2p1x: Crystal structure analysis of the complex between CyaY and Eu(III) -

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Basic information

Entry
Database: PDB / ID: 2p1x
TitleCrystal structure analysis of the complex between CyaY and Eu(III)
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 chaperone activity / iron-sulfur cluster assembly / ferroxidase activity / ferric iron binding / ferrous iron binding / 2 iron, 2 sulfur cluster binding / intracellular iron ion homeostasis / 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
EUROPIUM (III) ION / Iron-sulfur cluster assembly protein CyaY
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.42 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
DepositionMar 6, 2007Deposition site: RCSB / 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 / pdbx_struct_conn_angle / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _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)13,0026
Polymers12,2421
Non-polymers7605
Water2,036113
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)43.859, 43.859, 98.717
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 / 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-EU3 / EUROPIUM (III) ION


Mass: 151.964 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Eu
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 113 / 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: 2.22 Å3/Da / Density % sol: 44.48 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 5
Details: Crystallization conditions: protein concentration 15mg/ml, 0.1M sodium acetate, 0.2M CaCl2, 30% PEG 4000, 2mM beta mercaptoethanol Soaking conditions: EuCl3 in the stabilizing solution, pH 5. ...Details: Crystallization conditions: protein concentration 15mg/ml, 0.1M sodium acetate, 0.2M CaCl2, 30% PEG 4000, 2mM beta mercaptoethanol Soaking conditions: EuCl3 in the stabilizing solution, pH 5.0, 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: 1.1 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Nov 8, 2005
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.1 Å / Relative weight: 1
ReflectionResolution: 1.42→30 Å / Num. obs: 36600 / % possible obs: 97.2 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 5 % / Rmerge(I) obs: 0.086 / Net I/σ(I): 15.9
Reflection shellResolution: 1.42→1.44 Å / Rmerge(I) obs: 0.419 / Mean I/σ(I) obs: 3.1 / % possible all: 99.9

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Processing

Software
NameClassification
MAR345dtbdata collection
AMoREphasing
SHELXL-97refinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1EW4

1ew4


Resolution: 1.42→25 Å / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / σ(F): 2 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.222 3664 -RANDOM
Rwork0.199 ---
obs0.201 36600 10 %-
all-36600 --
Refinement stepCycle: LAST / Resolution: 1.42→25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms860 0 5 113 978
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONs_bond_d0.006
X-RAY DIFFRACTIONs_angle_d1.3

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