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- PDB-4hs5: Frataxin from Psychromonas ingrahamii as a model to study stabili... -

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Basic information

Entry
Database: PDB / ID: 4hs5
TitleFrataxin from Psychromonas ingrahamii as a model to study stability modulation within CyaY protein family
ComponentsProtein CyaY
KeywordsMETAL BINDING PROTEIN / pFXN / frataxin / CyaY / Psychromonas ingrahamii / Frataxin-like domain / CyaY protein family (pfam ID PF01491) / Iron homeostasis-redox balance
Function / homology
Function and homology information


iron-sulfur cluster assembly / ferric iron binding / ferrous iron binding / 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 speciesPsychromonas ingrahamii (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.45 Å
AuthorsRoman, E.A. / Cousido-siah, A. / Mitschler, A. / Podjarny, A. / Santos, J.
CitationJournal: Biochim.Biophys.Acta / Year: 2013
Title: Frataxin from Psychromonas ingrahamii as a model to study stability modulation within the CyaY protein family
Authors: Roman, E.A. / Faraj, S.E. / Cousido-Siah, A. / Mitschler, A. / Podjarny, A. / Santos, J.
History
DepositionOct 29, 2012Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Mar 13, 2013Provider: repository / Type: Initial release
Revision 1.1Jul 31, 2013Group: Database references
Revision 1.2Nov 8, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Protein CyaY
B: Protein CyaY


Theoretical massNumber of molelcules
Total (without water)24,5912
Polymers24,5912
Non-polymers00
Water4,954275
1
A: Protein CyaY


Theoretical massNumber of molelcules
Total (without water)12,2951
Polymers12,2951
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Protein CyaY


Theoretical massNumber of molelcules
Total (without water)12,2951
Polymers12,2951
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)39.841, 50.133, 45.748
Angle α, β, γ (deg.)90.00, 91.35, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Protein CyaY


Mass: 12295.387 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: Kanamycin resistance, IPTG inducible / Source: (gene. exp.) Psychromonas ingrahamii (bacteria) / Strain: 37 / Gene: cyaY, Ping_0042 / Plasmid: pJexpress411:56977 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 DE3 / References: UniProt: A1SR01
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 275 / 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: 1.86 Å3/Da / Density % sol: 33.78 %
Crystal growTemperature: 297 K / Method: vapor diffusion, hanging drop / pH: 4.8
Details: 20mM sodium acetate, 200mM MgCl2, 29.5% PEG 4000, pH 4.80, VAPOR DIFFUSION, HANGING DROP, temperature 297K

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Data collection

DiffractionMean temperature: 177 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 0.9191 Å
DetectorType: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Apr 2, 2012
RadiationMonochromator: Bartels Monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9191 Å / Relative weight: 1
ReflectionResolution: 1.45→50 Å / Num. all: 31292 / Num. obs: 31292 / % possible obs: 97.1 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.4 % / Rmerge(I) obs: 0.036 / Net I/σ(I): 26.5
Reflection shellResolution: 1.45→1.5 Å / % possible all: 97.1

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Processing

SoftwareName: PHENIX / Version: (phenix.refine: 1.8_1069) / Classification: refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ID 1EW4

1ew4


Resolution: 1.45→31.186 Å / Occupancy max: 1 / Occupancy min: 0 / FOM work R set: 0.8479 / SU ML: 0.17 / σ(F): 0 / Phase error: 22.53 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.2016 1581 5.05 %random 5%
Rwork0.1864 ---
all0.1872 31292 --
obs0.1872 31285 96.93 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 58.38 Å2 / Biso mean: 15.7965 Å2 / Biso min: 2.92 Å2
Refinement stepCycle: LAST / Resolution: 1.45→31.186 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1736 0 0 275 2011
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0061797
X-RAY DIFFRACTIONf_angle_d1.1282435
X-RAY DIFFRACTIONf_dihedral_angle_d13.461657
X-RAY DIFFRACTIONf_chiral_restr0.079260
X-RAY DIFFRACTIONf_plane_restr0.004323
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 11

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.4466-1.49330.28471330.24712541267492
1.4933-1.54670.27321830.23592620280396
1.5467-1.60860.23971440.21362688283297
1.6086-1.68180.2581420.21312704284697
1.6818-1.77050.24811140.21492736285097
1.7705-1.88140.23811440.21492722286698
1.8814-2.02660.21711470.19282706285398
2.0266-2.23050.19791430.18152753289699
2.2305-2.55320.21941270.18692780290799
2.5532-3.21620.17531490.18442766291599
3.2162-31.19290.16811550.15812688284394

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