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- PDB-9jb5: Crystal structure of Arabidopsis theliana FRATAXIN HOMOLOG -

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Basic information

Entry
Database: PDB / ID: 9jb5
TitleCrystal structure of Arabidopsis theliana FRATAXIN HOMOLOG
ComponentsFrataxin, mitochondrial
KeywordsTRANSPORT PROTEIN / Arabidopsis / metal-binding / iron transport / heme biosynthesis
Function / homology
Function and homology information


regulation of iron-sulfur cluster assembly / iron incorporation into metallo-sulfur cluster / embryo development ending in seed dormancy / heme biosynthetic process / ferroxidase / ferroxidase activity / aerobic respiration / ferric iron binding / chloroplast / response to hydrogen peroxide ...regulation of iron-sulfur cluster assembly / iron incorporation into metallo-sulfur cluster / embryo development ending in seed dormancy / heme biosynthetic process / ferroxidase / ferroxidase activity / aerobic respiration / ferric iron binding / chloroplast / response to hydrogen peroxide / iron ion transport / intracellular iron ion homeostasis / response to oxidative stress / mitochondrion / cytosol
Similarity search - Function
Frataxin / Frataxin/CyaY / Frataxin conserved site / Frataxin-like domain / Frataxin family signature. / Frataxin family profile. / Frataxin-like domain / Frataxin/CyaY superfamily
Similarity search - Domain/homology
Frataxin, mitochondrial
Similarity search - Component
Biological speciesArabidopsis thaliana (thale cress)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.8 Å
AuthorsZhang, J. / Wang, J. / Liu, L.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)32201041 China
CitationJournal: Biochimie / Year: 2024
Title: Characterization of Arabidopsis thaliana FRATAXIN HOMOLOG in heme catabolism.
Authors: Zhang, J. / Zhou, Y. / Duan, Q. / Xu, X. / Wang, X. / Wang, J. / Liu, L.
History
DepositionAug 26, 2024Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Jan 1, 2025Provider: repository / Type: Initial release
Revision 1.1Jan 8, 2025Group: Database references / Category: citation / Item: _citation.pdbx_database_id_PubMed / _citation.title

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Frataxin, mitochondrial
B: Frataxin, mitochondrial


Theoretical massNumber of molelcules
Total (without water)30,4542
Polymers30,4542
Non-polymers00
Water181
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1980 Å2
ΔGint-7 kcal/mol
Surface area12330 Å2
MethodPISA
Unit cell
Length a, b, c (Å)52.944, 139.413, 83.292
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221

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Components

#1: Protein Frataxin, mitochondrial / Fxn


Mass: 15226.913 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Gene: FH, At4g03240, F4C21.17 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9ZR07, ferroxidase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationN

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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: 2.52 Å3/Da / Density % sol: 51.26 %
Crystal growTemperature: 277.15 K / Method: vapor diffusion / Details: 2.4 M Sodium malonate pH 7.0

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL18U1 / Wavelength: 0.979 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: May 18, 2024
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2.8→50 Å / Num. obs: 7924 / % possible obs: 99.6 % / Redundancy: 5.5 % / CC1/2: 0.972 / CC star: 0.993 / Rmerge(I) obs: 0.154 / Rpim(I) all: 0.072 / Rrim(I) all: 0.17 / Χ2: 1.073 / Net I/σ(I): 4.2 / Num. measured all: 43905
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2CC starRpim(I) allRrim(I) allΧ2% possible all
2.8-2.950.7157510.6230.8760.3580.8030.797.9
2.9-3.025.20.6877840.6980.9070.3360.7670.7199.2
3.02-3.155.80.5337660.7830.9370.2480.5890.73499.7
3.15-3.325.80.347950.9130.9770.1570.3760.84199.7
3.32-3.535.60.2487820.9580.9890.1140.2741.02299.7
3.53-3.85.70.1937880.9780.9940.0880.2131.014100
3.8-4.185.90.1477860.9830.9960.0660.1611.255100
4.18-4.795.70.1177940.9880.9970.0540.1291.42199.9
4.79-6.035.70.1118110.9840.9960.0510.1231.36100
6.03-505.10.18670.9930.9980.0480.1111.58499.4

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Processing

Software
NameVersionClassification
PHENIX(1.20.1_4487: ???)refinement
HKL-3000data scaling
HKL-3000data reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.8→32.21 Å / SU ML: 0.51 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 29.29 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2758 410 5.23 %
Rwork0.2168 --
obs0.2197 7839 99.33 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.8→32.21 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1901 0 0 1 1902
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.002
X-RAY DIFFRACTIONf_angle_d0.456
X-RAY DIFFRACTIONf_dihedral_angle_d13.658725
X-RAY DIFFRACTIONf_chiral_restr0.043281
X-RAY DIFFRACTIONf_plane_restr0.004350
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.8-3.210.33271380.29652391X-RAY DIFFRACTION98
3.21-4.040.28341400.23242452X-RAY DIFFRACTION100
4.04-32.210.25681320.18962586X-RAY DIFFRACTION100

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