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- PDB-6fco: Structural and functional characterisation of Frataxin (FXN) like... -

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Basic information

Entry
Database: PDB / ID: 6fco
TitleStructural and functional characterisation of Frataxin (FXN) like protein from Chaetomium thermophilum
ComponentsMitochondrial frataxin-like protein
KeywordsTRANSPORT PROTEIN / iron sulphur cluster / iron chaperone / Friedreich's ataxia
Function / homology
Function and homology information


iron-sulfur cluster assembly / heme biosynthetic process / ferroxidase / ferroxidase activity / monoatomic ion transport / ferric iron binding / intracellular iron ion homeostasis / mitochondrion
Similarity search - Function
Frataxin/CyaY / Frataxin / Frataxin/CyaY / Frataxin conserved site / Frataxin-like domain / Frataxin family signature. / Frataxin family profile. / Frataxin-like domain / Metal Transport, Frataxin; Chain A / Frataxin/CyaY superfamily ...Frataxin/CyaY / Frataxin / Frataxin/CyaY / Frataxin conserved site / Frataxin-like domain / Frataxin family signature. / Frataxin family profile. / Frataxin-like domain / Metal Transport, Frataxin; Chain A / Frataxin/CyaY superfamily / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
MALONIC ACID / Ferroxidase
Similarity search - Component
Biological speciesChaetomium thermophilum var. thermophilum DSM 1495 (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.03 Å
AuthorsJamshidiha, M. / Rasheed, M. / Pastore, A. / Cota, E.
CitationJournal: FEBS J. / Year: 2019
Title: Structural and functional characterization of a frataxin from a thermophilic organism.
Authors: Rasheed, M. / Jamshidiha, M. / Puglisi, R. / Yan, R. / Cota, E. / Pastore, A.
History
DepositionDec 20, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 23, 2019Provider: repository / Type: Initial release
Revision 1.1Feb 13, 2019Group: Data collection / Database references / Category: citation / pdbx_database_proc
Item: _citation.journal_volume / _citation.page_first / _citation.page_last

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Mitochondrial frataxin-like protein
B: Mitochondrial frataxin-like protein
C: Mitochondrial frataxin-like protein
D: Mitochondrial frataxin-like protein
E: Mitochondrial frataxin-like protein
F: Mitochondrial frataxin-like protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)85,78810
Polymers85,3726
Non-polymers4164
Water2,612145
1
A: Mitochondrial frataxin-like protein
D: Mitochondrial frataxin-like protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,6654
Polymers28,4572
Non-polymers2082
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1760 Å2
ΔGint-15 kcal/mol
Surface area11710 Å2
MethodPISA
2
B: Mitochondrial frataxin-like protein
C: Mitochondrial frataxin-like protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,6654
Polymers28,4572
Non-polymers2082
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1870 Å2
ΔGint-15 kcal/mol
Surface area12370 Å2
MethodPISA
3
E: Mitochondrial frataxin-like protein
F: Mitochondrial frataxin-like protein


Theoretical massNumber of molelcules
Total (without water)28,4572
Polymers28,4572
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2130 Å2
ΔGint-17 kcal/mol
Surface area10110 Å2
MethodPISA
Unit cell
Length a, b, c (Å)89.058, 89.058, 185.620
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
12A
22C
13A
23D
14A
24E
15A
25F
16B
26C
17B
27D
18B
28E
19B
29F
110C
210D
111C
211E
112C
212F
113D
213E
114D
214F
115E
215F

NCS domain segments:
Dom-IDComponent-IDEns-IDRefine codeAuth asym-IDAuth seq-ID
1010A1 - 117
2010B1 - 117
1020A0 - 117
2020C0 - 117
1030A1 - 118
2030D1 - 118
1040A1 - 118
2040E1 - 118
1050A1 - 118
2050F1 - 118
1060B1 - 117
2060C1 - 117
1070B1 - 118
2070D1 - 118
1080B1 - 118
2080E1 - 118
1090B1 - 118
2090F1 - 118
10100C1 - 118
20100D1 - 118
10110C1 - 120
20110E1 - 120
10120C1 - 120
20120F1 - 120
10130D1 - 118
20130E1 - 118
10140D1 - 118
20140F1 - 118
10150E1 - 120
20150F1 - 120

NCS ensembles :
ID
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15

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Components

#1: Protein
Mitochondrial frataxin-like protein


Mass: 14228.637 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Chaetomium thermophilum var. thermophilum DSM 1495 (fungus)
Gene: CTHT_0015430 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: G0S1Z8
#2: Chemical
ChemComp-MLA / MALONIC ACID / DICARBOXYLIC ACID C3 / PROPANEDIOLIC ACID / METHANEDICARBOXYLIC ACID / Malonic acid


Mass: 104.061 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Formula: C3H4O4
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 145 / 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: 44.54 % / Description: Large rectangle
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 2.4 M Sodium malonate and 0.1 M BIS-TRIS propane pH 7.0
PH range: 6-7 / Temp details: 293

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Data collection

DiffractionMean temperature: 100 K / Ambient temp details: no detail nitogen cooled
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I24 / Wavelength: 0.96861 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Oct 20, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.96861 Å / Relative weight: 1
ReflectionResolution: 2.03→80.29 Å / Num. obs: 48810 / % possible obs: 100 % / Redundancy: 1 % / Biso Wilson estimate: 33.45 Å2 / CC1/2: 1 / Rmerge(I) obs: 0.079 / Net I/σ(I): 15.1
Reflection shellResolution: 2.03→2.106 Å / Num. unique obs: 48810 / Rpim(I) all: 0.8 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.8.0158refinement
iMOSFLM7.2.1data reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: SAD / Resolution: 2.03→80.29 Å / Cor.coef. Fo:Fc: 0.955 / Cor.coef. Fo:Fc free: 0.949 / Cross valid method: THROUGHOUT / ESU R: 0.211 / ESU R Free: 0.183 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.25956 2444 5 %RANDOM
Rwork0.21876 ---
obs0.22079 46368 99.96 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 39.341 Å2
Baniso -1Baniso -2Baniso -3
1-0.95 Å20 Å20 Å2
2--0.95 Å20 Å2
3----1.89 Å2
Refinement stepCycle: 1 / Resolution: 2.03→80.29 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5209 0 28 145 5382
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.025326
X-RAY DIFFRACTIONr_bond_other_d00.024772
X-RAY DIFFRACTIONr_angle_refined_deg1.6541.9867262
X-RAY DIFFRACTIONr_angle_other_deg3.813311049
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.9585675
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.95525.721229
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.86215845
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.7241519
X-RAY DIFFRACTIONr_chiral_restr0.1020.2839
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.0215974
X-RAY DIFFRACTIONr_gen_planes_other0.0110.02973
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it3.4334.032731
X-RAY DIFFRACTIONr_mcbond_other3.424.0282726
X-RAY DIFFRACTIONr_mcangle_it4.8426.0133393
X-RAY DIFFRACTIONr_mcangle_other4.8426.0133394
X-RAY DIFFRACTIONr_scbond_it4.0684.1992595
X-RAY DIFFRACTIONr_scbond_other4.0434.1982593
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other5.8486.1773869
X-RAY DIFFRACTIONr_long_range_B_refined7.69245.4445640
X-RAY DIFFRACTIONr_long_range_B_other7.69445.4195626
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Weight position: 0.05

Ens-IDDom-IDAuth asym-IDNumberRms dev position (Å)
11A66440.1
12B66440.1
21A68780.07
22C68780.07
31A64360.09
32D64360.09
41A62980.08
42E62980.08
51A63460.07
52F63460.07
61B66080.11
62C66080.11
71B66160.07
72D66160.07
81B62400.08
82E62400.08
91B62380.08
92F62380.08
101C64320.1
102D64320.1
111C63300.09
112E63300.09
121C63700.08
122F63700.08
131D62780.08
132E62780.08
141D62640.09
142F62640.09
151E64300.08
152F64300.08
LS refinement shellResolution: 2.034→2.087 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.356 174 -
Rwork0.291 3350 -
obs--99.97 %

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