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- PDB-6jo2: Ferredoxin I from Thermosynechococcus elongatus -

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Basic information

Entry
Database: PDB / ID: 6jo2
TitleFerredoxin I from Thermosynechococcus elongatus
ComponentsFerredoxin-1
KeywordsELECTRON TRANSPORT / Photosynthesis
Function / homology
Function and homology information


2 iron, 2 sulfur cluster binding / electron transfer activity / metal ion binding
Similarity search - Function
Ferredoxin [2Fe-2S], plant / 2Fe-2S ferredoxin, iron-sulphur binding site / 2Fe-2S ferredoxin-type iron-sulfur binding region signature. / 2Fe-2S iron-sulfur cluster binding domain / Beta-grasp domain superfamily / 2Fe-2S ferredoxin-type iron-sulfur binding domain profile. / 2Fe-2S ferredoxin-type iron-sulfur binding domain / 2Fe-2S ferredoxin-like superfamily
Similarity search - Domain/homology
BENZAMIDINE / FE2/S2 (INORGANIC) CLUSTER / Ferredoxin-1
Similarity search - Component
Biological speciesThermosynechococcus elongatus BP-1 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.55 Å
AuthorsMotomura, T.
CitationJournal: Biochim Biophys Acta Bioenerg / Year: 2019
Title: An alternative plant-like cyanobacterial ferredoxin with unprecedented structural and functional properties.
Authors: Motomura, T. / Zuccarello, L. / Setif, P. / Boussac, A. / Umena, Y. / Lemaire, D. / Tripathy, J.N. / Sugiura, M. / Hienerwadel, R. / Shen, J.R. / Berthomieu, C.
History
DepositionMar 19, 2019Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Sep 18, 2019Provider: repository / Type: Initial release
Revision 1.1Dec 11, 2019Group: Database references / Category: citation
Item: _citation.journal_id_ISSN / _citation.journal_volume ..._citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title
Revision 2.0Aug 18, 2021Group: Atomic model / Data collection ...Atomic model / Data collection / Database references / Derived calculations / Non-polymer description / Structure summary
Category: atom_site / atom_site_anisotrop ...atom_site / atom_site_anisotrop / chem_comp / database_2 / entity / pdbx_entity_nonpoly / pdbx_nonpoly_scheme / struct_site / struct_site_gen
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_comp_id / _atom_site.label_comp_id / _atom_site_anisotrop.U[1][1] / _atom_site_anisotrop.U[1][2] / _atom_site_anisotrop.U[1][3] / _atom_site_anisotrop.U[2][2] / _atom_site_anisotrop.U[2][3] / _atom_site_anisotrop.U[3][3] / _atom_site_anisotrop.pdbx_auth_comp_id / _atom_site_anisotrop.pdbx_label_comp_id / _chem_comp.formula / _chem_comp.formula_weight / _chem_comp.id / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _entity.formula_weight / _pdbx_entity_nonpoly.comp_id / _pdbx_nonpoly_scheme.mon_id / _pdbx_nonpoly_scheme.pdb_mon_id / _struct_site.details / _struct_site.pdbx_auth_comp_id / _struct_site_gen.auth_comp_id / _struct_site_gen.label_comp_id
Revision 2.1Nov 22, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Ferredoxin-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)11,2355
Polymers10,7231
Non-polymers5124
Water1,72996
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: mass spectrometry
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area240 Å2
ΔGint-16 kcal/mol
Surface area5090 Å2
MethodPISA
Unit cell
Length a, b, c (Å)56.172, 53.222, 32.293
Angle α, β, γ (deg.)90.000, 92.670, 90.000
Int Tables number5
Space group name H-MC121

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Components

#1: Protein Ferredoxin-1 / / Ferredoxin I


Mass: 10722.764 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermosynechococcus elongatus BP-1 (bacteria)
Gene: petF1, petF, tsl1009
Production host: Thermosynechococcus elongatus BP-1 (bacteria)
References: UniProt: P0A3C9
#2: Chemical ChemComp-BEN / BENZAMIDINE / Benzamidine


Mass: 120.152 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C7H8N2
#3: Chemical ChemComp-FES / FE2/S2 (INORGANIC) CLUSTER / Iron–sulfur cluster


Mass: 175.820 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Fe2S2
#4: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 96 / 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: 2.25 Å3/Da / Density % sol: 45.3 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 100 mM Sodium Citrate (pH 6.5) 2.5 M ammonium Sulfate 0.2%(w/v) benzamidine hydrochloride 3%(w/v) 1,6-hexanediol

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL41XU / Wavelength: 1 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Feb 9, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.55→38.61 Å / Num. obs: 13408 / % possible obs: 96.5 % / Redundancy: 3.3 % / Net I/σ(I): 12.04
Reflection shell
Resolution (Å)Redundancy (%)Mean I/σ(I) obsNum. unique obsDiffraction-ID% possible all
1.55-1.642.952.91983190.1
1.64-1.751
1.75-1.91
1.9-2.081
2.08-2.321
2.32-2.681
2.68-3.271
3.27-4.611
4.61-38.611

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
REFMAC5.8.0073refinement
XDSdata reduction
XSCALEdata scaling
MOLREPphasing
PDB_EXTRACT3.24data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5AUI

5aui


Resolution: 1.55→38.61 Å / Cor.coef. Fo:Fc: 0.971 / Cor.coef. Fo:Fc free: 0.957 / WRfactor Rfree: 0.1783 / WRfactor Rwork: 0.1339 / FOM work R set: 0.8757 / SU B: 3.321 / SU ML: 0.053 / SU R Cruickshank DPI: 0.1031 / SU Rfree: 0.0771 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.103 / ESU R Free: 0.077 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.1759 655 4.9 %RANDOM
Rwork0.1327 ---
obs0.1349 12752 96.51 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 54.46 Å2 / Biso mean: 14.938 Å2 / Biso min: 4.26 Å2
Baniso -1Baniso -2Baniso -3
1--0.67 Å20 Å2-0.59 Å2
2--1.74 Å20 Å2
3----1.01 Å2
Refinement stepCycle: final / Resolution: 1.55→38.61 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms748 0 27 97 872
Biso mean--23.68 29.39 -
Num. residues----97
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.022895
X-RAY DIFFRACTIONr_bond_other_d00.02801
X-RAY DIFFRACTIONr_angle_refined_deg1.4081.9841225
X-RAY DIFFRACTIONr_angle_other_deg1.0112.9831871
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.925122
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.71426.66745
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.26315154
X-RAY DIFFRACTIONr_dihedral_angle_4_deg25.09154
X-RAY DIFFRACTIONr_chiral_restr0.1180.2138
X-RAY DIFFRACTIONr_gen_planes_refined0.0120.021058
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02182
X-RAY DIFFRACTIONr_rigid_bond_restr5.49331696
X-RAY DIFFRACTIONr_sphericity_free32.914523
X-RAY DIFFRACTIONr_sphericity_bonded8.66351744
LS refinement shellResolution: 1.548→1.588 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.343 24 -
Rwork0.217 820 -
all-844 -
obs--86.3 %
Refinement TLS params.Method: refined / Origin x: -15.912 Å / Origin y: -0.1129 Å / Origin z: 1.8159 Å
111213212223313233
T0.0158 Å20.003 Å2-0.0033 Å2-0.0035 Å2-0.0038 Å2--0.0461 Å2
L0.4441 °20.1969 °2-0.2533 °2-0.253 °20.1243 °2--0.6061 °2
S-0.02 Å °0.0055 Å °0.0293 Å °0.0063 Å °-0.0105 Å °-0.0047 Å °0.0366 Å °-0.0306 Å °0.0305 Å °

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