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- PDB-6iri: Crystal structure of the minor ferredoxin from Thermosynechococcu... -

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Basic information

Entry
Database: PDB / ID: 6iri
TitleCrystal structure of the minor ferredoxin from Thermosynechococcus elongatus
ComponentsFerredoxin
KeywordsELECTRON TRANSPORT / PHOTOSYNTHESIS
Function / homology
Function and homology information


electron transport chain / 2 iron, 2 sulfur cluster binding / electron transfer activity / metal ion binding
Similarity search - Function
Ferredoxin [2Fe-2S], plant / 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
FE2/S2 (INORGANIC) CLUSTER / Ferredoxin
Similarity search - Component
Biological speciesThermosynechococcus elongatus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.38 Å
AuthorsMotomura, T. / Shen, J.R. / Umena, Y.
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
DepositionNov 13, 2018Deposition 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 1.2Nov 22, 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

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Assembly

Deposited unit
A: Ferredoxin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)12,1483
Polymers11,8761
Non-polymers2722
Water1,964109
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 area5790 Å2
MethodPISA
Unit cell
Length a, b, c (Å)27.946, 51.121, 31.570
Angle α, β, γ (deg.)90.000, 116.150, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Ferredoxin


Mass: 11876.442 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Thermosynechococcus elongatus (strain BP-1) (bacteria)
Strain: BP-1 / References: UniProt: Q8DJI7
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: SO4
#3: Chemical ChemComp-FES / FE2/S2 (INORGANIC) CLUSTER


Mass: 175.820 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Fe2S2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 109 / 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: 1.72 Å3/Da / Density % sol: 28.63 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5 / Details: 100 mM HEPES (pH 7.5), 2.4 M ammonium sulfate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL38B1 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Jan 31, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.38→28.34 Å / Num. obs: 16325 / % possible obs: 99.3 % / Redundancy: 3.68 % / CC1/2: 0.999 / Rmerge(I) obs: 0.056 / Net I/σ(I): 12.82
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsCC1/2% possible all
1.38-1.473.620.585225930.71898.9
1.47-1.57
1.57-1.69
1.69-1.85
1.85-2.07
2.07-2.39
2.39-2.92
2.92-4.11
4.11-28.34

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Phasing

PhasingMethod: molecular replacement
Phasing MRR rigid body: 0.599
Highest resolutionLowest resolution
Rotation25.56 Å1.52 Å

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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: 1.38→28.34 Å / Cor.coef. Fo:Fc: 0.986 / Cor.coef. Fo:Fc free: 0.98 / SU B: 2.696 / SU ML: 0.047 / SU R Cruickshank DPI: 0.0626 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.063 / ESU R Free: 0.056
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.157 793 4.9 %RANDOM
Rwork0.1124 ---
obs0.1146 15531 99.7 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 78.61 Å2 / Biso mean: 18.168 Å2 / Biso min: 6.68 Å2
Baniso -1Baniso -2Baniso -3
1--0.03 Å20 Å2-0.32 Å2
2--1.18 Å20 Å2
3----0.57 Å2
Refinement stepCycle: final / Resolution: 1.38→28.34 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms821 0 9 114 944
Biso mean--28.76 35.56 -
Num. residues----107
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0210.019924
X-RAY DIFFRACTIONr_bond_other_d0.0010.02856
X-RAY DIFFRACTIONr_angle_refined_deg2.0861.9571261
X-RAY DIFFRACTIONr_angle_other_deg1.1543.0041976
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.4485124
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.0322542
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.44615150
X-RAY DIFFRACTIONr_dihedral_angle_4_deg10.182155
X-RAY DIFFRACTIONr_chiral_restr0.1320.2145
X-RAY DIFFRACTIONr_gen_planes_refined0.010.021095
X-RAY DIFFRACTIONr_gen_planes_other0.0040.02204
X-RAY DIFFRACTIONr_rigid_bond_restr9.15931780
X-RAY DIFFRACTIONr_sphericity_free39.356535
X-RAY DIFFRACTIONr_sphericity_bonded10.8651831
LS refinement shellResolution: 1.382→1.418 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.228 67 -
Rwork0.226 1097 -
all-1164 -
obs--98.81 %
Refinement TLS params.Method: refined / Origin x: 2.811 Å / Origin y: -0.7295 Å / Origin z: 12.3016 Å
111213212223313233
T0.02 Å2-0.0004 Å2-0.0044 Å2-0.0005 Å20.0008 Å2--0.0383 Å2
L0.6819 °2-0.0285 °20.2764 °2-0.2802 °20.1528 °2--0.5518 °2
S-0.008 Å °0.0136 Å °0.0103 Å °-0.0013 Å °0.0059 Å °-0.0209 Å °-0.0085 Å °0.0051 Å °0.002 Å °

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