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- PDB-6lk1: Ultrahigh resolution X-ray structure of Ferredoxin I from C. rein... -

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Basic information

Entry
Database: PDB / ID: 6lk1
TitleUltrahigh resolution X-ray structure of Ferredoxin I from C. reinhardtii
ComponentsFerredoxin, chloroplastic
KeywordsELECTRON TRANSPORT / [2Fe2S] cluster
Function / homology
Function and homology information


iron-sulfur cluster binding / chloroplast / electron transport chain / 2 iron, 2 sulfur cluster binding / electron transfer activity / metal ion binding
Similarity search - Function
Ferredoxin, chloroplast transit peptide / Ferredoxin chloroplastic transit peptide / 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 / THIOCYANATE ION / Ferredoxin, chloroplastic
Similarity search - Component
Biological speciesChlamydomonas reinhardtii (plant)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 0.9 Å
AuthorsOnishi, Y. / Kurisu, G. / Tanaka, H.
Funding support Japan, 1items
OrganizationGrant numberCountry
Ministry of Education, Culture, Sports, Science and Technology (Japan) Japan
CitationJournal: J.Biochem. / Year: 2020
Title: X-ray dose-dependent structural changes of the [2Fe-2S] ferredoxin from Chlamydomonas reinhardtii.
Authors: Ohnishi, Y. / Muraki, N. / Kiyota, D. / Okumura, H. / Baba, S. / Kawano, Y. / Kumasaka, T. / Tanaka, H. / Kurisu, G.
History
DepositionDec 17, 2019Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0May 27, 2020Provider: repository / Type: Initial release
Revision 1.1Jun 10, 2020Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
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, chloroplastic
B: Ferredoxin, chloroplastic
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,67716
Polymers19,9702
Non-polymers1,70714
Water2,828157
1
A: Ferredoxin, chloroplastic
hetero molecules


Theoretical massNumber of molelcules
Total (without water)11,03610
Polymers9,9851
Non-polymers1,0519
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area250 Å2
ΔGint-17 kcal/mol
Surface area4710 Å2
MethodPISA
2
B: Ferredoxin, chloroplastic
hetero molecules


Theoretical massNumber of molelcules
Total (without water)10,6416
Polymers9,9851
Non-polymers6565
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area250 Å2
ΔGint-17 kcal/mol
Surface area4780 Å2
MethodPISA
Unit cell
Length a, b, c (Å)25.955, 60.090, 50.085
Angle α, β, γ (deg.)90.000, 102.400, 90.000
Int Tables number4
Space group name H-MP1211

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein Ferredoxin, chloroplastic


Mass: 9984.993 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Chlamydomonas reinhardtii (plant) / Gene: PETF / Production host: Escherichia coli (E. coli) / References: UniProt: P07839

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Non-polymers , 5 types, 171 molecules

#2: Chemical ChemComp-FES / FE2/S2 (INORGANIC) CLUSTER


Mass: 175.820 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Fe2S2 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical
ChemComp-BEN / BENZAMIDINE


Mass: 120.152 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: C7H8N2
#4: Chemical ChemComp-SCN / THIOCYANATE ION


Mass: 58.082 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: CNS
#5: Chemical ChemComp-SO4 / SULFATE ION


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


Mass: 18.015 Da / Num. of mol.: 157 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY

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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: 1.91 Å3/Da / Density % sol: 35.61 %
Crystal growTemperature: 298 K / Method: vapor diffusion
Details: Ammonium sulfate Sodium citrate Sodium thiocyanate Benzamidine Hydrochloride

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL44XU / Wavelength: 0.9 Å
DetectorType: RAYONIX MX300HE / Detector: CCD / Date: Jan 17, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9 Å / Relative weight: 1
ReflectionResolution: 0.9→37.96 Å / Num. obs: 109765 / % possible obs: 99.2 % / Redundancy: 4.736 % / Rmerge(I) obs: 0.061 / Net I/σ(I): 12.9
Reflection shellResolution: 0.9→0.92 Å / Redundancy: 3.188 % / Rmerge(I) obs: 0.729 / Mean I/σ(I) obs: 1.7 / Num. unique obs: 7995 / Rrim(I) all: 0.35 / % possible all: 97.6

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Processing

Software
NameVersionClassification
SHELXrefinement
PDB_EXTRACT3.25data extraction
MOSFLMdata reduction
Aimlessdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1AWD

1awd


Resolution: 0.9→37.96 Å / Cross valid method: THROUGHOUT
RfactorNum. reflection% reflectionSelection details
Rfree0.1713 --every 12th reflection was excluded for R-free calculation
Rwork0.1449 ---
obs-109765 99.2 %-
Displacement parametersBiso max: 136.17 Å2 / Biso min: 3.93 Å2
Refinement stepCycle: LAST / Resolution: 0.9→37.96 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1377 0 106 157 1640

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