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- PDB-7akt: CrPetF variant - A39G_A41V -

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Basic information

Entry
Database: PDB / ID: 7akt
TitleCrPetF variant - A39G_A41V
ComponentsFerredoxin, chloroplastic
KeywordsELECTRON TRANSPORT / ferredoxin
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 / Ferredoxin, chloroplastic
Similarity search - Component
Biological speciesChlamydomonas reinhardtii (plant)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.11 Å
AuthorsKurisu, G. / Ohnishi, Y. / Engelbrecht, V. / Happe, T.
Funding support Germany, 2items
OrganizationGrant numberCountry
German Research Foundation (DFG)GRK 2341 Germany
Volkswagen FoundationLigH2t Germany
CitationJournal: To Be Published
Title: Ferredoxin 2.0: an electron transfer protein designed into a photosystem I-driven hydrogenase
Authors: Engelbrecht, V. / Hemschemeier, A. / Heghmanns, M. / Thomsen, J. / Rutz, A. / Yadav, S. / Ohnishi, Y. / Apfel, U.-P. / Kasanmascheff, M. / Kurisu, G. / Happe, T.
History
DepositionOct 2, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 13, 2021Provider: repository / Type: Initial release
Revision 1.1Jan 31, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / diffrn_source / pdbx_initial_refinement_model
Item: _diffrn_source.pdbx_synchrotron_site

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Ferredoxin, chloroplastic
hetero molecules


Theoretical massNumber of molelcules
Total (without water)12,1916
Polymers11,7161
Non-polymers4755
Water1,40578
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area710 Å2
ΔGint-25 kcal/mol
Surface area6230 Å2
Unit cell
Length a, b, c (Å)25.966, 51.231, 32.255
Angle α, β, γ (deg.)90.00, 112.13, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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Protein , 1 types, 1 molecules A

#1: Protein Ferredoxin, chloroplastic


Mass: 11715.953 Da / Num. of mol.: 1 / Mutation: A39G, A41V
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Chlamydomonas reinhardtii (plant) / Gene: PETF / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): Rosetta / References: UniProt: P07839

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Non-polymers , 5 types, 83 molecules

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


Mass: 175.820 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Fe2S2 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-BEN / BENZAMIDINE


Mass: 120.152 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C7H8N2
#4: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#5: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 78 / 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: 1.7 Å3/Da / Density % sol: 27.49 %
Crystal growTemperature: 281.15 K / Method: vapor diffusion, hanging drop / pH: 5.6
Details: 2 % (w/v) benzamidine hydrochloride, 1.8 M (NH4)2SO4 and 0.2 M NaSCN in 0.1 M sodium citrate buffer

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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: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jun 19, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9 Å / Relative weight: 1
ReflectionResolution: 1.11→25.9 Å / Num. obs: 31128 / % possible obs: 99.4 % / Redundancy: 3.38 % / CC1/2: 0.997 / Rmerge(I) obs: 0.065 / Net I/σ(I): 8.92
Reflection shellResolution: 1.11→1.14 Å / Rmerge(I) obs: 0.783 / Num. unique obs: 2302 / CC1/2: 0.566

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Processing

Software
NameVersionClassification
XDSdata processing
XDSdata reduction
XSCALEdata scaling
PHENIXphasing
PHENIXVersion 1.14-3260refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6LK1

6lk1


Resolution: 1.11→25.81 Å / SU ML: 0.17 / Cross valid method: NONE / σ(F): 1.55 / Phase error: 20.11 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1913 3140 10.1 %
Rwork0.175 --
obs0.1767 31103 98.66 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.11→25.81 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms779 0 24 78 881
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.007889
X-RAY DIFFRACTIONf_angle_d1.2471221
X-RAY DIFFRACTIONf_dihedral_angle_d9.806458
X-RAY DIFFRACTIONf_chiral_restr0.083133
X-RAY DIFFRACTIONf_plane_restr0.006167
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.11-1.12010.56641020.55321025X-RAY DIFFRACTION79
1.1201-1.13840.40361540.40361269X-RAY DIFFRACTION99
1.1384-1.15810.37161310.34761271X-RAY DIFFRACTION100
1.1581-1.17910.28141520.281294X-RAY DIFFRACTION99
1.1791-1.20180.25831480.24731226X-RAY DIFFRACTION100
1.2018-1.22630.27491370.22671307X-RAY DIFFRACTION100
1.2263-1.2530.22431390.21111277X-RAY DIFFRACTION100
1.253-1.28220.20441460.19921295X-RAY DIFFRACTION99
1.2822-1.31420.21131500.20131261X-RAY DIFFRACTION100
1.3142-1.34980.21991400.19891283X-RAY DIFFRACTION100
1.3498-1.38950.20371470.19571275X-RAY DIFFRACTION100
1.3895-1.43430.20791440.18421305X-RAY DIFFRACTION100
1.4343-1.48560.17421350.16481268X-RAY DIFFRACTION100
1.4856-1.5450.17831490.15931280X-RAY DIFFRACTION100
1.545-1.61530.15431520.15421280X-RAY DIFFRACTION99
1.6153-1.70050.17281420.15261288X-RAY DIFFRACTION100
1.7005-1.8070.18291430.15231276X-RAY DIFFRACTION100
1.807-1.94650.16841470.15361285X-RAY DIFFRACTION100
1.9465-2.14230.15651460.15351296X-RAY DIFFRACTION100
2.1423-2.45210.16641380.15871292X-RAY DIFFRACTION100
2.4521-3.08850.21841460.17121293X-RAY DIFFRACTION100
3.0885-25.810.17381520.15941317X-RAY DIFFRACTION99

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