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- PDB-2pvo: Crystal srtucture of the ternary complex between thioredoxin f, f... -

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Basic information

Entry
Database: PDB / ID: 2pvo
TitleCrystal srtucture of the ternary complex between thioredoxin f, ferredoxin, and ferredoxin: thioredoxin reductase
Components
  • (Ferredoxin-thioredoxin reductase, ...) x 2
  • Ferredoxin-1
  • Thioredoxin F-type, chloroplast
KeywordsELECTRON TRANSPORT / Thioredoxin / ferredoxin. redox / iron-sulfur cluster / protein-protein complex
Function / homology
Function and homology information


ferredoxin-thioredoxin reductase activity / ferredoxin:thioredoxin reductase / oxidoreductase activity, acting on iron-sulfur proteins as donors / photosynthesis / chloroplast / 2 iron, 2 sulfur cluster binding / 4 iron, 4 sulfur cluster binding / electron transfer activity / oxidoreductase activity / metal ion binding
Similarity search - Function
Ferredoxin Thioredoxin Reductase / Ferredoxin thioredoxin reductase catalytic beta subunit / Ferredoxin-thioredoxin reductase catalytic subunit, cyanobacteria-type / Ferredoxin thioredoxin reductase, alpha chain / Ferredoxin-thioredoxin reductase, variable chain / Ferredoxin thioredoxin reductase variable alpha chain / Ferredoxin thioredoxin reductase catalytic beta subunit / Ferredoxin thioredoxin reductase catalytic beta subunit superfamily / Ferredoxin thioredoxin reductase catalytic beta chain / Ferredoxin [2Fe-2S], plant ...Ferredoxin Thioredoxin Reductase / Ferredoxin thioredoxin reductase catalytic beta subunit / Ferredoxin-thioredoxin reductase catalytic subunit, cyanobacteria-type / Ferredoxin thioredoxin reductase, alpha chain / Ferredoxin-thioredoxin reductase, variable chain / Ferredoxin thioredoxin reductase variable alpha chain / Ferredoxin thioredoxin reductase catalytic beta subunit / Ferredoxin thioredoxin reductase catalytic beta subunit superfamily / Ferredoxin thioredoxin reductase catalytic beta chain / Ferredoxin [2Fe-2S], plant / SH3 type barrels. - #50 / Electron transport accessory-like domain superfamily / 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 / Thioredoxin / Thioredoxin, conserved site / Thioredoxin family active site. / 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 / Thioredoxin domain profile. / Thioredoxin domain / Glutaredoxin / Glutaredoxin / SH3 type barrels. / Ubiquitin-like (UB roll) / Thioredoxin-like superfamily / Roll / Roll / Alpha-Beta Complex / 3-Layer(aba) Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
FE2/S2 (INORGANIC) CLUSTER / IRON/SULFUR CLUSTER / Thioredoxin F-type, chloroplastic / Ferredoxin-1 / Ferredoxin-thioredoxin reductase, catalytic chain / Ferredoxin-thioredoxin reductase, variable chain
Similarity search - Component
Biological speciesSynechocystis sp. (bacteria)
Spinacia oleracea (spinach)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.4 Å
AuthorsDai, S.
CitationJournal: Nature / Year: 2007
Title: Structural snapshots along the reaction pathway of ferredoxin-thioredoxin reductase.
Authors: Dai, S. / Friemann, R. / Glauser, D.A. / Bourquin, F. / Manieri, W. / Schurmann, P. / Eklund, H.
History
DepositionMay 9, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 10, 2007Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 18, 2017Group: Refinement description / Category: software
Item: _software.classification / _software.contact_author ..._software.classification / _software.contact_author / _software.contact_author_email / _software.date / _software.language / _software.location / _software.name / _software.type / _software.version
Revision 1.4Oct 20, 2021Group: Database references / Derived calculations
Category: database_2 / struct_conn ...database_2 / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Ferredoxin-thioredoxin reductase, catalytic chain
B: Ferredoxin-thioredoxin reductase, variable chain
C: Thioredoxin F-type, chloroplast
D: Ferredoxin-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,3288
Polymers43,6084
Non-polymers7204
Water0
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5950 Å2
ΔGint-92 kcal/mol
Surface area18300 Å2
MethodPISA
Unit cell
Length a, b, c (Å)130.426, 130.426, 63.837
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number154
Space group name H-MP3221

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Components

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Ferredoxin-thioredoxin reductase, ... , 2 types, 2 molecules AB

#1: Protein Ferredoxin-thioredoxin reductase, catalytic chain /


Mass: 12541.291 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Synechocystis sp. (bacteria) / Gene: ftrC / Plasmid: pET-3C / Species (production host): Escherichia coli / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: UniProt: Q55389
#2: Protein Ferredoxin-thioredoxin reductase, variable chain / / FTR-V / Ferredoxin- thioredoxin reductase subunit A


Mass: 8455.659 Da / Num. of mol.: 1 / Mutation: C49S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Synechocystis sp. (bacteria) / Gene: ftrV / Plasmid: pET-3C / Species (production host): Escherichia coli / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: UniProt: Q55781

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Protein , 2 types, 2 molecules CD

#3: Protein Thioredoxin F-type, chloroplast / TRX-F


Mass: 12360.387 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Spinacia oleracea (spinach) / Plasmid: pET-3C / Species (production host): Escherichia coli / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: UniProt: P09856
#4: Protein Ferredoxin-1 / / Ferredoxin I


Mass: 10251.063 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Synechocystis sp. (bacteria) / Gene: petF, fed / Production host: Escherichia coli (E. coli) / References: UniProt: P27320

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Non-polymers , 3 types, 4 molecules

#5: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#6: Chemical ChemComp-SF4 / IRON/SULFUR CLUSTER / Iron–sulfur cluster


Mass: 351.640 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Fe4S4
#7: Chemical ChemComp-FES / FE2/S2 (INORGANIC) CLUSTER / Iron–sulfur cluster


Mass: 175.820 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Fe2S2

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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: 3.59 Å3/Da / Density % sol: 65.76 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.6
Details: pH 5.6, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.2.1 / Wavelength: 0.9797 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Feb 3, 2006
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9797 Å / Relative weight: 1
ReflectionResolution: 3.3→50 Å / Num. obs: 9413 / % possible obs: 97 % / Redundancy: 8.2 % / Rmerge(I) obs: 0.195 / Χ2: 1.067 / Net I/σ(I): 4.5
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2% possible all
3.3-3.4270.6759550.84399.5
3.42-3.558.40.5369650.9299.4
3.55-3.7290.4469490.98899.4
3.72-3.918.90.3159341.05999.3
3.91-4.168.80.2539611.05999.2
4.16-4.488.60.1819291.12696.9
4.48-4.938.30.1599281.19696.3
4.93-5.648.10.1439281.14596.2
5.64-7.180.1259461.13295.7
7.1-507.20.0699181.20789.1

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
CNSrefinement
PDB_EXTRACT2data extraction
ADSCQuantumdata collection
HKL-2000data reduction
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.4→15 Å / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.263 534 6.1 %RANDOM 6%
Rwork0.202 ---
obs-8467 97 %-
Solvent computationBsol: 13.549 Å2
Displacement parametersBiso mean: 48.174 Å2
Baniso -1Baniso -2Baniso -3
1--3.882 Å2-18.994 Å20 Å2
2---3.882 Å20 Å2
3---7.764 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.45 Å0.32 Å
Luzzati d res low-5 Å
Luzzati sigma a0.44 Å0.37 Å
Refinement stepCycle: LAST / Resolution: 3.4→15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3049 0 22 0 3071
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.0081.5
X-RAY DIFFRACTIONc_angle_deg1.32
X-RAY DIFFRACTIONc_dihedral_angle_d23.82
X-RAY DIFFRACTIONc_improper_angle_d0.852.5
LS refinement shellResolution: 3.4→3.61 Å / Rfactor Rfree error: 0.033
RfactorNum. reflection% reflection
Rfree0.306 85 -
Rwork0.24 --
obs-1345 99.4 %
Xplor file
Refine-IDSerial noParam file
X-RAY DIFFRACTION1CNS_TOPPAR:protein_rep.param
X-RAY DIFFRACTION2CNS_TOPPAR:water_rep.param
X-RAY DIFFRACTION3CNS_TOPPAR:ion.param
X-RAY DIFFRACTION4fs4.par.new
X-RAY DIFFRACTION5fs2.par.new

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