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- PDB-1dj7: CRYSTAL STRUCTURE OF FERREDOXIN THIOREDOXIN REDUCTASE -

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Basic information

Entry
Database: PDB / ID: 1dj7
TitleCRYSTAL STRUCTURE OF FERREDOXIN THIOREDOXIN REDUCTASE
Components
  • FERREDOXIN THIOREDOXIN REDUCTASE: CATALYTIC CHAIN
  • FERREDOXIN THIOREDOXIN REDUCTASE: VARIABLE CHAIN
KeywordsELECTRON TRANSPORT / 4FE-4S CLUSTER BINDING FOLD WITH CXCX16CXCX8CXC BINDING MOTIF
Function / homology
Function and homology information


ferredoxin:thioredoxin reductase / ferredoxin-thioredoxin reductase activity / oxidoreductase activity, acting on iron-sulfur proteins as donors / photosynthesis / 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 / SH3 type barrels. - #50 ...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 / SH3 type barrels. - #50 / Electron transport accessory-like domain superfamily / SH3 type barrels. / Roll / Alpha-Beta Complex / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
IRON/SULFUR CLUSTER / Ferredoxin-thioredoxin reductase, catalytic chain / Ferredoxin-thioredoxin reductase, variable chain
Similarity search - Component
Biological speciesSynechocystis sp. (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 1.6 Å
AuthorsDai, S. / Schwendtmayer, C. / Schurmann, P. / Ramaswamy, S. / Eklund, H.
CitationJournal: Science / Year: 2000
Title: Redox signaling in chloroplasts: cleavage of disulfides by an iron-sulfur cluster.
Authors: Dai, S. / Schwendtmayer, C. / Schurmann, P. / Ramaswamy, S. / Eklund, H.
History
DepositionDec 2, 1999Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 14, 2000Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Source and taxonomy / Version format compliance
Revision 1.3Oct 4, 2017Group: Refinement description / Category: software
Revision 1.4Oct 11, 2017Group: Data collection / Category: reflns_shell
Item: _reflns_shell.number_unique_all / _reflns_shell.percent_possible_all

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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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,2934
Polymers21,8462
Non-polymers4482
Water2,648147
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2190 Å2
ΔGint-41 kcal/mol
Surface area9240 Å2
MethodPISA
Unit cell
Length a, b, c (Å)45.296, 45.296, 172.147
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212

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Components

#1: Protein FERREDOXIN THIOREDOXIN REDUCTASE: CATALYTIC CHAIN


Mass: 13274.975 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Synechocystis sp. (bacteria) / Strain: PCC 6803 / Plasmid: PET3 / Production host: Escherichia coli (E. coli) / References: UniProt: Q55389
#2: Protein FERREDOXIN THIOREDOXIN REDUCTASE: VARIABLE CHAIN


Mass: 8570.746 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Synechocystis sp. (bacteria) / Strain: PCC 6803 / Plasmid: PET3 / Production host: Escherichia coli (E. coli) / References: UniProt: Q55781
#3: Chemical ChemComp-SF4 / IRON/SULFUR CLUSTER


Mass: 351.640 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Fe4S4
#4: Chemical ChemComp-SO4 / SULFATE ION


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


Mass: 18.015 Da / Num. of mol.: 147 / 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: 2.02 Å3/Da / Density % sol: 39.11 %
Crystal growTemperature: 297 K / Method: vapor diffusion, hanging drop / pH: 5.1
Details: AMSO4, SODIUM ACETATE, MGCL2, TRIETHANOLAMINE-CL BUFFER PH 7.3, pH 5.1, VAPOR DIFFUSION, HANGING DROP, temperature 297K
Crystal grow
*PLUS
pH: 7.3
Details: drop consists of equal volume of protein and reservoir solutions
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
117 mg/mlprotein1drop
220 mMtriethanolamine-HCl1drop
32.0 Mammonium sulfate1reservoir
42.0 Mammonium sulfate1reservoir
50.1 M1reservoirNaAc
6100 mM1reservoirMgCl2

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: EMBL/DESY, Hamburg / Beamline: BW7B / Wavelength: 0.8345
DetectorType: MARRESEARCH / Detector: AREA DETECTOR / Date: Jul 18, 1998
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.8345 Å / Relative weight: 1
ReflectionResolution: 1.5→15 Å / Num. all: 30061 / Num. obs: 26709 / % possible obs: 88.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3 % / Biso Wilson estimate: 17.6 Å2 / Rmerge(I) obs: 0.049 / Net I/σ(I): 10.93
Reflection shellResolution: 1.5→1.6 Å / Redundancy: 2.6 % / Rmerge(I) obs: 0.196 / Num. unique all: 5155

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Processing

Software
NameClassification
XDSdata scaling
XDSdata reduction
SHARPphasing
REFMACrefinement
RefinementResolution: 1.6→10 Å / σ(F): 0 / σ(I): 0 / Stereochemistry target values: ENGH & HUBER / Details: MAXIMUL LIKELYHOOD ON FS
RfactorNum. reflection% reflectionSelection details
Rfree0.278 1187 -RANDOM
Rwork0.238 ---
all0.264 23142 --
obs0.264 21955 93.9 %-
Refinement stepCycle: LAST / Resolution: 1.6→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1396 0 13 147 1556
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONp_bond_d0.01
X-RAY DIFFRACTIONp_angle_d1.8
X-RAY DIFFRACTIONp_angle_deg
X-RAY DIFFRACTIONp_planar_d
X-RAY DIFFRACTIONp_hb_or_metal_coord
X-RAY DIFFRACTIONp_mcbond_it
X-RAY DIFFRACTIONp_mcangle_it
X-RAY DIFFRACTIONp_scbond_it
X-RAY DIFFRACTIONp_scangle_it
X-RAY DIFFRACTIONp_plane_restr
X-RAY DIFFRACTIONp_chiral_restr
X-RAY DIFFRACTIONp_singtor_nbd
X-RAY DIFFRACTIONp_multtor_nbd
X-RAY DIFFRACTIONp_xhyhbond_nbd
X-RAY DIFFRACTIONp_xyhbond_nbd
X-RAY DIFFRACTIONp_planar_tor
X-RAY DIFFRACTIONp_staggered_tor
X-RAY DIFFRACTIONp_orthonormal_tor
X-RAY DIFFRACTIONp_transverse_tor
X-RAY DIFFRACTIONp_special_tor

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