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- PDB-2puo: Crystal srtucture of the NEM modified ferredoxin:thioredoxin reductase -

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Basic information

Entry
Database: PDB / ID: 2puo
TitleCrystal srtucture of the NEM modified ferredoxin:thioredoxin reductase
Components(Ferredoxin-thioredoxin reductase, ...) x 2
KeywordsELECTRON TRANSPORT / Thioredoxin / redox / iron-sulfur
Function / homology
Function and homology information


ferredoxin-thioredoxin reductase activity / ferredoxin:thioredoxin reductase / oxidoreductase activity, acting on iron-sulfur proteins as donors / photosynthesis / 4 iron, 4 sulfur cluster binding / oxidoreductase activity / electron transfer 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
N-ETHYLMALEIMIDE / IRON/SULFUR CLUSTER / Ferredoxin-thioredoxin reductase, catalytic chain / Ferredoxin-thioredoxin reductase, variable chain
Similarity search - Component
Biological speciesSynechocystis sp. (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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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)21,3525
Polymers20,7802
Non-polymers5733
Water1,67593
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2530 Å2
ΔGint-40 kcal/mol
Surface area9660 Å2
MethodPISA
Unit cell
Length a, b, c (Å)44.650, 53.595, 79.393
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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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: 12453.121 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: 8326.545 Da / Num. of mol.: 1
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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Non-polymers , 4 types, 96 molecules

#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#4: Chemical ChemComp-SF4 / IRON/SULFUR CLUSTER


Mass: 351.640 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Fe4S4
#5: Chemical ChemComp-NEQ / N-ETHYLMALEIMIDE


Mass: 125.125 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H7NO2
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 93 / 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: 2.28 Å3/Da / Density % sol: 46.16 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 5.4
Details: pH 5.4, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.2.1 / Wavelength: 1.0781 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Jan 1, 2004
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0781 Å / Relative weight: 1
ReflectionResolution: 1.7→50 Å / Num. obs: 20362 / % possible obs: 93.9 % / Redundancy: 6.6 % / Biso Wilson estimate: 26.98 Å2 / Rmerge(I) obs: 0.06 / Χ2: 1.4 / Net I/σ(I): 18.3
Reflection shell
Resolution (Å)Rmerge(I) obsNum. unique allΧ2% possible all
1.7-1.760.512821.03560.6
1.76-1.830.42617901.08384.7
1.83-1.910.36920741.22196.9
1.91-2.020.25821201.36798.9
2.02-2.140.17221261.48499.1
2.14-2.310.12321271.54799.3
2.31-2.540.09221531.60599.7
2.54-2.910.06921821.576100
2.91-3.660.04622111.389100
3.66-500.04222971.30698.3

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
CNSrefinement
PDB_EXTRACT2data extraction
ADSCQuantumdata collection
HKL-2000data reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.7→500 Å / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.255 986 4.6 %Random 5%
Rwork0.234 ---
obs-20302 94 %-
Solvent computationBsol: 51.279 Å2
Displacement parametersBiso mean: 40.528 Å2
Baniso -1Baniso -2Baniso -3
1--5.809 Å20 Å20 Å2
2---7.452 Å20 Å2
3---13.261 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.3 Å0.26 Å
Luzzati d res low-5 Å
Luzzati sigma a0.3 Å0.28 Å
Refinement stepCycle: LAST / Resolution: 1.7→500 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1453 0 22 93 1568
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_angle_deg1.11.5
X-RAY DIFFRACTIONc_bond_d0.0052
X-RAY DIFFRACTIONc_dihedral_angle_d22.72
X-RAY DIFFRACTIONc_scangle_it0.732.5
LS refinement shellResolution: 1.7→1.81 Å / Rfactor Rfree error: 0.037
RfactorNum. reflection% reflection
Rfree0.394 116 -
Rwork0.355 --
obs-2316 68.9 %
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
X-RAY DIFFRACTION5neq.par

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