[English] 日本語
Yorodumi
- PDB-2pu9: Crystal srtucture of the binary complex between ferredoxin: thior... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 2pu9
TitleCrystal srtucture of the binary complex between ferredoxin: thioredoxin reductase and thioredoxin f
Components
  • (Ferredoxin-thioredoxin reductase, ...) x 2
  • Thioredoxin F-type, chloroplast
KeywordsELECTRON TRANSPORT / Thioredoxin / protein-protein complex / 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 / protein-disulfide reductase activity / photosynthesis / chloroplast / 4 iron, 4 sulfur cluster binding / oxidoreductase activity / electron transfer activity / metal ion binding / cytosol
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 / Thioredoxin / Thioredoxin, conserved site / Thioredoxin family active site. / Thioredoxin domain profile. / Thioredoxin domain / Glutaredoxin / Glutaredoxin / SH3 type barrels. / Thioredoxin-like superfamily / Roll / Alpha-Beta Complex / 3-Layer(aba) Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
IRON/SULFUR CLUSTER / Thioredoxin F-type, chloroplastic / Ferredoxin-thioredoxin reductase, catalytic chain / Ferredoxin-thioredoxin reductase, variable chain
Similarity search - Component
Biological speciesSynechocystis sp. (bacteria)
Spinacia oleracea (spinach)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.65 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_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_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

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


Theoretical massNumber of molelcules
Total (without water)34,28510
Polymers33,3573
Non-polymers9287
Water5,296294
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4870 Å2
ΔGint-111 kcal/mol
Surface area14380 Å2
MethodPISA
2
B: Ferredoxin-thioredoxin reductase, variable chain

A: Ferredoxin-thioredoxin reductase, catalytic chain
C: Thioredoxin F-type, chloroplast
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,28510
Polymers33,3573
Non-polymers9287
Water543
TypeNameSymmetry operationNumber
crystal symmetry operation2_554-x+1/2,-y,z-1/21
identity operation1_555x,y,z1
Buried area4360 Å2
ΔGint-117 kcal/mol
Surface area14890 Å2
MethodPISA
Unit cell
Length a, b, c (Å)61.322, 66.788, 69.698
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

-
Components

-
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
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

-
Protein , 1 types, 1 molecules C

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


Mass: 12360.387 Da / Num. of mol.: 1 / Mutation: C49S
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

-
Non-polymers , 3 types, 301 molecules

#4: Chemical
ChemComp-SO4 / SULFATE ION


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


Mass: 351.640 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Fe4S4
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 294 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 4

-
Sample preparation

CrystalDensity Matthews: 2.14 Å3/Da / Density % sol: 42.48 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6
Details: pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 298.0K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RUH2R / Wavelength: 1.54 Å
DetectorType: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Jan 1, 2004
RadiationMonochromator: Osmic mirrors / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionRedundancy: 14.1 % / Av σ(I) over netI: 15.6 / Number: 473696 / Rmerge(I) obs: 0.073 / Χ2: 1.44 / D res high: 1.65 Å / D res low: 50 Å / Num. obs: 33522 / % possible obs: 95.7
Diffraction reflection shell
Highest resolution (Å)Lowest resolution (Å)% possible obs (%)IDRmerge(I) obsChi squaredRedundancy
3.555099.210.0461.89716.8
2.823.5598.310.0591.71217.8
2.462.8297.510.0951.63317.9
2.242.4696.710.1211.48218
2.082.2495.910.1571.30917.8
1.962.0895.110.2171.26314.2
1.861.9694.610.2791.14111.5
1.781.8693.510.3631.0619.7
1.711.7893.110.4930.9878.8
1.651.7192.310.6620.9287.7
ReflectionResolution: 1.65→50 Å / Num. obs: 33522 / % possible obs: 95.7 % / Redundancy: 14.1 % / Biso Wilson estimate: 23.8 Å2 / Rmerge(I) obs: 0.073 / Χ2: 1.436 / Net I/σ(I): 15.6
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2% possible all
1.65-1.717.70.66232050.92892.3
1.71-1.788.80.49331880.98793.1
1.78-1.869.70.36332401.06193.5
1.86-1.9611.50.27932691.14194.6
1.96-2.0814.20.21732931.26395.1
2.08-2.2417.80.15733351.30995.9
2.24-2.46180.12133741.48296.7
2.46-2.8217.90.09534281.63397.5
2.82-3.5517.80.05934891.71298.3
3.55-5016.80.04637011.89799.2

-
Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
CNSrefinement
PDB_EXTRACT2data extraction
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.65→500 Å / FOM work R set: 0.862 / σ(F): 0
RfactorNum. reflection% reflection
Rfree0.231 1658 4.7 %
Rwork0.205 --
obs-33478 95.3 %
Solvent computationBsol: 49.785 Å2
Displacement parametersBiso mean: 28.854 Å2
Baniso -1Baniso -2Baniso -3
1--0.571 Å20 Å20 Å2
2--1.152 Å20 Å2
3----0.582 Å2
Refinement stepCycle: LAST / Resolution: 1.65→500 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2335 0 38 294 2667
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.004
X-RAY DIFFRACTIONc_angle_d1.162
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 33

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection obs
1.65-1.670.449440.428786830
1.67-1.680.366590.361911970
1.68-1.70.318660.323897963
1.7-1.720.389450.306930975
1.72-1.740.283490.28914963
1.74-1.760.327530.255923976
1.76-1.790.295440.24952996
1.79-1.810.264410.226949990
1.81-1.830.273590.218904963
1.83-1.860.19450.207952997
1.86-1.890.2410.196938979
1.89-1.920.305500.211940990
1.92-1.950.226470.217946993
1.95-1.980.224430.29791022
1.98-2.020.236430.199947990
2.02-2.060.269490.2229631012
2.06-2.10.268540.2069551009
2.1-2.150.278450.2019661011
2.15-2.20.217590.1949601019
2.2-2.250.216490.29621011
2.25-2.310.3550.2139661021
2.31-2.380.201450.2069931038
2.38-2.460.252510.2129771028
2.46-2.540.229520.1969711023
2.54-2.650.293520.2169941046
2.65-2.770.298510.2279981049
2.77-2.910.207480.22110081056
2.91-3.10.315470.229981045
3.1-3.330.212520.210181070
3.33-3.670.197570.18710141071
3.67-4.20.156630.16610311094
4.2-5.290.169540.16410451099
5.29-500.010.259460.21211331179
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

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbjlvh1.pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more