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

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 2puk
TitleCrystal structure of the binary complex between ferredoxin: thioredoxin reductase and thioredoxin m
Components
  • Ferredoxin-thioredoxin reductase, catalytic chain
  • Ferredoxin-thioredoxin reductase, variable chain
  • Thioredoxin M-type, chloroplast (TRX-M)
KeywordsELECTRON TRANSPORT / Thioredoxin / protein-protein complex / redox / iron-sulfur
Function / homology
Function and homology information


ferredoxin:thioredoxin reductase / ferredoxin-thioredoxin reductase activity / oxidoreductase activity, acting on iron-sulfur proteins as donors / protein-disulfide reductase activity / photosynthesis / enzyme activator activity / chloroplast / 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 / Thioredoxin / 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 M-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 / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3 Å
AuthorsDai, S. / Friemann, R. / Schurmann, P. / Eklund, H.
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 1.3Sep 18, 2013Group: Derived calculations
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 M-type, chloroplast (TRX-M)
E: Ferredoxin-thioredoxin reductase, catalytic chain
F: Ferredoxin-thioredoxin reductase, variable chain
G: Thioredoxin M-type, chloroplast (TRX-M)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)65,9928
Polymers65,2886
Non-polymers7032
Water00
1
A: Ferredoxin-thioredoxin reductase, catalytic chain
B: Ferredoxin-thioredoxin reductase, variable chain
C: Thioredoxin M-type, chloroplast (TRX-M)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,9964
Polymers32,6443
Non-polymers3521
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1850 Å2
ΔGint-32 kcal/mol
Surface area10670 Å2
2
E: Ferredoxin-thioredoxin reductase, catalytic chain
F: Ferredoxin-thioredoxin reductase, variable chain
G: Thioredoxin M-type, chloroplast (TRX-M)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,9964
Polymers32,6443
Non-polymers3521
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1910 Å2
ΔGint-33 kcal/mol
Surface area10780 Å2
Unit cell
Length a, b, c (Å)53.952, 42.223, 145.344
Angle α, β, γ (deg.)90.00, 90.29, 90.00
Int Tables number4
Space group name H-MP1211

-
Components

#1: Protein Ferredoxin-thioredoxin reductase, catalytic chain


Mass: 12453.121 Da / Num. of mol.: 2
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.: 2 / Mutation: C40S
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
#3: Protein Thioredoxin M-type, chloroplast (TRX-M)


Mass: 11864.448 Da / Num. of mol.: 2
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: P07591
#4: Chemical ChemComp-SF4 / IRON/SULFUR CLUSTER


Mass: 351.640 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Fe4S4

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
Sample preparation

CrystalDensity Matthews: 2.53 Å3/Da / Density % sol: 51.47 %
Crystal growTemperature: 288 K / Method: vapor diffusion, hanging drop / pH: 6
Details: pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 288K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-4
DetectorType: ADSC QUANTUM 315 / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthRelative weight: 1
ReflectionResolution: 3→145.865 Å / Num. obs: 13477 / % possible obs: 99.8 % / Redundancy: 3.6 % / Rmerge(I) obs: 0.1 / Rsym value: 0.1 / Net I/σ(I): 5.5
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRsym value% possible all
3-3.163.50.2912.5667819200.29199.7
3.16-3.353.60.2083.4654218290.20899.9
3.35-3.593.60.1663.9637417610.166100
3.59-3.873.60.1394.7588616280.13999.9
3.87-4.243.60.0937540114870.093100
4.24-4.743.60.0768.5493113580.076100
4.74-5.483.60.079431811970.07100
5.48-6.713.50.06310.6369410420.063100
6.71-9.493.40.05710.227248010.057100
9.49-72.742.90.0696.113374540.06995.6

-
Processing

Software
NameVersionClassificationNB
SCALAdata scaling
REFMACrefinement
PDB_EXTRACT2data extraction
ADSCQuantumdata collection
MOSFLMdata reduction
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3→30 Å / Cor.coef. Fo:Fc: 0.907 / Cor.coef. Fo:Fc free: 0.863 / SU B: 23.935 / SU ML: 0.424 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.518 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.284 663 4.9 %RANDOM
Rwork0.235 ---
obs0.237 13469 99.85 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 51.898 Å2
Baniso -1Baniso -2Baniso -3
1-4.21 Å20 Å22.01 Å2
2---1.43 Å20 Å2
3----2.76 Å2
Refinement stepCycle: LAST / Resolution: 3→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4562 0 16 0 4578
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0224705
X-RAY DIFFRACTIONr_angle_refined_deg1.5051.9826477
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.0155568
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.66724.698215
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.67115810
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.7921524
X-RAY DIFFRACTIONr_chiral_restr0.0660.2710
X-RAY DIFFRACTIONr_gen_planes_refined0.0020.023534
X-RAY DIFFRACTIONr_nbd_refined0.1940.22131
X-RAY DIFFRACTIONr_nbtor_refined0.3010.23120
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1080.2107
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1940.252
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1280.24
X-RAY DIFFRACTIONr_mcbond_it0.3181.52964
X-RAY DIFFRACTIONr_mcangle_it0.57824678
X-RAY DIFFRACTIONr_scbond_it0.4831977
X-RAY DIFFRACTIONr_scangle_it0.8174.51675
LS refinement shellResolution: 3→3.077 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.414 46 -
Rwork0.322 888 -
obs-934 99.05 %

+
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://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