[English] 日本語
Yorodumi
- PDB-2eio: Design of Disulfide-linked Thioredoxin Dimers and Multimers Throu... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 2eio
TitleDesign of Disulfide-linked Thioredoxin Dimers and Multimers Through Analysis of Crystal Contacts
ComponentsThioredoxin 1
KeywordsELECTRON TRANSPORT / THIOREDOXIN / MUTANT / DI-SULFIDE BOND
Function / homology
Function and homology information


DNA polymerase processivity factor activity / protein-disulfide reductase activity / cell redox homeostasis / cytoplasm / cytosol
Similarity search - Function
Thioredoxin / Thioredoxin / Thioredoxin, conserved site / Thioredoxin family active site. / Thioredoxin domain profile. / Thioredoxin domain / Glutaredoxin / Glutaredoxin / Thioredoxin-like superfamily / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.6 Å
AuthorsKobayashi, M.
CitationJournal: J.Mol.Biol. / Year: 2007
Title: Design of Disulfide-linked Thioredoxin Dimers and Multimers Through Analysis of Crystal Contacts
Authors: Das, M. / Kobayashi, M. / Yamada, Y. / Sreeramulu, S. / Ramakrishnan, C. / Wakatsuki, S. / Kato, R. / Varadarajan, R.
History
DepositionMar 13, 2007Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Sep 11, 2007Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 10, 2021Group: Database references / Category: database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details
Revision 1.3Oct 25, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.4Nov 6, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Thioredoxin 1
B: Thioredoxin 1
C: Thioredoxin 1
D: Thioredoxin 1


Theoretical massNumber of molelcules
Total (without water)46,6464
Polymers46,6464
Non-polymers00
Water1,02757
1
A: Thioredoxin 1


Theoretical massNumber of molelcules
Total (without water)11,6611
Polymers11,6611
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Thioredoxin 1


Theoretical massNumber of molelcules
Total (without water)11,6611
Polymers11,6611
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Thioredoxin 1


Theoretical massNumber of molelcules
Total (without water)11,6611
Polymers11,6611
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Thioredoxin 1


Theoretical massNumber of molelcules
Total (without water)11,6611
Polymers11,6611
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)101.731, 59.209, 75.061
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212

-
Components

#1: Protein
Thioredoxin 1 / TRX1 / TRX / THIOREDOXIN 11P


Mass: 11661.417 Da / Num. of mol.: 4 / Mutation: E101C
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Production host: Escherichia coli (E. coli) / References: UniProt: P0AA25
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 57 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.42 Å3/Da / Density % sol: 49.22 %
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 20% PEG 3350, 0.1M TRIS, 0.2M MAGNESIUM CHLORIDE, pH 8.50, VAPOR DIFFUSION, HANGING DROP, temperature 289K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: AR-NW12A / Wavelength: 1
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Feb 17, 2005 / Details: MIRROR
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.6→50 Å / Num. obs: 14472 / % possible obs: 100 % / Redundancy: 7.2 % / Biso Wilson estimate: 27.7 Å2 / Rmerge(I) obs: 0.081 / Rsym value: 0.081 / Net I/σ(I): 24.3
Reflection shellResolution: 2.6→2.69 Å / Redundancy: 7.3 % / Rmerge(I) obs: 0.258 / Mean I/σ(I) obs: 6.7 / Rsym value: 0.258 / % possible all: 99.9

-
Processing

Software
NameVersionClassification
MOLREPphasing
CNS1.1refinement
HKL-2000data reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2TRX

2trx


Resolution: 2.6→38.58 Å / Rfactor Rfree error: 0.008 / Data cutoff high absF: 148038.94 / Data cutoff low absF: 0 / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.292 1405 9.9 %RANDOM
Rwork0.231 ---
obs0.231 14183 97.8 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 21.8641 Å2 / ksol: 0.35 e/Å3
Displacement parametersBiso mean: 24 Å2
Baniso -1Baniso -2Baniso -3
1--4.01 Å20 Å20 Å2
2--9.32 Å20 Å2
3----5.31 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.46 Å0.33 Å
Luzzati d res low-5 Å
Luzzati sigma a0.42 Å0.26 Å
Refinement stepCycle: LAST / Resolution: 2.6→38.58 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3252 0 0 57 3309
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.006
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.3
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d23.9
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.83
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it1.331.5
X-RAY DIFFRACTIONc_mcangle_it2.282
X-RAY DIFFRACTIONc_scbond_it1.912
X-RAY DIFFRACTIONc_scangle_it2.912.5
LS refinement shellResolution: 2.6→2.76 Å / Rfactor Rfree error: 0.024 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.338 196 8.9 %
Rwork0.248 2013 -
obs--93.6 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2water.paramwater.top

+
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