[English] 日本語
Yorodumi
- PDB-1i5g: TRYPAREDOXIN II COMPLEXED WITH GLUTATHIONYLSPERMIDINE -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1i5g
TitleTRYPAREDOXIN II COMPLEXED WITH GLUTATHIONYLSPERMIDINE
ComponentsTRYPAREDOXIN II
KeywordsELECTRON TRANSPORT / tryparedoxin
Function / homology
Function and homology information


protein-disulfide reductase / thioredoxin-disulfide reductase (NADPH) activity
Similarity search - Function
: / TryX and NRX, thioredoxin domain / Thioredoxin-like / Thioredoxin-like fold / Thioredoxin domain profile. / Thioredoxin domain / Glutaredoxin / Glutaredoxin / Thioredoxin-like superfamily / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
GLUTATHIONYLSPERMIDINE / protein-disulfide reductase
Similarity search - Component
Biological speciesCrithidia fasciculata (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.4 Å
AuthorsHofmann, B. / Budde, H. / Bruns, K. / Guerrero, S.A. / Kalisz, H.M. / Menge, U. / Montemartini, M. / Nogoceke, E. / Steinert, P. / Wissing, J.B. ...Hofmann, B. / Budde, H. / Bruns, K. / Guerrero, S.A. / Kalisz, H.M. / Menge, U. / Montemartini, M. / Nogoceke, E. / Steinert, P. / Wissing, J.B. / Flohe, L. / Hecht, H.-J.
CitationJournal: Biol.Chem. / Year: 2001
Title: Structures of tryparedoxins revealing interaction with trypanothione.
Authors: Hofmann, B. / Budde, H. / Bruns, K. / Guerrero, S.A. / Kalisz, H.M. / Menge, U. / Montemartini, M. / Nogoceke, E. / Steinert, P. / Wissing, J.B. / Flohe, L. / Hecht, H.J.
History
DepositionFeb 27, 2001Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 14, 2001Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 27, 2021Group: Database references / Derived calculations
Category: database_2 / struct_conn ...database_2 / struct_conn / 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_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Aug 9, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: TRYPAREDOXIN II
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,7803
Polymers16,2241
Non-polymers5572
Water5,026279
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)41.211, 50.510, 67.259
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

-
Components

#1: Protein TRYPAREDOXIN II


Mass: 16223.512 Da / Num. of mol.: 1 / Mutation: C44S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Crithidia fasciculata (eukaryote) / Strain: HS6 / Plasmid: PET22B / Production host: Escherichia coli (E. coli) / References: UniProt: O77093
#2: Chemical ChemComp-TRS / 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL / TRIS BUFFER


Mass: 122.143 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H12NO3 / Comment: pH buffer*YM
#3: Chemical ChemComp-TS5 / GLUTATHIONYLSPERMIDINE


Mass: 434.554 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C17H34N6O5S
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 279 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.16 Å3/Da / Density % sol: 42.95 %
Crystal growTemperature: 292 K / Method: vapor diffusion, sitting drop / pH: 6.9
Details: PEG 8000, Mes Tris glutathionylspermidine, pH 6.9, VAPOR DIFFUSION, SITTING DROP, temperature 292K
Crystal grow
*PLUS
Temperature: 19 ℃
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
129 %PEG80001reservoirpH6.9
20.1MES/Tris1reservoir
30.1 Mammonium sulfate1drop
42.5 mMN1-glutathionylspermidine1drop

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: MPG/DESY, HAMBURG / Beamline: BW6 / Wavelength: 0.95 Å
DetectorType: MARRESEARCH / Detector: CCD / Date: Sep 25, 2000 / Details: mirrors
RadiationMonochromator: Si 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.95 Å / Relative weight: 1
ReflectionResolution: 1.4→28.87 Å / Num. all: 24911 / Num. obs: 24911 / % possible obs: 89 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.3 % / Biso Wilson estimate: 9.2 Å2 / Rmerge(I) obs: 0.074 / Rsym value: 0.065 / Net I/σ(I): 4.6
Reflection shellResolution: 1.4→1.48 Å / Redundancy: 4.1 % / Rmerge(I) obs: 0.088 / Mean I/σ(I) obs: 8.8 / Num. unique all: 3735 / Rsym value: 0.077 / % possible all: 92.1
Reflection
*PLUS
Num. obs: 24680 / % possible obs: 89 % / Rmerge(I) obs: 0.065

-
Processing

Software
NameVersionClassification
AMoREphasing
REFMAC5refinement
MOSFLMdata reduction
CCP4(SCALA)data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1FG4

1fg4


Resolution: 1.4→40.49 Å / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.203 1229 4.9 %RANDOM
Rwork0.168 ---
all0.17 24911 --
obs0.1703 23682 87.87 %-
Displacement parametersBiso mean: 7 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2---0 Å20 Å2
3----0 Å2
Refine analyzeLuzzati coordinate error free: 0.075 Å
Refinement stepCycle: LAST / Resolution: 1.4→40.49 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1147 0 37 279 1463
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONp_mcbond_d0.0131.098
X-RAY DIFFRACTIONp_mcangle_d2.3981.789
X-RAY DIFFRACTIONp_scbond_d1.481
X-RAY DIFFRACTIONp_scangle_d2.292
Software
*PLUS
Name: REFMAC / Version: 5 / Classification: refinement
Refinement
*PLUS
σ(F): 0 / % reflection Rfree: 4.9 % / Rfactor obs: 0.176
Solvent computation
*PLUS
Displacement parameters
*PLUS

+
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