[English] 日本語
Yorodumi
- PDB-1o6j: Tryparedoxin II from C.fasciculata solved by sulphur phasing -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1o6j
TitleTryparedoxin II from C.fasciculata solved by sulphur phasing
ComponentsTRYPAREDOXIN II
KeywordsELECTRON TRANSPORT / TRYPAREDOXIN II / SULPHUR PHASING / SAD / S-SAD
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
protein-disulfide reductase
Similarity search - Component
Biological speciesCRITHIDIA FASCICULATA (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / OTHER / Resolution: 2.35 Å
AuthorsLeonard, G.A. / Micossi, E. / Hunter, W.N.
CitationJournal: Acta Crystallogr.,Sect.D / Year: 2002
Title: De Novo Phasing of Two Crystal Forms of Tryparedoxin II Using the Anomalous Scattering from S Atoms: A Combination of Small Signal and Medium Resolution Reveals This to be a General Tool for ...Title: De Novo Phasing of Two Crystal Forms of Tryparedoxin II Using the Anomalous Scattering from S Atoms: A Combination of Small Signal and Medium Resolution Reveals This to be a General Tool for Solving Protein Crystal Structures
Authors: Micossi, E. / Hunter, W.N. / Leonard, G.A.
History
DepositionOct 4, 2002Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 7, 2002Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3May 8, 2024Group: Data collection / Database references / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: TRYPAREDOXIN II
B: TRYPAREDOXIN II


Theoretical massNumber of molelcules
Total (without water)33,8572
Polymers33,8572
Non-polymers00
Water1,982110
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)114.200, 114.200, 102.600
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212
Components on special symmetry positions
IDModelComponents
11A-2009-

HOH

21A-2030-

HOH

31A-2047-

HOH

Noncrystallographic symmetry (NCS)NCS oper: (Code: given
Matrix: (0.769, 0.404, -0.495), (-0.639, 0.474, -0.605), (-0.01, 0.782, 0.623)
Vector: 38.135, -27.456, 36.293)

-
Components

#1: Protein TRYPAREDOXIN II


Mass: 16928.457 Da / Num. of mol.: 2 / Fragment: RESIDUES 16-165
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) CRITHIDIA FASCICULATA (eukaryote) / Plasmid: PET15B / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: O77093
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 110 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsCONSTRUCT STARTS AT RESIDUE 16

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 2

-
Sample preparation

CrystalDensity Matthews: 4.4 Å3/Da / Density % sol: 72 %
Crystal growpH: 7.5 / Details: pH 7.50
Crystal grow
*PLUS
Temperature: 277 K / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
11.4 Msodium citrate1reservoir
2100 mMsodium HEPES1reservoirpH7.5

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-2 / Wavelength: 1.77
DetectorType: MARRESEARCH / Detector: CCD / Date: Mar 15, 2001
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.77 Å / Relative weight: 1
ReflectionResolution: 2.35→40 Å / Num. obs: 28025 / % possible obs: 97.5 % / Observed criterion σ(I): 0 / Redundancy: 4.8 % / Biso Wilson estimate: 52.2 Å2 / Rmerge(I) obs: 0.053 / Net I/σ(I): 29.8
Reflection shellResolution: 2.35→2.39 Å / Rmerge(I) obs: 0.249 / Mean I/σ(I) obs: 9.6 / % possible all: 99.9
Reflection
*PLUS
Highest resolution: 2.35 Å / Lowest resolution: 40 Å / Num. obs: 35567 / % possible obs: 100 % / Num. measured all: 531442 / Rmerge(I) obs: 0.058
Reflection shell
*PLUS
Highest resolution: 2.7 Å / Lowest resolution: 2.76 Å / % possible obs: 100 % / Rmerge(I) obs: 0.299 / Mean I/σ(I) obs: 9.5

-
Processing

Software
NameClassification
DENZOdata reduction
SCALEPACKdata scaling
SOLVEphasing
SHARPphasing
REFMACrefinement
RefinementMethod to determine structure: OTHER / Resolution: 2.35→30 Å / SU B: 6.529 / SU ML: 0.16 / Cross valid method: THROUGHOUT / ESU R: 0.184 / ESU R Free: 0.157 / Details: CNS USED IN INITIAL STAGES
RfactorNum. reflection% reflectionSelection details
Rfree0.215 1414 5.1 %RANDOM
Rwork0.20083 ---
obs0.20155 26560 97.5 %-
Displacement parametersBiso mean: 44.7 Å2
Baniso -1Baniso -2Baniso -3
1--2.08 Å20 Å20 Å2
2---2.08 Å20 Å2
3---4.16 Å2
Refinement stepCycle: LAST / Resolution: 2.35→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2343 0 0 110 2453
Refinement
*PLUS
Lowest resolution: 30 Å / % reflection Rfree: 5 % / Rfactor Rwork: 0.201
Solvent computation
*PLUS
Displacement parameters
*PLUS
LS refinement shell
*PLUS
Highest resolution: 2.351 Å / Lowest resolution: 2.412 Å / Rfactor Rfree: 0.287 / Rfactor Rwork: 0.256 / Num. reflection Rwork: 126 / Total num. of bins used: 20

+
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