[English] 日本語
Yorodumi
- PDB-5nyo: Crystal structure of an atypical poplar thioredoxin-like2.1 varia... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5nyo
TitleCrystal structure of an atypical poplar thioredoxin-like2.1 variant in dimeric form
ComponentsThioredoxin-like protein 2.1
KeywordsOXIDOREDUCTASE / atypical thioredoxin / disulfide exchange / oxidoredutase
Function / homologyThioredoxin-like 3-1/3-2 / chloroplast stroma / Thioredoxin / Thioredoxin domain profile. / Thioredoxin domain / Thioredoxin-like superfamily / Thioredoxin-like protein 2.1
Function and homology information
Biological speciesPopulus tremula x Populus tremuloides (plant)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.25 Å
AuthorsChibani, K. / Saul, F.A. / Haouz, A. / Rouhier, N.
Funding support France, 2items
OrganizationGrant numberCountry
INRA-FORMAS program France
Institut Pasteur France
CitationJournal: FEBS Lett. / Year: 2018
Title: Structural snapshots along the reaction mechanism of the atypical poplar thioredoxin-like2.1.
Authors: Chibani, K. / Saul, F. / Didierjean, C. / Rouhier, N. / Haouz, A.
History
DepositionMay 11, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 28, 2018Provider: repository / Type: Initial release
Revision 1.1Apr 4, 2018Group: Data collection / Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.2May 1, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.3Nov 13, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Thioredoxin-like protein 2.1
B: Thioredoxin-like protein 2.1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,5094
Polymers28,3172
Non-polymers1922
Water1,76598
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: covalently linked dimer
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1480 Å2
ΔGint-28 kcal/mol
Surface area12640 Å2
MethodPISA
Unit cell
Length a, b, c (Å)62.547, 62.547, 138.415
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212

-
Components

#1: Protein Thioredoxin-like protein 2.1


Mass: 14158.645 Da / Num. of mol.: 2 / Mutation: C45S Engineered mutation
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Populus tremula x Populus tremuloides (plant)
Plasmid: pET3d / Details (production host): T7 expression system / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: I0BZV0
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 98 / 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: 2.4 Å3/Da / Density % sol: 48.75 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / Details: 0.2M sodium formate, 20% (w/v) PEG3350

-
Data collection

DiffractionMean temperature: 110 K
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 1 / Wavelength: 0.98011 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Sep 16, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98011 Å / Relative weight: 1
ReflectionResolution: 2.25→46.4 Å / Num. obs: 13773 / % possible obs: 100 % / Redundancy: 8.5 % / Biso Wilson estimate: 62.95 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.068 / Rpim(I) all: 0.035 / Net I/σ(I): 14.9
Reflection shellResolution: 2.25→2.32 Å / Redundancy: 8.8 % / Rmerge(I) obs: 1.078 / Mean I/σ(I) obs: 2.1 / Num. unique obs: 1242 / CC1/2: 0.745 / Rpim(I) all: 0.552 / % possible all: 100

-
Processing

Software
NameVersionClassification
BUSTER2.10.2refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: wild-type Thioredoxin-like protein 2.1

Resolution: 2.25→46.4 Å / Cor.coef. Fo:Fc: 0.9518 / Cor.coef. Fo:Fc free: 0.9108 / SU R Cruickshank DPI: 0.282 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.312 / SU Rfree Blow DPI: 0.239 / SU Rfree Cruickshank DPI: 0.232
RfactorNum. reflection% reflectionSelection details
Rfree0.2684 700 5.1 %RANDOM
Rwork0.2069 ---
obs0.2098 13714 99.99 %-
Displacement parametersBiso mean: 67.23 Å2
Baniso -1Baniso -2Baniso -3
1-4.4184 Å20 Å20 Å2
2--4.4184 Å20 Å2
3----8.8368 Å2
Refine analyzeLuzzati coordinate error obs: 0.318 Å
Refinement stepCycle: 1 / Resolution: 2.25→46.4 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1938 0 10 98 2046
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.011992HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.122693HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d718SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes49HARMONIC2
X-RAY DIFFRACTIONt_gen_planes273HARMONIC5
X-RAY DIFFRACTIONt_it1992HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_omega_torsion2.93
X-RAY DIFFRACTIONt_other_torsion18.81
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion261SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact2329SEMIHARMONIC4
LS refinement shellResolution: 2.25→2.43 Å / Total num. of bins used: 7
RfactorNum. reflection% reflection
Rfree0.2598 147 5.35 %
Rwork0.2534 2601 -
all0.2538 2748 -
obs--100 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
13.00011.0004-0.33684.7519-0.60782.17470.0132-0.0004-0.2873-0.1669-0.1885-0.29690.069-0.03540.1752-0.14680.0417-0.0163-0.0210.0128-0.037-15.3793-0.0718-13.8717
23.82680.369-0.46693.2182-1.02786.31890.0823-0.3131-0.00540.0302-0.06-0.0284-0.1050.3872-0.0223-0.1204-0.0478-0.0344-0.05130.038-0.1193-34.501312.41279.5434
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1{ A|* }
2X-RAY DIFFRACTION2{ B|* }

+
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