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- PDB-7asw: Crystal structure of chloroplastic thioredoxin z defines a novel ... -

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Basic information

Entry
Database: PDB / ID: 7asw
TitleCrystal structure of chloroplastic thioredoxin z defines a novel type-specific target recognition
ComponentsThioredoxin-related protein CITRX
KeywordsISOMERASE / Ribose-5-phosphate / Rossmann fold / enzyme / chloroplast / photosynthese / Chlamydomonas
Function / homology
Function and homology information


oxidoreductase activity, acting on a sulfur group of donors, disulfide as acceptor / protein-disulfide reductase (NAD(P)H) activity / protein-disulfide reductase activity / cell redox homeostasis / cytoplasm
Similarity search - Function
Thioredoxin / Thioredoxin, conserved site / Thioredoxin family active site. / Thioredoxin domain profile. / Thioredoxin domain / Thioredoxin-like superfamily
Similarity search - Domain/homology
Thioredoxin-related protein CITRX
Similarity search - Component
Biological speciesChlamydomonas reinhardtii (plant)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.444 Å
AuthorsLe Moigne, T. / Gurrieri, L. / Crozet, P. / Marchand, C.H. / Zaffagnini, M. / Sparla, F. / Lemaire, S.D. / Henri, J.
CitationJournal: Plant J. / Year: 2021
Title: Crystal structure of chloroplastic thioredoxin z defines a type-specific target recognition.
Authors: Le Moigne, T. / Gurrieri, L. / Crozet, P. / Marchand, C.H. / Zaffagnini, M. / Sparla, F. / Lemaire, S.D. / Henri, J.
History
DepositionOct 28, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 19, 2021Provider: repository / Type: Initial release
Revision 1.1Sep 15, 2021Group: Database references / Category: citation / citation_author / database_2
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.2Jan 31, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Thioredoxin-related protein CITRX


Theoretical massNumber of molelcules
Total (without water)16,2121
Polymers16,2121
Non-polymers00
Water181
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: SAXS
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area6830 Å2
MethodPISA
Unit cell
Length a, b, c (Å)61.985, 61.985, 61.138
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number154
Space group name H-MP3221

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Components

#1: Protein Thioredoxin-related protein CITRX


Mass: 16211.506 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Chlamydomonas reinhardtii (plant) / Gene: CITRX, CHLRE_02g142800v5, CHLREDRAFT_195890 / Production host: Escherichia coli (E. coli) / References: UniProt: A8J0Q8
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

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

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Sample preparation

CrystalDensity Matthews: 2.09 Å3/Da / Density % sol: 41.19 %
Crystal growTemperature: 293.1 K / Method: vapor diffusion, hanging drop
Details: 1.26 mol.L-1 ammonium sulfate 0,1 mol.L-1 HEPES pH=7.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 2 / Wavelength: 0.983995 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Jan 29, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.983995 Å / Relative weight: 1
ReflectionResolution: 2.44→30.99 Å / Num. obs: 5268 / % possible obs: 99.36 % / Redundancy: 39.1 % / Biso Wilson estimate: 65.65 Å2 / CC1/2: 0.997 / CC star: 0.999 / Net I/σ(I): 27.43
Reflection shellResolution: 2.44→2.53 Å / Mean I/σ(I) obs: 2.04 / Num. unique obs: 485 / CC1/2: 0.662 / CC star: 0.893

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
PHENIX1.14_3260refinement
PHASERphasing
PDB_EXTRACT3.25data extraction
XDSdata collection
XDSdata reduction
XDSdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6I1C

6i1c


Resolution: 2.444→30.99 Å / SU ML: 0.25 / Cross valid method: FREE R-VALUE / σ(F): 1.39 / Phase error: 27.8 / Stereochemistry target values: MLHL
RfactorNum. reflection% reflection
Rfree0.233 525 9.96 %
Rwork0.2272 4744 -
obs-5268 99.36 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 111.93 Å2 / Biso mean: 70.15 Å2 / Biso min: 30 Å2
Refinement stepCycle: final / Resolution: 2.444→30.99 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms864 0 0 1 865
Biso mean---30 -
Num. residues----113
LS refinement shellResolution: 2.4444→2.6903 Å / Rfactor Rfree error: 0
RfactorNum. reflection% reflection
Rfree0.3357 115 -
Rwork0.2843 1169 -
obs--98 %

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