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- PDB-7c65: Crystal structure of thioredoxin m1 -

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Basic information

Entry
Database: PDB / ID: 7c65
TitleCrystal structure of thioredoxin m1
ComponentsThioredoxin M1, chloroplastic
KeywordsELECTRON TRANSPORT / Trx m1
Function / homology
Function and homology information


stromule / oxidoreductase activity, acting on a sulfur group of donors, disulfide as acceptor / regulation of carbohydrate metabolic process / glycerol ether metabolic process / protein-disulfide reductase (NAD(P)H) activity / negative regulation of catalytic activity / apoplast / thylakoid / chloroplast envelope / enzyme inhibitor activity ...stromule / oxidoreductase activity, acting on a sulfur group of donors, disulfide as acceptor / regulation of carbohydrate metabolic process / glycerol ether metabolic process / protein-disulfide reductase (NAD(P)H) activity / negative regulation of catalytic activity / apoplast / thylakoid / chloroplast envelope / enzyme inhibitor activity / chloroplast stroma / positive regulation of catalytic activity / protein-disulfide reductase activity / enzyme activator activity / response to cold / cell redox homeostasis / chloroplast / extracellular region / cytoplasm
Similarity search - Function
Thioredoxin / Thioredoxin / Thioredoxin, conserved site / Thioredoxin family active site. / Thioredoxin domain profile. / Thioredoxin domain / Thioredoxin-like superfamily
Similarity search - Domain/homology
Thioredoxin M1, chloroplastic
Similarity search - Component
Biological speciesArabidopsis thaliana (thale cress)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.1 Å
AuthorsKurisu, G. / Juniar, L. / Tanaka, H.
Funding support Japan, 1items
OrganizationGrant numberCountry
Japan Society for the Promotion of Science (JSPS)16H06560 Japan
CitationJournal: Protein Sci. / Year: 2020
Title: Structural basis for thioredoxin isoform-based fine-tuning of ferredoxin-thioredoxin reductase activity.
Authors: Juniar, L. / Tanaka, H. / Yoshida, K. / Hisabori, T. / Kurisu, G.
History
DepositionMay 21, 2020Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Oct 14, 2020Provider: repository / Type: Initial release
Revision 1.1Dec 9, 2020Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title / _citation_author.identifier_ORCID
Revision 1.2Nov 29, 2023Group: 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Thioredoxin M1, chloroplastic
hetero molecules


Theoretical massNumber of molelcules
Total (without water)12,0192
Polymers11,9961
Non-polymers231
Water2,108117
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area130 Å2
ΔGint-9 kcal/mol
Surface area5650 Å2
MethodPISA
Unit cell
Length a, b, c (Å)24.004, 64.333, 29.487
Angle α, β, γ (deg.)90.000, 96.010, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Thioredoxin M1, chloroplastic / AtTrxm1


Mass: 11995.627 Da / Num. of mol.: 1 / Mutation: C37S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Cell: chloroplast / Gene: At1g03680, F21B7.28, F21B7_7 / Details (production host): pET23 / Production host: Escherichia coli BL21 (bacteria) / References: UniProt: O48737
#2: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 117 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 1.89 Å3/Da / Density % sol: 34.75 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, hanging drop / pH: 7.5 / Details: 0.1M HEPES 7.5, 10% 2-propanol, 20% PEG 4000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL44XU / Wavelength: 0.9 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Oct 10, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9 Å / Relative weight: 1
ReflectionResolution: 1.1→26.68 Å / Num. obs: 35880 / % possible obs: 99.69 % / Redundancy: 6.2 % / CC1/2: 0.998 / Rmerge(I) obs: 0.058 / Rrim(I) all: 0.063 / Net I/σ(I): 20.98
Reflection shellResolution: 1.1→1.13 Å / Redundancy: 6.3 % / Rmerge(I) obs: 0.252 / Mean I/σ(I) obs: 9.8 / Num. unique obs: 5726 / CC1/2: 0.98 / Rrim(I) all: 0.274 / % possible all: 98.7

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Processing

Software
NameVersionClassification
SHELXrefinement
PDB_EXTRACT3.25data extraction
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2PUK

2puk


Resolution: 1.1→26.68 Å / Cross valid method: THROUGHOUT
RfactorNum. reflection% reflection
Rfree0.1877 --
Rwork0.1437 --
obs-35799 99 %
Displacement parametersBiso max: 83.59 Å2 / Biso mean: 19.1522 Å2 / Biso min: 7.6 Å2
Refinement stepCycle: LAST / Resolution: 1.1→26.68 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms821 0 1 117 939
LS refinement shellResolution: 1.1→1.14 Å
RfactorNum. reflection% reflection
Rwork0.156 3467 -
obs--99 %

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