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- PDB-6x0b: Crystal Structure of Thioredoxin NaTrxh from Nicotiana alata -

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Basic information

Entry
Database: PDB / ID: 6x0b
TitleCrystal Structure of Thioredoxin NaTrxh from Nicotiana alata
ComponentsThioredoxin H
KeywordsOXIDOREDUCTASE / NaTrxh / Thioredoxin h / S-RNase / self-incompatibility
Function / homologyglycerol ether metabolic process / Thioredoxin / Thioredoxin / protein-disulfide reductase activity / Thioredoxin domain profile. / Thioredoxin domain / Thioredoxin-like superfamily / Thioredoxin H
Function and homology information
Biological speciesNicotiana alata (Persian tobacco)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.702 Å
AuthorsGonzalez-Segura, L. / Torres-Rodriguez, M.D. / Cruz-Garcia, F.
Funding support Mexico, 2items
OrganizationGrant numberCountry
Consejo Nacional de Ciencia y Tecnologia (CONACYT)236602 Mexico
Programa de Apoyo a Proyectos de Investigacion e Innovacion Tecnologica (PAPIIT)IN220919 Mexico
CitationJournal: J.Struct.Biol. / Year: 2020
Title: High resolution crystal structure of NaTrxh from Nicotiana alata and its interaction with the S-RNase.
Authors: Torres-Rodriguez, M.D. / Gonzalez-Segura, L. / Rodriguez-Sotres, R. / Juarez-DiaZ, J.A. / Cruz-Zamora, Y. / Cruz-Garcia, F.
History
DepositionMay 15, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 22, 2020Provider: repository / Type: Initial release
Revision 1.1Aug 5, 2020Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.identifier_ORCID / _citation_author.name
Revision 1.2Aug 19, 2020Group: Database references / Category: citation_author / Item: _citation_author.name
Revision 1.3Oct 7, 2020Group: Database references / Category: citation / citation_author / Item: _citation.journal_volume / _citation_author.name
Revision 1.4Oct 18, 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 H
B: Thioredoxin H
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,7654
Polymers33,6402
Non-polymers1242
Water2,270126
1
A: Thioredoxin H
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,8822
Polymers16,8201
Non-polymers621
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Thioredoxin H
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,8822
Polymers16,8201
Non-polymers621
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)45.990, 68.851, 70.807
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Thioredoxin H


Mass: 16820.211 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: Stylar transmitting tract tissue / Source: (gene. exp.) Nicotiana alata (Persian tobacco) / Tissue: Stylar transmitting tract tissue / Gene: Trxh / Organ: Pistil / Plasmid: pGEX 4T-2
Details (production host): Glutathione S-transferase fusion vector. Thrombin protease site to cleave protein from fusion.
Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): pLysS / References: UniProt: Q4U0W0
#2: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6O2
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 126 / 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: 2.15 Å3/Da / Density % sol: 26.18 %
Crystal growTemperature: 291.15 K / Method: vapor diffusion, sitting drop / pH: 6
Details: 20% (w/v) PEG 3,350, 200 mM ammonium formate and 0.025% (v/v) dichloromethane

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.9792 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Jun 13, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 1.7→49.362 Å / Num. obs: 47203 / % possible obs: 98.73 % / Redundancy: 8.6 % / CC1/2: 1 / Rmerge(I) obs: 0.106 / Rpim(I) all: 0.038 / Net I/σ(I): 25.2
Reflection shellResolution: 1.7→1.7 Å / Rmerge(I) obs: 1.032 / Mean I/σ(I) obs: 2.6 / Num. unique obs: 2344 / CC1/2: 0.863 / Rpim(I) all: 0.384

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Processing

Software
NameVersionClassification
PHENIX1.13_2998refinement
PDB_EXTRACT3.25data extraction
HKL-3000data reduction
HKL-3000data scaling
HKL-3000phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2IWT

2iwt


Resolution: 1.702→49.362 Å / SU ML: 0.21 / Cross valid method: THROUGHOUT / σ(F): 0.83 / Phase error: 25.76 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2202 2295 4.88 %
Rwork0.1854 44730 -
obs0.1871 47025 98.73 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 131.52 Å2 / Biso mean: 31.1829 Å2 / Biso min: 16.16 Å2
Refinement stepCycle: final / Resolution: 1.702→49.362 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1827 0 8 126 1961
Biso mean--62.92 44.68 -
Num. residues----231
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.702-1.73870.31881460.2967260794
1.7387-1.77910.31141320.2636281099
1.7791-1.82360.29741580.2411282699
1.8236-1.87290.26071640.2425276399
1.8729-1.92810.30671550.2414276698
1.9281-1.99030.25061400.2154278198
1.9903-2.06140.24551710.20112786100
2.0614-2.1440.22951430.1992284599
2.144-2.24150.22511140.1864282199
2.2415-2.35970.21551250.1927282298
2.3597-2.50760.24181120.19952841100
2.5076-2.70120.24261380.20192842100
2.7012-2.97290.26681420.198282799
2.9729-3.40310.21681710.1777277199
3.4031-4.28710.16171300.1492833100
4.2871-4.28710.18471540.1581278999

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