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- PDB-6mos: Structure of thioredoxin 1 from the thermophilic eubacterium Ther... -

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Basic information

Entry
Database: PDB / ID: 6mos
TitleStructure of thioredoxin 1 from the thermophilic eubacterium Thermosipho africanus TCF52B
ComponentsThioredoxin
KeywordsOXIDOREDUCTASE / thioredoxin / thermophile / Thermosipho africanus / protein stability / catalysis
Function / homologyThioredoxin / Thioredoxin domain / Thioredoxin-like superfamily / Thioredoxin
Function and homology information
Biological speciesThermosipho africanus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.80013732031 Å
AuthorsSahtout, N. / Kuttiyatveetil, J.R. / Sanders, D.A.R.
Citation
Journal: Biochim Biophys Acta Proteins Proteom / Year: 2019
Title: Structure and function of the putative thioredoxin 1 from the thermophilic eubacterium Thermosipho africanus strain TCF52B.
Authors: Sahtout, N. / Kuttiyatveetil, J.R.A. / Sanders, D.A.R.
#1: Journal: Acta Crystallogr F Struct Biol Commun / Year: 2016
Title: Putative thioredoxin Trx1 from Thermosipho africanus strain TCF52B: expression, purification and structural determination using S-SAD.
Authors: Sahtout, N. / Kuttiyatveetil, J.R. / Fodje, M. / Sanders, D.A.
History
DepositionOct 4, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 14, 2019Provider: repository / Type: Initial release
Revision 1.1Mar 6, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / software
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _software.name
Revision 1.2Nov 20, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Thioredoxin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,0122
Polymers13,8491
Non-polymers1631
Water37821
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area210 Å2
ΔGint-1 kcal/mol
Surface area5800 Å2
Unit cell
Length a, b, c (Å)40.454, 41.023, 55.822
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x,y+1/2,-z+1/2
#4: -x+1/2,-y,z+1/2

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Components

#1: Protein Thioredoxin


Mass: 13848.891 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermosipho africanus (strain TCF52B) (bacteria)
Strain: TCF52B / Gene: THA_37 / Cell line (production host): BL21-CodonPlus-RIL / Production host: Escherichia coli (E. coli) / References: UniProt: B7IEN1
#2: Chemical ChemComp-TAM / TRIS(HYDROXYETHYL)AMINOMETHANE


Mass: 163.215 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C7H17NO3 / Comment: pH buffer*YM
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 21 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 1.67 Å3/Da / Density % sol: 26.55 % / Description: large irregular-shaped trapezoid crystals
Crystal growTemperature: 289 K / Method: microbatch
Details: 0.2 M MgCl2 , 0.1 M bis-tris pH 6.5, 25%(w/v) PEG 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: CLSI / Beamline: 08ID-1 / Wavelength: 0.9795 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Dec 4, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 1.8→41.02 Å / Num. obs: 8989 / % possible obs: 99.1 % / Redundancy: 6.1 % / Biso Wilson estimate: 25.4388546055 Å2 / Net I/σ(I): 28.2
Reflection shellResolution: 1.8→1.9 Å / Redundancy: 3.3 % / Mean I/σ(I) obs: 7.3 / Num. unique obs: 1198 / % possible all: 95

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Processing

Software
NameClassification
autoPROCdata collection
SCALAdata scaling
PHENIXrefinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.80013732031→33.0566043115 Å / SU ML: 0.154539013252 / Cross valid method: NONE / σ(F): 1.33595773055 / Phase error: 30.8445965544
RfactorNum. reflection% reflection
Rfree0.24563185947 433 4.84123434705 %
Rwork0.210661817761 --
obs0.212317242433 8944 98.8396507901 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 32.5232942362 Å2
Refinement stepCycle: LAST / Resolution: 1.80013732031→33.0566043115 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms730 0 11 21 762
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00623932333739761
X-RAY DIFFRACTIONf_angle_d0.843075747141028
X-RAY DIFFRACTIONf_chiral_restr0.0544356261178120
X-RAY DIFFRACTIONf_plane_restr0.00405494837583127
X-RAY DIFFRACTIONf_dihedral_angle_d11.2951731028485
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.8001-2.06060.2753319768721350.1905398229592728X-RAY DIFFRACTION96.722972973
2.0606-2.5960.2781803368731420.2369815435932819X-RAY DIFFRACTION99.7977755308
2.596-33.06220.230478433371560.2050981594022964X-RAY DIFFRACTION99.935938501

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