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- PDB-1thx: THIOREDOXIN-2 -

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Basic information

Entry
Database: PDB / ID: 1thx
TitleTHIOREDOXIN-2
ComponentsTHIOREDOXIN
KeywordsELECTRON TRANSPORT / OXIDO-REDUCTASE
Function / homology
Function and homology information


glycerol ether metabolic process / protein-disulfide reductase activity / cell redox homeostasis
Similarity search - Function
Thioredoxin / Thioredoxin / Thioredoxin, conserved site / Thioredoxin family active site. / Thioredoxin domain profile. / Thioredoxin domain / Glutaredoxin / Glutaredoxin / Thioredoxin-like superfamily / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Biological speciesNostoc sp. (bacteria)
MethodX-RAY DIFFRACTION / Resolution: 1.6 Å
AuthorsSaarinen, M. / Gleason, F.K. / Eklund, H.
Citation
Journal: Structure / Year: 1995
Title: Crystal structure of thioredoxin-2 from Anabaena.
Authors: Saarinen, M. / Gleason, F.K. / Eklund, H.
#1: Journal: J.Bacteriol. / Year: 1992
Title: Activities of Two Dissimilar Thioredoxins from the Cyanobacterium Anabaena Sp. Pcc 7120
Authors: Gleason, F.K.
#2: Journal: J.Bacteriol. / Year: 1989
Title: Isolation, Sequence, and Expression in Escherichia Coli of an Unusual Thioredoxin Gene from the Cyanobacterium Anabaena Sp. Strain Pcc 7120
Authors: Alam, J. / Curtis, S.E. / Gleason, F.K. / Gerami-Nejad, M. / Fuchs, J.A.
History
DepositionJul 7, 1995Processing site: BNL
Revision 1.0Oct 15, 1995Provider: repository / Type: Initial release
Revision 1.1Mar 3, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Source and taxonomy / Version format compliance
Revision 1.3Jun 5, 2024Group: Data collection / Database references / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.process_site

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: THIOREDOXIN


Theoretical massNumber of molelcules
Total (without water)12,8121
Polymers12,8121
Non-polymers00
Water1,33374
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)40.480, 39.780, 60.080
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Atom site foot note1: CIS PROLINE - PRO 76

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Components

#1: Protein THIOREDOXIN / THIOREDOXIN 2


Mass: 12811.778 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Nostoc sp. (bacteria) / Strain: PCC 7120 / Gene: TRXA / Plasmid: PAN673.2 / Gene (production host): TRXA / Production host: Escherichia coli (E. coli) / References: UniProt: P20857
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 74 / 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: 2

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Sample preparation

CrystalDensity Matthews: 1.89 Å3/Da / Density % sol: 34.81 %
Crystal grow
*PLUS
Temperature: 20 ℃ / Method: vapor diffusion, sitting drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
110 mg/mlprotein1drop
220-25 %(w/w)PEG14501reservoircan be replaced with PEG-mono methyl ether 2000
3100 mMMES1reservoir

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Data collection

Diffraction sourceWavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IIC / Detector: IMAGE PLATE / Date: Nov 22, 1993
RadiationMonochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionNum. obs: 10467 / % possible obs: 78.6 % / Redundancy: 3.3 % / Rmerge(I) obs: 0.035
Reflection
*PLUS
Highest resolution: 1.6 Å / Lowest resolution: 34 Å / Observed criterion σ(I): 13.9 / Num. measured all: 34399 / Rmerge(I) obs: 0.035
Reflection shell
*PLUS
Highest resolution: 1.6 Å / Lowest resolution: 1.64 Å / % possible obs: 49.5 %

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Processing

Software
NameClassification
DENZO/CCP4data collection
X-PLORmodel building
X-PLORrefinement
DENZOdata reduction
CCP4data reduction
X-PLORphasing
RefinementResolution: 1.6→7 Å / σ(F): 2
Details: RESIDUES SER 1 AND LYS 2 COULD BE BUILT IN TWO ALTERNATE ORIENTATIONS ROTATED 180 DEGREES AROUND THE C-ALPHA - C BOND OF LYS 2. MOST OF THESE ATOMS HAVE GOOD ELECTRON DENSITY IN BOTH ...Details: RESIDUES SER 1 AND LYS 2 COULD BE BUILT IN TWO ALTERNATE ORIENTATIONS ROTATED 180 DEGREES AROUND THE C-ALPHA - C BOND OF LYS 2. MOST OF THESE ATOMS HAVE GOOD ELECTRON DENSITY IN BOTH ORIENTATIONS, AND A POSITIVE DIFFERENCE FOURIER DENSITY SHOWS THE PRESENCE OF THE OTHER ORIENTATION, IN EITHER OF THE CASES.
RfactorNum. reflection
Rfree0.229 -
Rwork0.175 -
obs0.175 10103
Displacement parametersBiso mean: 18.41 Å2
Refinement stepCycle: LAST / Resolution: 1.6→7 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms844 0 0 74 918
Software
*PLUS
Name: X-PLOR / Classification: refinement
Refinement
*PLUS
Rfactor obs: 0.174 / Rfactor Rwork: 0.174
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.009
X-RAY DIFFRACTIONx_angle_deg1.63
X-RAY DIFFRACTIONx_dihedral_angle_deg23.3

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