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- PDB-6h1y: CRYSTAL STRUCTURE OF A CHIMERIC VARIANT OF THIOREDOXIN FROM ESCHE... -

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Basic information

Entry
Database: PDB / ID: 6h1y
TitleCRYSTAL STRUCTURE OF A CHIMERIC VARIANT OF THIOREDOXIN FROM ESCHERICHIA COLI
ComponentsThioredoxin 1,Thioredoxin (TrxA-1),Thioredoxin 1
KeywordsOXIDOREDUCTASE / protein thermal stability / loop size optimization / fundamental rules / chimeric proteins / protein stabilization
Function / homology
Function and homology information


DNA polymerase processivity factor activity / protein-disulfide reductase activity / cell redox homeostasis / cytosol / cytoplasm
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
Thioredoxin 1 / Thioredoxin (TrxA-1)
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
Sulfolobus solfataricus (archaea)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.99 Å
AuthorsRuggiero, A. / Smaldone, G. / Esposito, L. / Balasco, N. / Vitagliano, L.
CitationJournal: Febs J. / Year: 2019
Title: Loop size optimization induces a strong thermal stabilization of the thioredoxin fold.
Authors: Ruggiero, A. / Smaldone, G. / Esposito, L. / Balasco, N. / Vitagliano, L.
History
DepositionJul 12, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 6, 2019Provider: repository / Type: Initial release
Revision 1.1May 15, 2019Group: Data collection / Database references
Category: citation / database_PDB_rev ...citation / database_PDB_rev / database_PDB_rev_record / pdbx_database_proc
Item: _citation.journal_abbrev / _citation.journal_id_ISSN ..._citation.journal_abbrev / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.2Jan 17, 2024Group: 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

Downloads & links

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Assembly

Deposited unit
A: Thioredoxin 1,Thioredoxin (TrxA-1),Thioredoxin 1
B: Thioredoxin 1,Thioredoxin (TrxA-1),Thioredoxin 1


Theoretical massNumber of molelcules
Total (without water)23,5692
Polymers23,5692
Non-polymers00
Water0
1
A: Thioredoxin 1,Thioredoxin (TrxA-1),Thioredoxin 1


Theoretical massNumber of molelcules
Total (without water)11,7851
Polymers11,7851
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Thioredoxin 1,Thioredoxin (TrxA-1),Thioredoxin 1


Theoretical massNumber of molelcules
Total (without water)11,7851
Polymers11,7851
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)95.340, 95.340, 39.646
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number144
Space group name H-MP31

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Components

#1: Protein Thioredoxin 1,Thioredoxin (TrxA-1),Thioredoxin 1 / Trx-1


Mass: 11784.570 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli), (gene. exp.) Sulfolobus solfataricus (archaea)
Strain: K12, ATCC 35092 / DSM 1617 / JCM 11322 / P2 / Gene: trxA, fipA, tsnC, b3781, JW5856, trxA-1, SSO0368 / Production host: Escherichia coli (E. coli) / References: UniProt: P0AA25, UniProt: Q980E5

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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: 4.41 Å3/Da / Density % sol: 72.13 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: Crystals were obtained with a protein concentration of 20-25 mg/ml. The composition of the reservoir solution was 17% (w/v) PEG10000, 0.1 M ammonium acetate and 0.1 M BIS-TRIS buffer, pH 5.5.

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 / Wavelength: 1.54 Å
DetectorType: RIGAKU SATURN 944 / Detector: CCD / Date: Feb 19, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 2.99→82.57 Å / Num. obs: 7669 / % possible obs: 93.6 % / Redundancy: 2.7 % / Rmerge(I) obs: 0.079 / Net I/σ(I): 14.8
Reflection shellResolution: 2.99→3.13 Å

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Processing

Software
NameVersionClassification
REFMAC5.8.0049refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2TRX

2trx


Resolution: 2.99→82.57 Å / Cor.coef. Fo:Fc: 0.933 / Cor.coef. Fo:Fc free: 0.893 / SU B: 18.35 / SU ML: 0.323 / Cross valid method: THROUGHOUT / ESU R: 3.049 / ESU R Free: 0.412 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.25945 963 12.6 %RANDOM
Rwork0.19761 ---
obs0.20583 6695 93.6 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 53.326 Å2
Baniso -1Baniso -2Baniso -3
1-0.04 Å20.02 Å2-0 Å2
2--0.04 Å20 Å2
3----0.12 Å2
Refinement stepCycle: 1 / Resolution: 2.99→82.57 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1656 0 0 0 1656
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.021688
X-RAY DIFFRACTIONr_bond_other_d0.0010.021672
X-RAY DIFFRACTIONr_angle_refined_deg1.4961.982288
X-RAY DIFFRACTIONr_angle_other_deg0.79833864
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.7125212
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.54826.28670
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.79515304
X-RAY DIFFRACTIONr_dihedral_angle_4_deg23.803154
X-RAY DIFFRACTIONr_chiral_restr0.0820.2264
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0211882
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02342
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it3.2325.114854
X-RAY DIFFRACTIONr_mcbond_other3.2345.106853
X-RAY DIFFRACTIONr_mcangle_it5.3227.6531064
X-RAY DIFFRACTIONr_mcangle_other5.327.6621065
X-RAY DIFFRACTIONr_scbond_it3.3255.443834
X-RAY DIFFRACTIONr_scbond_other3.3245.449835
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other5.6117.9861225
X-RAY DIFFRACTIONr_long_range_B_refined8.23239.8051873
X-RAY DIFFRACTIONr_long_range_B_other8.23239.8441874
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.988→3.066 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.423 69 -
Rwork0.433 404 -
obs--76.17 %

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