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- PDB-1r26: Crystal structure of thioredoxin from Trypanosoma brucei brucei -

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Basic information

Entry
Database: PDB / ID: 1r26
TitleCrystal structure of thioredoxin from Trypanosoma brucei brucei
ComponentsThioredoxin
KeywordsELECTRON TRANSPORT / redox-active disulfide / thioredoxin
Function / homology
Function and homology information


disulfide oxidoreductase activity / protein disulfide isomerase activity / cell redox homeostasis / mitochondrion
Similarity search - Function
: / 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 speciesTrypanosoma (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.4 Å
AuthorsFriemann, R. / Schmidt, H. / Ramaswamy, S. / Forstner, M. / Krauth-Siegel, R.L. / Eklund, H.
CitationJournal: FEBS Lett. / Year: 2003
Title: Structure of thioredoxin from Trypanosoma brucei brucei
Authors: Friemann, R. / Schmidt, H. / Ramaswamy, S. / Forstner, M. / Krauth-Siegel, R.L. / Eklund, H.
History
DepositionSep 26, 2003Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 9, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Source and taxonomy / Version format compliance
Revision 1.3Aug 23, 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 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details
Revision 1.4Nov 6, 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


Theoretical massNumber of molelcules
Total (without water)14,4841
Polymers14,4841
Non-polymers00
Water2,270126
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)37.878, 51.725, 57.389
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Cell settingorthorhombic
Space group name H-MP212121

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Components

#1: Protein Thioredoxin


Mass: 14483.934 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: reduced form / Source: (gene. exp.) Trypanosoma (eukaryote) / Species: Trypanosoma brucei / Strain: brucei / Gene: trx / Plasmid: pQE-60 / Production host: Escherichia coli (E. coli) / Strain (production host): SG13009 / References: UniProt: Q9NG23
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 126 / 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: 1.94 Å3/Da / Density % sol: 36.4 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 4.6
Details: 2M sodium formate, 0.1M sodium acetate, pH 4.6, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal grow
*PLUS
Temperature: 293 K / pH: 7.2 / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formulaDetails
16.8 mg/mlprotein1drop
2250 mMimidazole1drop
3300 mM1dropNaCl
450 mMsodium phosphate1droppH7.2
52 Msodium formate1reservoir
60.1 Msodium acetate1reservoirpH4.6

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.915 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Jan 31, 2001
RadiationMonochromator: cryogenically cooled high resolution Si (311) and lower resolution Si (111)
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.915 Å / Relative weight: 1
ReflectionResolution: 1.4→30 Å / Num. all: 22807 / Num. obs: 22807 / % possible obs: 99.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 10 % / Rmerge(I) obs: 0.078 / Rsym value: 0.078 / Net I/σ(I): 5.8
Reflection shellResolution: 1.4→1.45 Å / Redundancy: 10.4 % / Rmerge(I) obs: 0.515 / Mean I/σ(I) obs: 1 / Num. unique all: 23274 / Rsym value: 0.01 / % possible all: 100
Reflection
*PLUS
Highest resolution: 1.4 Å / Redundancy: 10 % / Num. measured all: 232960
Reflection shell
*PLUS
Highest resolution: 1.4 Å / % possible obs: 99.6 %

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Processing

Software
NameVersionClassification
d*TREKdata scaling
d*TREKdata reduction
AMoREphasing
REFMAC5.1refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: Pdb entry 1ert polyala

1ert


Resolution: 1.4→30 Å / Cor.coef. Fo:Fc: 0.97 / Cor.coef. Fo:Fc free: 0.957 / SU B: 0.982 / SU ML: 0.039 / Isotropic thermal model: isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.058 / ESU R Free: 0.062 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.19841 1165 5.1 %RANDOM
Rwork0.16762 ---
all0.16827 21601 --
obs0.1691 21601 99.68 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 14.589 Å2
Baniso -1Baniso -2Baniso -3
1-0.57 Å20 Å20 Å2
2---0.36 Å20 Å2
3----0.21 Å2
Refinement stepCycle: LAST / Resolution: 1.4→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms904 0 0 126 1030
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.022920
X-RAY DIFFRACTIONr_bond_other_d0.0020.02879
X-RAY DIFFRACTIONr_angle_refined_deg1.3271.9511240
X-RAY DIFFRACTIONr_angle_other_deg0.76332033
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.5115111
X-RAY DIFFRACTIONr_chiral_restr0.0830.2141
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.02989
X-RAY DIFFRACTIONr_gen_planes_other0.0060.02190
X-RAY DIFFRACTIONr_nbd_refined0.2830.2164
X-RAY DIFFRACTIONr_nbd_other0.250.2936
X-RAY DIFFRACTIONr_nbtor_other0.0820.2527
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1870.272
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1680.26
X-RAY DIFFRACTIONr_symmetry_vdw_other0.260.261
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1370.221
X-RAY DIFFRACTIONr_mcbond_it0.881.5564
X-RAY DIFFRACTIONr_mcangle_it1.672920
X-RAY DIFFRACTIONr_scbond_it2.4783356
X-RAY DIFFRACTIONr_scangle_it4.2294.5320
LS refinement shellResolution: 1.4→1.436 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.265 95
Rwork0.23 1555
Refinement
*PLUS
Highest resolution: 1.4 Å / Lowest resolution: 30 Å / Rfactor Rfree: 0.198 / Rfactor Rwork: 0.168
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONr_bond_d0.012
X-RAY DIFFRACTIONr_angle_d
X-RAY DIFFRACTIONr_angle_deg1.3

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