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- PDB-2e0q: Crystal structure of K53E thioredoxin from Sulfolobus tokodaii strain7 -

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Basic information

Entry
Database: PDB / ID: 2e0q
TitleCrystal structure of K53E thioredoxin from Sulfolobus tokodaii strain7
Componentsthioredoxin
KeywordsELECTRON TRANSPORT / thioredoxin
Function / homology
Function and homology information


protein-disulfide reductase activity
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 speciesSulfolobus tokodaii (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.49 Å
AuthorsMing, H. / Tanokura, M.
CitationJournal: Proteins / Year: 2007
Title: Crystal structure of thioredoxin domain of ST2123 from thermophilic archaea Sulfolobus tokodaii strain7
Authors: Ming, H. / Kato, Y. / Miyazono, K. / Ito, K. / Kamo, M. / Nagata, K. / Tanokura, M.
History
DepositionOct 11, 2006Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Oct 2, 2007Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 10, 2021Group: Database references / Category: database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details
Revision 1.3Oct 30, 2024Group: Data collection / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / 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)11,6241
Polymers11,6241
Non-polymers00
Water2,054114
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)27.951, 52.123, 33.794
Angle α, β, γ (deg.)90.00, 93.52, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein thioredoxin


Mass: 11624.176 Da / Num. of mol.: 1 / Fragment: Residues 37-140 / Mutation: K53E
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Sulfolobus tokodaii (archaea) / Strain: strain7 / Plasmid: pET28a / Production host: Escherichia coli (E. coli) / References: UniProt: Q96YQ0, UniProt: F9VP91*PLUS
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 114 / 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: 2.11 Å3/Da / Density % sol: 41.77 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8
Details: 16% PEG-3000, 0.1M acetate (pH 4.1), 25% glycerol, pH 8.0, VAPOR DIFFUSION, SITTING DROP, temperature 293.0K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL41XU / Wavelength: 1 Å
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.49→50 Å / Num. obs: 57836 / % possible obs: 99.9 % / Biso Wilson estimate: 15.2 Å2

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Processing

Software
NameVersionClassification
REFMAC5.1.24refinement
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.49→15 Å / Cor.coef. Fo:Fc: 0.966 / Cor.coef. Fo:Fc free: 0.961 / SU B: 1.161 / SU ML: 0.045 / Cross valid method: THROUGHOUT / ESU R: 0.075 / ESU R Free: 0.072 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.19185 789 5 %RANDOM
Rwork0.17186 ---
obs0.17294 15049 99.97 %-
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: 14.866 Å2
Baniso -1Baniso -2Baniso -3
1--0.6 Å20 Å20.18 Å2
2---0.21 Å20 Å2
3---0.83 Å2
Refinement stepCycle: LAST / Resolution: 1.49→15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms819 0 0 114 933
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.021840
X-RAY DIFFRACTIONr_bond_other_d0.0020.02764
X-RAY DIFFRACTIONr_angle_refined_deg1.5831.9621145
X-RAY DIFFRACTIONr_angle_other_deg0.84631782
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.6535103
X-RAY DIFFRACTIONr_dihedral_angle_2_deg
X-RAY DIFFRACTIONr_dihedral_angle_3_deg
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.0880.2128
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.02933
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02160
X-RAY DIFFRACTIONr_nbd_refined0.2150.2170
X-RAY DIFFRACTIONr_nbd_other0.2450.2866
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other0.0860.2479
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1730.255
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1770.28
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2250.237
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2050.210
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.951.5520
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.742844
X-RAY DIFFRACTIONr_scbond_it2.6123320
X-RAY DIFFRACTIONr_scangle_it3.9844.5301
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.491→1.529 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.284 52
Rwork0.184 1096

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