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- PDB-4tn8: Crystal structure of Thermus Thermophilus thioredoxin solved by s... -

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Basic information

Entry
Database: PDB / ID: 4tn8
TitleCrystal structure of Thermus Thermophilus thioredoxin solved by sulfur SAD using Swiss Light Source data
ComponentsThioredoxin
KeywordsELECTRON TRANSPORT / SULFUR SAD
Function / homology
Function and homology information


protein-disulfide reductase activity / cell redox homeostasis / cytosol
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 speciesThermus thermophilus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.15 Å
AuthorsWeinert, T. / Waltersperger, S. / Olieric, V. / Panepucci, E. / Chen, L. / Rose, J.P. / Wang, M. / Wang, B.C. / Southeast Collaboratory for Structural Genomics (SECSG)
CitationJournal: Nat.Methods / Year: 2015
Title: Fast native-SAD phasing for routine macromolecular structure determination.
Authors: Weinert, T. / Olieric, V. / Waltersperger, S. / Panepucci, E. / Chen, L. / Zhang, H. / Zhou, D. / Rose, J. / Ebihara, A. / Kuramitsu, S. / Li, D. / Howe, N. / Schnapp, G. / Pautsch, A. / ...Authors: Weinert, T. / Olieric, V. / Waltersperger, S. / Panepucci, E. / Chen, L. / Zhang, H. / Zhou, D. / Rose, J. / Ebihara, A. / Kuramitsu, S. / Li, D. / Howe, N. / Schnapp, G. / Pautsch, A. / Bargsten, K. / Prota, A.E. / Surana, P. / Kottur, J. / Nair, D.T. / Basilico, F. / Cecatiello, V. / Pasqualato, S. / Boland, A. / Weichenrieder, O. / Wang, B.C. / Steinmetz, M.O. / Caffrey, M. / Wang, M.
History
DepositionJun 3, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 10, 2014Provider: repository / Type: Initial release
Revision 1.1Jan 14, 2015Group: Database references
Revision 1.2Feb 4, 2015Group: Derived calculations
Revision 1.3Feb 11, 2015Group: Database references
Revision 1.4Aug 12, 2015Group: Database references
Revision 1.5Nov 22, 2017Group: Derived calculations / Refinement description / Category: pdbx_struct_oper_list / software / Item: _pdbx_struct_oper_list.symmetry_operation
Revision 1.6Dec 27, 2023Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_special_symmetry
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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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)12,6897
Polymers12,4771
Non-polymers2136
Water61334
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)58.500, 58.500, 59.930
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212
Components on special symmetry positions
IDModelComponents
11A-205-

CL

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Components

#1: Protein Thioredoxin /


Mass: 12476.533 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermus thermophilus (bacteria) / Strain: HB27 / ATCC BAA-163 / DSM 7039 / Gene: TT_C1385 / Plasmid: PET11A / Production host: ESCHERICHIA COLI (E. coli) / References: UniProt: Q72HU9
#2: Chemical
ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Cl
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 34 / 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: 1

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Sample preparation

CrystalDensity Matthews: 2.04 Å3/Da / Density % sol: 39.59 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 7.3 / Details: 0.1 M HEPES buffer containing 4.3M NaCl, pH 7.3

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 2.066 Å
DetectorType: DECTRIS PILATUS 2M-F / Detector: PIXEL / Date: Aug 30, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 2.066 Å / Relative weight: 1
ReflectionResolution: 2.15→50 Å / Num. obs: 10426 / % possible obs: 95.5 % / Redundancy: 38.77 % / Rmerge(I) obs: 0.047 / Net I/σ(I): 40.45

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Processing

Software
NameVersionClassification
XDSdata reduction
SHELXDEphasing
CootFOLLOWED BY PHENIXmodel building
PHENIX(phenix.refine: 1.8.4_1496)refinement
SHELXCDphasing
SHELXDphasing
SHELXEFOLLOWED BY PHENIXmodel building
XSCALEdata scaling
RefinementResolution: 2.15→41.862 Å / SU ML: 0.29 / Cross valid method: FREE R-VALUE / σ(F): 1.58 / Phase error: 31.79 / Stereochemistry target values: MLHL
RfactorNum. reflection% reflection
Rfree0.2814 1004 10.04 %
Rwork0.226 --
obs0.2315 10001 92.64 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.15→41.862 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms813 0 6 34 853
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.003832
X-RAY DIFFRACTIONf_angle_d0.8821130
X-RAY DIFFRACTIONf_dihedral_angle_d13.668314
X-RAY DIFFRACTIONf_chiral_restr0.028127
X-RAY DIFFRACTIONf_plane_restr0.013145
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.15-2.26350.3429850.3211726X-RAY DIFFRACTION53
2.2635-2.40530.35631580.28651302X-RAY DIFFRACTION96
2.4053-2.5910.33811460.26651401X-RAY DIFFRACTION100
2.591-2.85170.29131640.27181385X-RAY DIFFRACTION100
2.8517-3.26420.38711430.26751400X-RAY DIFFRACTION100
3.2642-4.1120.24241610.191379X-RAY DIFFRACTION100
4.112-41.87010.23351470.19011404X-RAY DIFFRACTION100

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