4TN8 | pdb_00004tn8

Crystal structure of Thermus Thermophilus thioredoxin solved by sulfur SAD using Swiss Light Source data

• PDB DOI: https://doi.org/10.2210/pdb4TN8/pdb

• Classification: ELECTRON TRANSPORT
• Organism(s): Thermus thermophilus HB27
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2014-06-03 Released: 2014-12-10 
• Deposition Author(s): Weinert, T., Waltersperger, S., Olieric, V., Panepucci, E., Chen, L., Rose, J.P., Wang, M., Wang, B.C., Southeast Collaboratory for Structural Genomics (SECSG)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.15 Å
• R-Value Free: 
  0.281 (Depositor), 0.280 (DCC) 
• R-Value Work: 
  0.226 (Depositor), 0.231 (DCC) 
• R-Value Observed: 
  0.232 (Depositor) 

Literature

Fast native-SAD phasing for routine macromolecular structure determination.

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.

(2015) Nat Methods 12: 131-133

• PubMed: 25506719 
• DOI: https://doi.org/10.1038/nmeth.3211
• Primary Citation Related Structures: 
  4PGO, 4PII, 4R8T, 4R8U, 4TN8, 4TNO, 4WAB, 4WAU, 4WBQ, 4WBX


• PubMed Abstract: 
  

  We describe a data collection method that uses a single crystal to solve X-ray structures by native SAD (single-wavelength anomalous diffraction). We solved the structures of 11 real-life examples, including a human membrane protein, a protein-DNA complex and a 266-kDa multiprotein-ligand complex, using this method. The data collection strategy is suitable for routine structure determination and can be implemented at most macromolecular crystallography synchrotron beamlines.

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Organizational Affiliation: 
• Swiss Light Source at Paul Scherrer Institut, Villigen, Switzerland.
Department of Biochemistry and Molecular Biology, University of Georgia, Athens, Georgia, USA.
Laboratory of Biological Chemistry, Faculty of Applied Biological Sciences, Gifu University, Gifu, Japan.
Department of Biological Sciences, Graduate School of Science, Osaka University, Osaka, Japan.
Membrane Structural and Functional Biology Group, School of Medicine and School of Biochemistry and Immunology, Trinity College Dublin, Dublin, Ireland.
Boehringer Ingelheim Pharma GmbH and Co. KG, Biberach an der Riss, Germany.
Laboratory of Biomolecular Research, Department of Biology and Chemistry, Paul Scherrer Institut, Villigen, Switzerland.
National Centre for Biological Sciences, Bangalore, India.
Department of Experimental Oncology, European Institute of Oncology, Milan, Italy.
Department of Biochemistry, Max Planck Institute for Developmental Biology, Tübingen, Germany.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 12.69 kDa 
• Atom Count: 853 
• Modeled Residue Count: 103 
• Deposited Residue Count: 110 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Thioredoxin	A	110	Thermus thermophilus HB27	Mutation(s): 0  Gene Names: TT_C1385
UniProt
Find proteins for Q72HU9 (Thermus thermophilus (strain ATCC BAA-163 / DSM 7039 / HB27)) Explore Q72HU9  Go to UniProtKB:  Q72HU9

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
CL	B [auth A], C [auth A], D [auth A], E [auth A], F [auth A], G [auth A]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.15 Å
• R-Value Free:  0.281 (Depositor), 0.280 (DCC) 
• R-Value Work:  0.226 (Depositor), 0.231 (DCC) 
• R-Value Observed: 0.232 (Depositor) 

Space Group: P 4₃ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 58.5	α = 90
b = 58.5	β = 90
c = 59.93	γ = 90

Software Package:

Software Name	Purpose
XDS	data reduction
SHELXDE	phasing
Coot	model building
PHENIX	refinement
SHELXCD	phasing
SHELXD	phasing
SHELXE	model building
XSCALE	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2014-12-10 
Deposition Author(s): Weinert, T., Waltersperger, S., Olieric, V., Panepucci, E., Chen, L., Rose, J.P., Wang, M., Wang, B.C., Southeast Collaboratory for Structural Genomics (SECSG)

Revision History  

• Version 1.0: 2014-12-10
  Type: Initial release
  
• Version 1.1: 2015-01-14
  Changes: Database references
• Version 1.2: 2015-02-04
  Changes: Derived calculations
• Version 1.3: 2015-02-11
  Changes: Database references
• Version 1.4: 2015-08-12
  Changes: Database references
• Version 1.5: 2017-11-22
  Changes: Derived calculations, Refinement description
• Version 1.6: 2023-12-27
  Changes: Data collection, Database references, Derived calculations