5UM7 | pdb_00005um7

Crystal structure of the reduced state of the thiol-disulfide reductase SdbA from Streptococcus gordonii

• PDB DOI: https://doi.org/10.2210/pdb5UM7/pdb

• Classification: OXIDOREDUCTASE
• Organism(s): Streptococcus gordonii str. Challis substr. CH1
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2017-01-26 Released: 2017-02-15 
• Deposition Author(s): Stogios, P.J., Evdokimova, E., Wawrzak, Z., Yim, V., Savchenko, A., Anderson, W.F., Center for Structural Genomics of Infectious Diseases (CSGID)
• Funding Organization(s): National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.62 Å
• R-Value Free: 
  0.292 (Depositor), 0.289 (DCC) 
• R-Value Work: 
  0.238 (Depositor), 0.238 (DCC) 
• R-Value Observed: 
  0.246 (Depositor) 

Starting Model: experimental

Literature

Crystal structure of the reduced state of the thiol-disulfide reductase SdbA from Streptococcus gordonii

Stogios, P.J.

To be published.

Biological Assembly 1  

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

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

Biological Assembly 2  

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

Biological assembly 2 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 43.97 kDa 
• Atom Count: 2,796 
• Modeled Residue Count: 282 
• Deposited Residue Count: 374 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Thioredoxin signature protein	A, B	187	Streptococcus gordonii str. Challis substr. CH1	Mutation(s): 0  Gene Names: SGO_2006
UniProt
Find proteins for A8AZP5 (Streptococcus gordonii (strain Challis / ATCC 35105 / BCRC 15272 / CH1 / DL1 / V288)) Explore A8AZP5  Go to UniProtKB:  A8AZP5

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
ACT	C [auth A]	ACETATE ION C2 H3 O2 QTBSBXVTEAMEQO-UHFFFAOYSA-M

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.62 Å
• R-Value Free:  0.292 (Depositor), 0.289 (DCC) 
• R-Value Work:  0.238 (Depositor), 0.238 (DCC) 
• R-Value Observed: 0.246 (Depositor) 

Diffraction Data: https://doi.org/10.18430/m35um7

Space Group: C 2 2 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 49.25	α = 90
b = 49.32	β = 90
c = 196.54	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data reduction
Aimless	data scaling
BALBES	phasing
PHENIX	model building
Coot	model building

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2017-02-15 
Deposition Author(s): Stogios, P.J., Evdokimova, E., Wawrzak, Z., Yim, V., Savchenko, A., Anderson, W.F., Center for Structural Genomics of Infectious Diseases (CSGID)

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Funding Organization	Location	Grant Number
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)	United States	HHSCN27220120026C

Revision History  

• Version 1.0: 2017-02-15
  Type: Initial release
  
• Version 1.1: 2017-09-27
  Changes: Author supporting evidence
• Version 1.2: 2019-12-11
  Changes: Author supporting evidence, Database references
• Version 1.3: 2023-10-04
  Changes: Data collection, Database references, Refinement description