3LOR | pdb_00003lor

The Crystal Structure of a Thiol-disulfide Isomerase from Corynebacterium glutamicum to 2.2A

• PDB DOI: https://doi.org/10.2210/pdb3LOR/pdb

• Classification: ISOMERASE
• Organism(s): Corynebacterium glutamicum ATCC 13032
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2010-02-04 Released: 2010-03-16 
• Deposition Author(s): Stein, A.J., Osipiuk, J., Weger, A., Cobb, G., Joachimiak, A., Midwest Center for Structural Genomics (MCSG)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.20 Å
• R-Value Free: 
  0.259 (Depositor), 0.276 (DCC) 
• R-Value Work: 
  0.212 (Depositor), 0.228 (DCC) 
• R-Value Observed: 
  0.214 (Depositor) 

Literature

The Crystal Structure of a Thiol-disulfide Isomerase from Corynebacterium glutamicum to 2.2A

Stein, A.J., Osipiuk, J., Weger, A., Cobb, G., Joachimiak, A.

To be published.

Biological Assembly 1  

Global Symmetry: Dihedral - D2  (Explore in 3D)
Global Stoichiometry: Homo 4-mer - A4 

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

Macromolecule Content 

• Total Structure Weight: 73.38 kDa 
• Atom Count: 4,860 
• Modeled Residue Count: 610 
• Deposited Residue Count: 640 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Thiol-disulfide isomerase and thioredoxins	A, B, C, D	160	Corynebacterium glutamicum ATCC 13032	Mutation(s): 0  Gene Names: cg1043, Cgl0914
UniProt
Find proteins for Q8NRX7 (Corynebacterium glutamicum (strain ATCC 13032 / DSM 20300 / JCM 1318 / BCRC 11384 / CCUG 27702 / LMG 3730 / NBRC 12168 / NCIMB 10025 / NRRL B-2784 / 534)) Explore Q8NRX7  Go to UniProtKB:  Q8NRX7

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
ACT	H [auth B]	ACETATE ION C2 H3 O2 QTBSBXVTEAMEQO-UHFFFAOYSA-M
CA	G [auth B]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N
CL	E [auth A], F [auth B], I [auth C], J [auth D], K [auth D]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
MSE	A, B, C, D	L-PEPTIDE LINKING	C5 H11 N O2 Se		MET

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.20 Å
• R-Value Free:  0.259 (Depositor), 0.276 (DCC) 
• R-Value Work:  0.212 (Depositor), 0.228 (DCC) 
• R-Value Observed: 0.214 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 78.19	α = 90
b = 78.892	β = 90
c = 124.229	γ = 90

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction
SBC-Collect	data collection
SHELX	phasing
MLPHARE	phasing
DM	phasing
ARP/wARP	model building
Coot	model building

Structure Validation

Entry History 

Deposition Data

• Released Date: 2010-03-16 
Deposition Author(s): Stein, A.J., Osipiuk, J., Weger, A., Cobb, G., Joachimiak, A., Midwest Center for Structural Genomics (MCSG)

Revision History  

• Version 1.0: 2010-03-16
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Advisory, Version format compliance
• Version 1.2: 2017-11-01
  Changes: Refinement description
• Version 1.3: 2024-10-30
  Changes: Data collection, Database references, Derived calculations, Structure summary