3K20 | pdb_00003k20

X-ray structure of oxidoreductase from corynebacterium diphtheriae,hexagonal crystal form. northeast structural genomics consortium target cdr100d

• PDB DOI: https://doi.org/10.2210/pdb3K20/pdb

• Classification: OXIDOREDUCTASE
• Organism(s): Corynebacterium diphtheriae
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2009-09-29 Released: 2009-10-20 
• Deposition Author(s): Kuzin, A., Lew, S., Sahdev, S., Xiao, R., Ciccosanti, C., Wang, H., Everett, J.K., Nair, R., Acton, T.B., Rost, B., Montelione, G.T., Tong, L., Hunt, J.F., Northeast Structural Genomics Consortium (NESG)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.50 Å
• R-Value Free: 
  0.246 (Depositor), 0.235 (DCC) 
• R-Value Work: 
  0.229 (Depositor), 0.223 (DCC) 
• R-Value Observed: 
  0.230 (Depositor) 

Literature

Northeast Structural Genomics Consortium Target CdR100D

Kuzin, A., Lew, S., Seetharaman, J., Sahdev, S., Xiao, R., Ciccosanti, C., Wang, H., Everett, J.K., Nair, R., Acton, T.B., Rost, B., Montelione, G.T., Tong, L., Hunt, J.F.

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: 20.84 kDa 
• Atom Count: 1,381 
• Modeled Residue Count: 181 
• Deposited Residue Count: 191 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
oxidoreductase	A	191	Corynebacterium diphtheriae	Mutation(s): 0  Gene Names: DIP1437
UniProt
Find proteins for Q6NGS1 (Corynebacterium diphtheriae (strain ATCC 700971 / NCTC 13129 / Biotype gravis)) Explore Q6NGS1  Go to UniProtKB:  Q6NGS1

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
SO4	B [auth A], C [auth A], D [auth A], E [auth A]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L

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

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.50 Å
• R-Value Free:  0.246 (Depositor), 0.235 (DCC) 
• R-Value Work:  0.229 (Depositor), 0.223 (DCC) 
• R-Value Observed: 0.230 (Depositor) 

Space Group: P 6₄ 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 99.839	α = 90
b = 99.839	β = 90
c = 137.309	γ = 120

Software Package:

Software Name	Purpose
PHENIX	refinement
PDB_EXTRACT	data extraction
DENZO	data reduction
SCALEPACK	data scaling
PHENIX	phasing
REFMAC	refinement

Structure Validation

Entry History 

Deposition Data

• Released Date: 2009-10-20 
Deposition Author(s): Kuzin, A., Lew, S., Sahdev, S., Xiao, R., Ciccosanti, C., Wang, H., Everett, J.K., Nair, R., Acton, T.B., Rost, B., Montelione, G.T., Tong, L., Hunt, J.F., Northeast Structural Genomics Consortium (NESG)

Revision History  

• Version 1.0: 2009-10-20
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance
• Version 1.2: 2019-07-17
  Changes: Data collection, Derived calculations, Refinement description
• Version 1.3: 2024-11-06
  Changes: Data collection, Database references, Derived calculations, Structure summary