3NPI

Crystal structure of a TetR family regulatory protein (DIP1788) from CORYNEBACTERIUM DIPHTHERIAE at 2.96 A resolution

• PDB DOI: https://doi.org/10.2210/pdb3NPI/pdb

• Classification: GENE REGULATION
• Organism(s): Corynebacterium diphtheriae
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2010-06-28 Released: 2010-08-18 
• Deposition Author(s): Joint Center for Structural Genomics (JCSG)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.96 Å
• R-Value Free: 0.222 
• R-Value Work: 0.201 
• R-Value Observed: 0.202 

Literature

Crystal structure of a TetR family regulatory protein (DIP1788) from CORYNEBACTERIUM DIPHTHERIAE at 2.96 A resolution

Joint Center for Structural Genomics (JCSG)

To be published.

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

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

Biological Assembly Evidence: gel filtration, light scattering

Macromolecule Content

• Total Structure Weight: 57.2 kDa 
• Atom Count: 3,211 
• Modelled Residue Count: 423 
• Deposited Residue Count: 502 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
TetR family regulatory protein	A, B	251	Corynebacterium diphtheriae	Mutation(s): 0  Gene Names: DIP1788
UniProt
Find proteins for Q6NFU8 (Corynebacterium diphtheriae (strain ATCC 700971 / NCTC 13129 / Biotype gravis)) Explore Q6NFU8  Go to UniProtKB:  Q6NFU8

Small Molecules

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

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

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.96 Å
• R-Value Free: 0.222 
• R-Value Work: 0.201 
• R-Value Observed: 0.202 
• Space Group: P 3₂ 2 1
• Diffraction Data: https://doi.org/10.18430/M33NPI

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 137.238	α = 90
b = 137.238	β = 90
c = 54.725	γ = 120

Software Package:

Software Name	Purpose
SHELX	phasing
BUSTER-TNT	refinement
XSCALE	data processing
PDB_EXTRACT	data extraction
XDS	data reduction
XSCALE	data scaling
autoSHARP	phasing
BUSTER	refinement

Structure Validation

Entry History 

Deposition Data

• Released Date: 2010-08-18 
Deposition Author(s): Joint Center for Structural Genomics (JCSG)

Revision History  

• Version 1.0: 2010-08-18
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance
• Version 1.2: 2013-02-13
  Changes: Structure summary
• Version 1.3: 2017-10-25
  Changes: Author supporting evidence
• Version 1.4: 2023-02-01
  Changes: Database references, Derived calculations
• Version 1.5: 2024-11-20
  Changes: Data collection, Structure summary