2Q5C

Crystal structure of NtrC family transcriptional regulator from Clostridium acetobutylicum

• PDB DOI: https://doi.org/10.2210/pdb2Q5C/pdb

• Classification: TRANSCRIPTION
• Organism(s): Clostridium acetobutylicum ATCC 824
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2007-05-31 Released: 2007-07-03 
• Deposition Author(s): Ramagopal, U.A., Dickey, M., Toro, R., Iizuka, M., Groshong, K., Rodgers, L., Sauder, J.M., Burley, S.K., Almo, S.C., New York SGX Research Center for Structural Genomics (NYSGXRC)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.49 Å
• R-Value Free: 0.210 
• R-Value Work: 0.187 
• R-Value Observed: 0.188 

Literature

Crystal structure of NtrC family transcriptional regulator from Clostridium acetobutylicum.

Ramagopal, U.A., Dickey, M., Toro, R., Iizuka, M., Groshong, K., Rodgers, L., Sauder, J.M., Burley, S.K., Almo, S.C.

To be published.

Biological Assembly 1  

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

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

Biological Assembly 2  

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

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

Biological Assembly 3  

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

Biological assembly 3 generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 45.29 kDa 
• Atom Count: 3,566 
• Modelled Residue Count: 374 
• Deposited Residue Count: 392 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
NtrC family transcriptional regulator	A, B [auth D]	196	Clostridium acetobutylicum ATCC 824	Mutation(s): 0  Gene Names: CA_C0459
UniProt
Find proteins for Q97LU5 (Clostridium acetobutylicum (strain ATCC 824 / DSM 792 / JCM 1419 / IAM 19013 / LMG 5710 / NBRC 13948 / NRRL B-527 / VKM B-1787 / 2291 / W)) Explore Q97LU5  Go to UniProtKB:  Q97LU5

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
SO4	C [auth A], D [auth A], E [auth A], F [auth A], G [auth A], J [auth D], K [auth D], L [auth D], M [auth D], N [auth D], O [auth D]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L
GOL	H [auth A], I [auth A], P [auth D], Q [auth D]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.49 Å
• R-Value Free: 0.210 
• R-Value Work: 0.187 
• R-Value Observed: 0.188 
• Space Group: P 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 45.95	α = 72.94
b = 45.948	β = 72.98
c = 58.284	γ = 82.07

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction
HKL-2000	data reduction
SHELX	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2007-07-03 
Deposition Author(s): Ramagopal, U.A., Dickey, M., Toro, R., Iizuka, M., Groshong, K., Rodgers, L., Sauder, J.M., Burley, S.K., Almo, S.C., New York SGX Research Center for Structural Genomics (NYSGXRC)

Revision History  

• Version 1.0: 2007-07-03
  Type: Initial release
  
• Version 1.1: 2008-05-01
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Derived calculations, Version format compliance
• Version 1.3: 2017-10-18
  Changes: Refinement description
• Version 1.4: 2018-11-14
  Changes: Data collection, Structure summary
• Version 1.5: 2021-02-03
  Changes: Database references, Derived calculations, Structure summary
• Version 1.6: 2024-02-21
  Changes: Data collection, Database references