3JVD | pdb_00003jvd

Crystal structure of putative transcription regulation repressor (LACI family) FROM Corynebacterium glutamicum

• PDB DOI: https://doi.org/10.2210/pdb3JVD/pdb

• Classification: TRANSCRIPTION REGULATOR
• Organism(s): Corynebacterium glutamicum
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2009-09-16 Released: 2009-09-22 
• Deposition Author(s): Patskovsky, Y., Ramagopal, U., Toro, R., Foti, R., Freeman, J., Do, J., 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: 2.30 Å
• R-Value Free: 
  0.284 (Depositor), 0.286 (DCC) 
• R-Value Work: 
  0.224 (Depositor), 0.224 (DCC) 
• R-Value Observed: 
  0.226 (Depositor) 

Literature

Crystal structure of LACI family protein from Corynebacterium glutamicum

Patskovsky, Y., Ramagopal, U., Toro, R., Foti, R., Freeman, J., Do, J., Sauder, J.M., Burley, S.K., Almo, S.C.

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)

Macromolecule Content 

• Total Structure Weight: 71.85 kDa 
• Atom Count: 3,989 
• Modeled Residue Count: 513 
• Deposited Residue Count: 666 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Transcriptional regulators	A, B	333	Corynebacterium glutamicum	Mutation(s): 0  Gene Names: Cgl2044, ycza
UniProt
Find proteins for Q8NNY3 (Corynebacterium glutamicum (strain ATCC 13032 / DSM 20300 / JCM 1318 / BCRC 11384 / CCUG 27702 / LMG 3730 / NBRC 12168 / NCIMB 10025 / NRRL B-2784 / 534)) Explore Q8NNY3  Go to UniProtKB:  Q8NNY3

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
SO4	C [auth A], D [auth A], E [auth A]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L
GOL	F [auth B]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.30 Å
• R-Value Free:  0.284 (Depositor), 0.286 (DCC) 
• R-Value Work:  0.224 (Depositor), 0.224 (DCC) 
• R-Value Observed: 0.226 (Depositor) 

Space Group: P 6₅ 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 91.97	α = 90
b = 91.97	β = 90
c = 285.453	γ = 120

Software Package:

Software Name	Purpose
SHELX	model building
REFMAC	refinement
HKL-2000	data reduction
HKL-2000	data scaling
SHELX	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2009-09-22 
Deposition Author(s): Patskovsky, Y., Ramagopal, U., Toro, R., Foti, R., Freeman, J., Do, J., Sauder, J.M., Burley, S.K., Almo, S.C., New York SGX Research Center for Structural Genomics (NYSGXRC)

Revision History  

• Version 1.0: 2009-09-22
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Non-polymer description, Version format compliance
• Version 1.2: 2018-11-21
  Changes: Data collection, Structure summary
• Version 1.3: 2021-02-10
  Changes: Database references, Derived calculations, Structure summary
• Version 1.4: 2024-02-21
  Changes: Data collection, Database references