3K9C | pdb_00003k9c

Crystal structure of LacI Transcriptional regulator from Rhodococcus species.

• PDB DOI: https://doi.org/10.2210/pdb3K9C/pdb

• Classification: transcription regulator
• Organism(s): Rhodococcus jostii RHA1
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2009-10-15 Released: 2009-11-03 
• Deposition Author(s): Damodharan, L., Burley, S.K., Swaminathan, S., New York SGX Research Center for Structural Genomics (NYSGXRC)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.14 Å
• R-Value Free: 
  0.243 (Depositor), 0.240 (DCC) 
• R-Value Work: 
  0.209 (Depositor), 0.210 (DCC) 
• R-Value Observed: 
  0.209 (Depositor) 

Literature

Crystal structure of LacI Transcriptional regulator from Rhodococcus species.

Damodhran, L., Burley, S.K., Swaminathan, S.

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: 61.81 kDa 
• Atom Count: 4,180 
• Modeled Residue Count: 539 
• Deposited Residue Count: 578 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Transcriptional regulator, LacI family protein	A, B	289	Rhodococcus jostii RHA1	Mutation(s): 0  Gene Names: RHA1_ro05266
UniProt
Find proteins for Q0S5Y9 (Rhodococcus jostii (strain RHA1)) Explore Q0S5Y9  Go to UniProtKB:  Q0S5Y9

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
GOL	C [auth A], D [auth B]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N

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: 2.14 Å
• R-Value Free:  0.243 (Depositor), 0.240 (DCC) 
• R-Value Work:  0.209 (Depositor), 0.210 (DCC) 
• R-Value Observed: 0.209 (Depositor) 

Space Group: C 2 2 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 98.435	α = 90
b = 100.543	β = 90
c = 106.433	γ = 90

Software Package:

Software Name	Purpose
CBASS	data collection
SHARP	phasing
CNS	refinement
HKL-2000	data reduction
HKL-2000	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2009-11-03 
Deposition Author(s): Damodharan, L., Burley, S.K., Swaminathan, S., New York SGX Research Center for Structural Genomics (NYSGXRC)

Revision History  

• Version 1.0: 2009-11-03
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Source and taxonomy, Version format compliance
• Version 1.2: 2021-02-10
  Changes: Database references, Derived calculations, Structure summary
• Version 1.3: 2024-11-27
  Changes: Data collection, Database references, Structure summary