3DBI | pdb_00003dbi

CRYSTAL STRUCTURE OF SUGAR-BINDING TRANSCRIPTIONAL REGULATOR (LACI FAMILY) FROM ESCHERICHIA COLI COMPLEXED WITH PHOSPHATE

• PDB DOI: https://doi.org/10.2210/pdb3DBI/pdb

• Classification: TRANSCRIPTION REGULATOR
• Organism(s): Escherichia coli K-12
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2008-06-01 Released: 2008-07-01 
• Deposition Author(s): Patskovsky, Y., Ozyurt, S., Freeman, J., Wu, B., Maletic, M., Koss, J., Wasserman, S.R., 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: 2.45 Å
• R-Value Free: 
  0.270 (Depositor), 0.263 (DCC) 
• R-Value Work: 
  0.231 (Depositor), 0.229 (DCC) 
• R-Value Observed: 
  0.232 (Depositor) 

Literature

Crystal Structure of Sugar-Binding Transcriptional Regulator (LacI Family) from Escherichia Coli Complexed with Phosphate.

Patskovsky, Y., Ozyurt, S., Freeman, J., Wu, B., Maletic, M., Koss, J., Wasserman, S.R., 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)

Biological Assembly 2  

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

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

Macromolecule Content 

• Total Structure Weight: 113.1 kDa 
• Atom Count: 6,617 
• Modeled Residue Count: 833 
• Deposited Residue Count: 1,014 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
SUGAR-BINDING TRANSCRIPTIONAL REGULATOR, LACI FAMILY	A, B, C	338	Escherichia coli K-12	Mutation(s): 0  Gene Names: LACI
UniProt
Find proteins for P24242 (Escherichia coli (strain K12)) Explore P24242  Go to UniProtKB:  P24242

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
PO4	D [auth A], F [auth B], G [auth C]	PHOSPHATE ION O4 P NBIIXXVUZAFLBC-UHFFFAOYSA-K
GOL	E [auth A]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N

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

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.45 Å
• R-Value Free:  0.270 (Depositor), 0.263 (DCC) 
• R-Value Work:  0.231 (Depositor), 0.229 (DCC) 
• R-Value Observed: 0.232 (Depositor) 

Space Group: P 4₃ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 82.468	α = 90
b = 82.468	β = 90
c = 341.448	γ = 90

Software Package:

Software Name	Purpose
SHELXD	phasing
REFMAC	refinement
HKL-2000	data reduction
HKL-2000	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2008-07-01 
Deposition Author(s): Patskovsky, Y., Ozyurt, S., Freeman, J., Wu, B., Maletic, M., Koss, J., Wasserman, S.R., Sauder, J.M., Burley, S.K., Almo, S.C., New York SGX Research Center for Structural Genomics (NYSGXRC)

Revision History  

• Version 1.0: 2008-07-01
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Non-polymer description, Version format compliance
• Version 1.2: 2018-11-14
  Changes: Data collection, Structure summary
• Version 1.3: 2021-02-03
  Changes: Database references, Derived calculations, Structure summary
• Version 1.4: 2024-10-09
  Changes: Data collection, Database references, Refinement description, Structure summary