3L5Z | pdb_00003l5z

Crystal structure of transcriptional regulator, GntR family from Bacillus cereus

• PDB DOI: https://doi.org/10.2210/pdb3L5Z/pdb

• Classification: transcription regulator
• Organism(s): Bacillus cereus ATCC 10987
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2009-12-22 Released: 2010-01-05 
• Deposition Author(s): Chang, C., Hatzos, C., Feldmann, B., Clancy, S., Joachimiak, A., Midwest Center for Structural Genomics (MCSG)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.90 Å
• R-Value Free: 
  0.243 (Depositor), 0.247 (DCC) 
• R-Value Work: 
  0.204 (Depositor), 0.211 (DCC) 
• R-Value Observed: 
  0.206 (Depositor) 

Literature

Crystal structure of transcriptional regulator, GntR family from Bacillus cereus

Chang, C., Hatzos, C., Feldmann, B., Clancy, S., Joachimiak, A.

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: 36.02 kDa 
• Atom Count: 2,363 
• Modeled Residue Count: 286 
• Deposited Residue Count: 312 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Transcriptional regulator, GntR family	A, B	156	Bacillus cereus ATCC 10987	Mutation(s): 0  Gene Names: BCE_3424
UniProt
Find proteins for Q734I1 (Bacillus cereus (strain ATCC 10987 / NRS 248)) Explore Q734I1  Go to UniProtKB:  Q734I1

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
PG5	D [auth B]	1-METHOXY-2-[2-(2-METHOXY-ETHOXY]-ETHANE C8 H18 O4 YFNKIDBQEZZDLK-UHFFFAOYSA-N
EDO	C [auth B]	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-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: 2.90 Å
• R-Value Free:  0.243 (Depositor), 0.247 (DCC) 
• R-Value Work:  0.204 (Depositor), 0.211 (DCC) 
• R-Value Observed: 0.206 (Depositor) 

Space Group: P 4₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 121.191	α = 90
b = 121.191	β = 90
c = 114.693	γ = 90

Software Package:

Software Name	Purpose
SBC-Collect	data collection
HKL-3000	phasing
SHELXD	phasing
SHELXE	model building
MLPHARE	phasing
DM	model building
RESOLVE	model building
Coot	model building
ARP/wARP	model building
REFMAC	refinement
HKL-3000	data reduction
HKL-3000	data scaling
DM	phasing
RESOLVE	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2010-01-05 
Deposition Author(s): Chang, C., Hatzos, C., Feldmann, B., Clancy, S., Joachimiak, A., Midwest Center for Structural Genomics (MCSG)

Revision History  

• Version 1.0: 2010-01-05
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Advisory, Refinement description, Version format compliance
• Version 1.2: 2017-11-01
  Changes: Refinement description
• Version 1.3: 2024-11-20
  Changes: Data collection, Database references, Derived calculations, Structure summary