2PJU

Crystal structure of propionate catabolism operon regulatory protein prpR

• PDB DOI: https://doi.org/10.2210/pdb2PJU/pdb

• Classification: TRANSCRIPTION
• Organism(s): Escherichia coli
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): Yes 


• Deposited: 2007-04-16 Released: 2007-05-22 
• Deposition Author(s): Ramagopal, U.A., Toro, R., Gilmore, M., Wu, B., Koss, J., Groshong, C., Gheyi, T., 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: 2.10 Å
• R-Value Free: 
  0.252 (Depositor), 0.270 (DCC) 
• R-Value Work: 
  0.201 (Depositor), 0.230 (DCC) 
• R-Value Observed: 
  0.204 (Depositor) 

Literature

Crystal structure of propionate catabolism operon regulatory protein prpR

Ramagopal, U.A., Toro, R., Gilmore, M., Wu, B., Koss, J., Groshong, C., Gheyi, T., 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: 100.31 kDa 
• Atom Count: 6,218 
• Modelled Residue Count: 766 
• Deposited Residue Count: 900 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Propionate catabolism operon regulatory protein	A, B, C, D	225	Escherichia coli	Mutation(s): 1  Gene Names: prpR, b0330, JW0322
UniProt
Find proteins for P77743 (Escherichia coli (strain K12)) Explore P77743  Go to UniProtKB:  P77743

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.10 Å
• R-Value Free:  0.252 (Depositor), 0.270 (DCC) 
• R-Value Work:  0.201 (Depositor), 0.230 (DCC) 
• R-Value Observed: 0.204 (Depositor) 

Space Group: P 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 35.657	α = 85.03
b = 58.545	β = 88.56
c = 103.576	γ = 86.94

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction
MAR345	data collection
HKL-2000	data reduction
HKL2Map	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2007-05-22 
Deposition Author(s): Ramagopal, U.A., Toro, R., Gilmore, M., Wu, B., Koss, J., Groshong, C., Gheyi, T., Sauder, J.M., Burley, S.K., Almo, S.C., New York SGX Research Center for Structural Genomics (NYSGXRC)

Revision History  

• Version 1.0: 2007-05-22
  Type: Initial release
  
• Version 1.1: 2008-05-01
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: 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, Structure summary
• Version 1.6: 2021-10-20
  Changes: Database references
• Version 1.7: 2024-02-21
  Changes: Data collection