4RK6

Crystal structure of LacI family transcriptional regulator CCPA from Weissella paramesenteroides, Target EFI-512926, with bound glucose

• PDB DOI: https://doi.org/10.2210/pdb4RK6/pdb

• Classification: TRANSCRIPTION REGULATOR
• Organism(s): Weissella paramesenteroides ATCC 33313
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2014-10-11 Released: 2014-10-29 
• Deposition Author(s): Patskovsky, Y., Toro, R., Bhosle, R., Al Obaidi, N., Chamala, S., Attonito, J.D., Scott Glenn, A., Chowdhury, S., Lafleur, J., Siedel, R.D., Hillerich, B., Love, J., Whalen, K.L., Gerlt, J.A., Almo, S.C., Enzyme Function Initiative (EFI)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.76 Å
• R-Value Free: 0.198 
• R-Value Work: 0.168 
• R-Value Observed: 0.169 

Literature

Crystal structure of transcriptional regulator CCPA from Weissella paramesenteroides, Target EFI-512926

Patskovsky, Y., Toro, R., Bhosle, R., Al Obaidi, N., Chamala, S., Scott Glenn, A., Attonito, J.D., Chowdhury, S., Lafleur, J., Siedel, R.D., Hillerich, B., Love, J., Whalen, K.L., Gerlt, J.A., 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: 65.44 kDa 
• Atom Count: 4,718 
• Modelled Residue Count: 539 
• Deposited Residue Count: 574 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Glucose-resistance amylase regulator	A, B	287	Weissella paramesenteroides ATCC 33313	Mutation(s): 0  Gene Names: ccpA, HMPREF0877_1426
UniProt
Find proteins for C5RBT0 (Weissella paramesenteroides ATCC 33313) Explore C5RBT0  Go to UniProtKB:  C5RBT0

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
GLC	C [auth A], D [auth B]	alpha-D-glucopyranose C6 H12 O6 WQZGKKKJIJFFOK-DVKNGEFBSA-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: 1.76 Å
• R-Value Free: 0.198 
• R-Value Work: 0.168 
• R-Value Observed: 0.169 
• Space Group: P 4₃ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 102.564	α = 90
b = 102.564	β = 90
c = 128.055	γ = 90

Software Package:

Software Name	Purpose
CBASS	data collection
SHELX	model building
ARP/wARP	model building
REFMAC	refinement
HKL-2000	data reduction
HKL-2000	data scaling
SHELX	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2014-10-29 
Deposition Author(s): Patskovsky, Y., Toro, R., Bhosle, R., Al Obaidi, N., Chamala, S., Attonito, J.D., Scott Glenn, A., Chowdhury, S., Lafleur, J., Siedel, R.D., Hillerich, B., Love, J., Whalen, K.L., Gerlt, J.A., Almo, S.C., Enzyme Function Initiative (EFI)

Revision History  

• Version 1.0: 2014-10-29
  Type: Initial release
  
• Version 1.1: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Data collection, Database references, Derived calculations, Structure summary