6BXG

1.45 Angstrom Resolution Crystal Structure of PDZ domain of Carboxy-Terminal Protease from Vibrio cholerae in Complex with Peptide.

• PDB DOI: https://doi.org/10.2210/pdb6BXG/pdb

• Classification: HYDROLASE/PEPTIDE
• Organism(s): Vibrio cholerae O1 biovar El Tor str. N16961, Escherichia coli
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2017-12-18 Released: 2018-01-03 
• Deposition Author(s): Minasov, G., Shuvalova, L., Filippova, E.V., Kiryukhina, O., Grimshaw, S., Kwon, K., Anderson, W.F., Satchell, K.J.F., Joachimiak, A., Center for Structural Genomics of Infectious Diseases (CSGID)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.45 Å
• R-Value Free: 0.178 
• R-Value Work: 0.132 
• R-Value Observed: 0.135 

Literature

1.45 Angstrom Resolution Crystal Structure of PDZ domain of Carboxy-Terminal Protease from Vibrio cholerae in Complex with Peptide.

Minasov, G., Shuvalova, L., Filippova, E.V., Kiryukhina, O., Grimshaw, S., Kwon, K., Anderson, W.F., Satchell, K.J.F., Joachimiak, A., Center for Structural Genomics of Infectious Diseases (CSGID)

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors.

Biological Assembly 2  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 2 assigned by authors.

Macromolecule Content

• Total Structure Weight: 12.52 kDa 
• Atom Count: 895 
• Modelled Residue Count: 101 
• Deposited Residue Count: 105 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Tail-specific protease	A	102	Vibrio cholerae O1 biovar El Tor str. N16961	Mutation(s): 0  Gene Names: VC_1496
UniProt
Find proteins for Q9KRY7 (Vibrio cholerae serotype O1 (strain ATCC 39315 / El Tor Inaba N16961)) Explore Q9KRY7  Go to UniProtKB:  Q9KRY7

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
LEU-ILE-ALA	B	3	Escherichia coli	Mutation(s): 0

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
IOD	E [auth A], F [auth A], G [auth A], H [auth A], I [auth A], J [auth A], K [auth A], L [auth A], M [auth A], N [auth A]	IODIDE ION I XMBWDFGMSWQBCA-UHFFFAOYSA-M
CL	C [auth A], D [auth A]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M

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

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.45 Å
• R-Value Free: 0.178 
• R-Value Work: 0.132 
• R-Value Observed: 0.135 
• Space Group: P 6₅
• Diffraction Data: https://doi.org/10.18430/m36bxg

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 35.579	α = 90
b = 35.579	β = 90
c = 118.394	γ = 120

Software Package:

Software Name	Purpose
REFMAC	refinement
HKL-3000	data reduction
HKL-3000	data scaling
HKL-3000	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2018-01-03 
Deposition Author(s): Minasov, G., Shuvalova, L., Filippova, E.V., Kiryukhina, O., Grimshaw, S., Kwon, K., Anderson, W.F., Satchell, K.J.F., Joachimiak, A., Center for Structural Genomics of Infectious Diseases (CSGID)

Revision History  

• Version 1.0: 2018-01-03
  Type: Initial release
  
• Version 1.1: 2024-11-20
  Changes: Data collection, Database references, Structure summary