6X2D | pdb_00006x2d

Crystal Structure of DNase I Domain of Ribonuclease E from Vibrio cholerae

• PDB DOI: https://doi.org/10.2210/pdb6X2D/pdb

• Classification: RNA BINDING PROTEIN
• Organism(s): Vibrio cholerae O1 biovar El Tor str. N16961
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2020-05-20 Released: 2020-06-10 
• Deposition Author(s): Minasov, G., Shuvalova, L., Kiryukhina, O., Dubrovska, I., Wiersum, G., Satchell, K.J.F., Center for Structural Genomics of Infectious Diseases (CSGID)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.85 Å
• R-Value Free: 
  0.243 (Depositor), 0.247 (DCC) 
• R-Value Work: 
  0.207 (Depositor), 0.214 (DCC) 
• R-Value Observed: 
  0.208 (Depositor) 

Starting Model: experimental

Literature

Crystal Structure of DNase I Domain of Ribonuclease E from Vibrio cholerae.

Minasov, G., Shuvalova, L., Kiryukhina, O., Dubrovska, I., Wiersum, G., Satchell, K.J.F., Center for Structural Genomics of Infectious Diseases (CSGID)

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 Evidence: homology

Macromolecule Content 

• Total Structure Weight: 26.84 kDa 
• Atom Count: 1,810 
• Modeled Residue Count: 217 
• Deposited Residue Count: 230 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Ribonuclease E	A, B	115	Vibrio cholerae O1 biovar El Tor str. N16961	Mutation(s): 0  Gene Names: rne, VC_2030 EC: 3.1.26.12
UniProt
Find proteins for Q9KQG8 (Vibrio cholerae serotype O1 (strain ATCC 39315 / El Tor Inaba N16961)) Explore Q9KQG8  Go to UniProtKB:  Q9KQG8

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
IOD	C [auth A], D [auth A], E [auth A], F [auth A], G [auth B], H [auth B], I [auth B]	IODIDE ION I XMBWDFGMSWQBCA-UHFFFAOYSA-M

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: 1.85 Å
• R-Value Free:  0.243 (Depositor), 0.247 (DCC) 
• R-Value Work:  0.207 (Depositor), 0.214 (DCC) 
• R-Value Observed: 0.208 (Depositor) 

Diffraction Data: https://doi.org/10.18430/m36x2d

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 40.614	α = 90
b = 58.812	β = 108.16
c = 47.046	γ = 90

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Released Date: 2020-06-10 
Deposition Author(s): Minasov, G., Shuvalova, L., Kiryukhina, O., Dubrovska, I., Wiersum, G., Satchell, K.J.F., Center for Structural Genomics of Infectious Diseases (CSGID)

Revision History  

• Version 1.0: 2020-06-10
  Type: Initial release
  
• Version 1.1: 2023-10-18
  Changes: Data collection, Database references, Refinement description
• Version 1.2: 2023-11-15
  Changes: Data collection
• Version 1.3: 2024-10-23
  Changes: Structure summary