2W6K | pdb_00002w6k

The crystal structure at 1.7 A resolution of CobE, a protein from the cobalamin (vitamin B12) biosynthetic pathway

• PDB DOI: https://doi.org/10.2210/pdb2W6K/pdb
• Entry: 2W6K supersedes: 2BSN

• Classification: BIOSYNTHETIC PROTEIN
• Organism(s): Pseudomonas aeruginosa
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2008-12-18 Released: 2008-12-30 
• Deposition Author(s): Vevodova, J., Smith, D., McGoldrick, H., Deery, E., Murzin, A.G., Warren, M.J., Wilson, K.S.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.70 Å
• R-Value Free: 
  0.250 (Depositor), 0.256 (DCC) 
• R-Value Work: 
  0.199 (Depositor), 0.204 (DCC) 
• R-Value Observed: 
  0.202 (Depositor) 

Literature

The Crystal Structure at 1.7 A Resolution of Cobe, a Protein from the Cobalamin (Vitamin B12) Biosynthetic Pathway

Vevodova, J., Smith, D., Mcgoldrick, H., Deery, E., Murzin, A.G., Warren, M.J., Wilson, K.S.

To be published.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors and generated by PQS (software)

Macromolecule Content 

• Total Structure Weight: 15.9 kDa 
• Atom Count: 1,194 
• Modeled Residue Count: 142 
• Deposited Residue Count: 145 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
COBE	A	145	Pseudomonas aeruginosa	Mutation(s): 0
UniProt
Find proteins for Q9HZQ0 (Pseudomonas aeruginosa (strain ATCC 15692 / DSM 22644 / CIP 104116 / JCM 14847 / LMG 12228 / 1C / PRS 101 / PAO1)) Explore Q9HZQ0  Go to UniProtKB:  Q9HZQ0

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
SO4	B [auth A], C [auth A]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L
GOL	D [auth A], E [auth A], F [auth A]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N

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: 1.70 Å
• R-Value Free:  0.250 (Depositor), 0.256 (DCC) 
• R-Value Work:  0.199 (Depositor), 0.204 (DCC) 
• R-Value Observed: 0.202 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 31.729	α = 90
b = 41.271	β = 90
c = 87.94	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
DENZO	data reduction
SCALEPACK	data scaling
SOLVE	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2008-12-30 
Deposition Author(s): Vevodova, J., Smith, D., McGoldrick, H., Deery, E., Murzin, A.G., Warren, M.J., Wilson, K.S.
• This entry supersedes: 2BSN

Revision History  

• Version 1.0: 2008-12-30
  Type: Initial release
  
• Version 1.1: 2011-05-08
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2024-11-13
  Changes: Data collection, Database references, Derived calculations, Other, Structure summary