2GLU | pdb_00002glu

The crystal structure of YcgJ protein from Bacillus subitilis

• PDB DOI: https://doi.org/10.2210/pdb2GLU/pdb

• Classification: STRUCTURAL GENOMICS, UNKNOWN FUNCTION
• Organism(s): Bacillus subtilis
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): Yes 


• Deposited: 2006-04-05 Released: 2006-04-18 
• Deposition Author(s): Burke, T., Gorman, J., Shapiro, L., Burley, S.K., New York SGX Research Center for Structural Genomics (NYSGXRC)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.91 Å
• R-Value Free: 
  0.283 (Depositor), 0.289 (DCC) 
• R-Value Work: 
  0.192 (Depositor), 0.199 (DCC) 
• R-Value Observed: 
  0.197 (Depositor) 

Starting Model: experimental

Literature

The crystal structure of YcgJ protein from Bacillus subitilis

Burke, T., Gorman, J., Shapiro, L.

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: 56.38 kDa 
• Atom Count: 3,923 
• Modeled Residue Count: 468 
• Deposited Residue Count: 478 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
ycgJ	A, B	239	Bacillus subtilis	Mutation(s): 3  Gene Names: Ycgj EC: 2.1.1
UniProt
Find proteins for O31474 (Bacillus subtilis (strain 168)) Explore O31474  Go to UniProtKB:  O31474

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
SAM	G [auth A], O [auth B]	S-ADENOSYLMETHIONINE C15 H22 N6 O5 S MEFKEPWMEQBLKI-FCKMPRQPSA-N
SO4	C [auth A], D [auth A], E [auth A], F [auth A], H [auth B], I [auth B], J [auth B], K [auth B], L [auth B], M [auth B], N [auth B]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L

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: 2.91 Å
• R-Value Free:  0.283 (Depositor), 0.289 (DCC) 
• R-Value Work:  0.192 (Depositor), 0.199 (DCC) 
• R-Value Observed: 0.197 (Depositor) 

Space Group: C 2 2 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 69.899	α = 90
b = 73.639	β = 90
c = 245.742	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
ADSC	data collection
DENZO	data reduction
SCALEPACK	data scaling
AMoRE	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2006-04-18 
Deposition Author(s): Burke, T., Gorman, J., Shapiro, L., Burley, S.K., New York SGX Research Center for Structural Genomics (NYSGXRC)

Revision History  

• Version 1.0: 2006-04-18
  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: 2021-02-03
  Changes: Database references, Derived calculations, Structure summary
• Version 1.4: 2023-08-30
  Changes: Data collection, Database references, Refinement description
• Version 1.5: 2023-11-15
  Changes: Data collection
• Version 1.6: 2024-12-25
  Changes: Advisory, Derived calculations, Structure summary