2UYR | pdb_00002uyr

Crystal structure of Bacillus cereus sphingomyelinase mutant :N57A

• PDB DOI: https://doi.org/10.2210/pdb2UYR/pdb

• Classification: HYDROLASE
• Organism(s): Bacillus cereus
• Expression System: Bacillus subtilis
• Mutation(s): Yes 


• Deposited: 2007-04-12 Released: 2008-05-27 
• Deposition Author(s): Oda, M., Tsuge, H., Sakurai, J.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.40 Å
• R-Value Free: 
  0.235 (Depositor) 
• R-Value Work: 
  0.182 (Depositor), 0.180 (DCC) 
• R-Value Observed: 
  0.184 (Depositor) 

Starting Model: experimental

Literature

Crystal Structure of Bacillus Cereus Sphingomyelinase Mutant : N57A

Oda, M., Tsuge, H., Sakurai, J.

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: 34.3 kDa 
• Atom Count: 2,451 
• Modeled Residue Count: 299 
• Deposited Residue Count: 306 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
SPHINGOMYELINASE C	A [auth X]	306	Bacillus cereus	Mutation(s): 1  EC: 3.1.4.12
UniProt
Find proteins for P11889 (Bacillus cereus) Explore P11889  Go to UniProtKB:  P11889

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
MG	B [auth X]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.40 Å
• R-Value Free:  0.235 (Depositor) 
• R-Value Work:  0.182 (Depositor), 0.180 (DCC) 
• R-Value Observed: 0.184 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 55.09	α = 90
b = 63.927	β = 90
c = 101.69	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
HKL-2000	data reduction
SCALEPACK	data scaling
CCP4I	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2008-05-27 
Deposition Author(s): Oda, M., Tsuge, H., Sakurai, J.

Revision History  

• Version 1.0: 2008-05-27
  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: 2018-04-04
  Changes: Data collection
• Version 1.4: 2023-12-13
  Changes: Data collection, Database references, Derived calculations, Other, Refinement description
• Version 1.5: 2024-10-16
  Changes: Structure summary