4RWR | pdb_00004rwr

2.1 Angstrom Crystal Structure of Stage II Sporulation Protein D from Bacillus anthracis

• PDB DOI: https://doi.org/10.2210/pdb4RWR/pdb

• Classification: VIRAL PROTEIN
• Organism(s): Bacillus anthracis
• Expression System: Escherichia coli BL21
• Mutation(s): No 


• Deposited: 2014-12-05 Released: 2014-12-17 
• Deposition Author(s): Minasov, G., Wawrzak, Z., Nocadello, S., Shuvalova, L., Dubrovska, I., Flores, K., Bagnoli, F., Falugi, F., Bottomley, M., Grandi, G., Anderson, W.F., Center for Structural Genomics of Infectious Diseases (CSGID)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.10 Å
• R-Value Free: 
  0.243 (Depositor), 0.249 (DCC) 
• R-Value Work: 
  0.188 (Depositor), 0.196 (DCC) 
• R-Value Observed: 
  0.190 (Depositor) 

Literature

Crystal Structures of the SpoIID Lytic Transglycosylases Essential for Bacterial Sporulation.

Nocadello, S., Minasov, G., Shuvalova, L.S., Dubrovska, I., Sabini, E., Anderson, W.F.

(2016) J Biological Chem 291: 14915-14926

• PubMed: 27226615 
• DOI: https://doi.org/10.1074/jbc.M116.729749
• Primary Citation Related Structures: 
  4RWR, 5I1T


• PubMed Abstract: 
  

  Bacterial spores are the most resistant form of life known on Earth and represent a serious problem for (i) bioterrorism attack, (ii) horizontal transmission of microbial pathogens in the community, and (iii) persistence in patients and in a nosocomial environment. Stage II sporulation protein D (SpoIID) is a lytic transglycosylase (LT) essential for sporulation. The LT superfamily is a potential drug target because it is active in essential bacterial processes involving the peptidoglycan, which is unique to bacteria. However, the absence of structural information for the sporulation-specific LT enzymes has hindered mechanistic understanding of SpoIID. Here, we report the first crystal structures with and without ligands of the SpoIID family from two community relevant spore-forming pathogens, Bacillus anthracis and Clostridium difficile. The structures allow us to visualize the overall architecture, characterize the substrate recognition model, identify critical residues, and provide the structural basis for catalysis by this new family of enzymes.

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Organizational Affiliation: 
• From the Center for Structural Genomics of Infectious Diseases, Department of Biochemistry and Molecular Genetics, Northwestern University Feinberg School of Medicine, Chicago, Illinois 60611.
From the Center for Structural Genomics of Infectious Diseases, Department of Biochemistry and Molecular Genetics, Northwestern University Feinberg School of Medicine, Chicago, Illinois 60611 [e-mail].

Biological Assembly 1  

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

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

Biological Assembly 2  

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

Biological assembly 2 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 74.11 kDa 
• Atom Count: 4,642 
• Modeled Residue Count: 535 
• Deposited Residue Count: 662 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Stage II sporulation protein D	A, B	331	Bacillus anthracis	Mutation(s): 0  Gene Names: BAS5136, BA_5528, DH23_5378, DJ42_3419, DJ44_3608, DJ45_519, DJ48_4453, DJ49_4581, GBAA_5528, spoIID
UniProt
Find proteins for A0A6L7HNW1 (Bacillus anthracis) Explore A0A6L7HNW1  Go to UniProtKB:  A0A6L7HNW1

Small Molecules

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: 2.10 Å
• R-Value Free:  0.243 (Depositor), 0.249 (DCC) 
• R-Value Work:  0.188 (Depositor), 0.196 (DCC) 
• R-Value Observed: 0.190 (Depositor) 

Diffraction Data: https://doi.org/10.18430/m34rwr

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 46.616	α = 90
b = 144.477	β = 115.36
c = 47.076	γ = 90

Software Package:

Software Name	Purpose
Blu-Ice	data collection
PHENIX	model building
REFMAC	refinement
HKL-3000	data reduction
HKL-3000	data scaling
PHENIX	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2014-12-17 
Deposition Author(s): Minasov, G., Wawrzak, Z., Nocadello, S., Shuvalova, L., Dubrovska, I., Flores, K., Bagnoli, F., Falugi, F., Bottomley, M., Grandi, G., Anderson, W.F., Center for Structural Genomics of Infectious Diseases (CSGID)

Revision History  

• Version 1.0: 2014-12-17
  Type: Initial release
  
• Version 1.1: 2016-06-08
  Changes: Database references
• Version 1.2: 2016-08-03
  Changes: Database references
• Version 1.3: 2017-11-22
  Changes: Refinement description
• Version 1.4: 2024-11-06
  Changes: Data collection, Database references, Derived calculations, Structure summary