8IOF | pdb_00008iof

Crystal structure of N-methyl-Cis-4-hydroxy-D-proline dehydratase in Clostridium sp. FS41

• PDB DOI: https://doi.org/10.2210/pdb8IOF/pdb

• Classification: LYASE
• Organism(s): Clostridium sp. FS41
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2023-03-11 Released: 2024-03-27 
• Deposition Author(s): Jiang, L., Zhang, Y.
• Funding Organization(s): National Natural Science Foundation of China (NSFC)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.33 Å
• R-Value Free: 
  0.266 (Depositor), 0.266 (DCC) 
• R-Value Work: 
  0.190 (Depositor), 0.191 (DCC) 
• R-Value Observed: 
  0.191 (Depositor) 

Starting Model: other

Literature

Glycyl Radical Enzymes Catalyzing the Dehydration of Two Isomers of N-Methyl-4-hydroxyproline

Jiang, L., Yang, Y., Huang, L., Zhou, Y., An, J., Zheng, Y., Chen, Y., Liu, Y., Huang, J., Ang, E.L., Zhao, S., Zhao, H., Liao, R., Wei, Y., Zhang, Y.

(2024) ACS Catal 14: 4407-4422

• DOI: https://doi.org/10.1021/acscatal.4c00216

Biological Assembly 1  

Global Symmetry: Dihedral - D2  (Explore in 3D)
Global Stoichiometry: Homo 4-mer - A4 

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

Biological Assembly Evidence: gel filtration

Macromolecule Content 

• Total Structure Weight: 357.28 kDa 
• Atom Count: 26,216 
• Modeled Residue Count: 3,165 
• Deposited Residue Count: 3,172 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Benzylsuccinate synthase alpha subunit	A, B, C, D	793	Clostridium sp. FS41	Mutation(s): 0  Gene Names: bssA EC: 4.1.99.11
UniProt
Find proteins for A0A0F0CL90 (Clostridium sp. FS41) Explore A0A0F0CL90  Go to UniProtKB:  A0A0F0CL90

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
87I (Subject of Investigation/LOI)	E [auth A], F [auth B], G [auth C], H [auth D]	(2R,4R)-1-methyl-4-hydroxyl-pyrrolidine-2-carboxylic acid C6 H11 N O3 FMIPNAUMSPFTHK-RFZPGFLSSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.33 Å
• R-Value Free:  0.266 (Depositor), 0.266 (DCC) 
• R-Value Work:  0.190 (Depositor), 0.191 (DCC) 
• R-Value Observed: 0.191 (Depositor) 

Space Group: P 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 78.967	α = 83.13
b = 103.603	β = 75.71
c = 114.254	γ = 79.84

Software Package:

Software Name	Purpose
PHENIX	refinement
Aimless	data scaling
XDS	data reduction
PHENIX	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2024-03-27 
Deposition Author(s): Jiang, L., Zhang, Y.

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Funding Organization	Location	Grant Number
National Natural Science Foundation of China (NSFC)	China	--

Revision History  

• Version 1.0: 2024-03-27
  Type: Initial release
  
• Version 1.1: 2024-10-09
  Changes: Database references, Structure summary