7C18 | pdb_00007c18

Crystal structure of FumaraseC from Mannheimia succiniciproducens in complex with Fumarate

• PDB DOI: https://doi.org/10.2210/pdb7C18/pdb

• Classification: LYASE
• Organism(s): [Mannheimia] succiniciproducens MBEL55E
• Expression System: Escherichia coli K-12
• Mutation(s): Yes 


• Deposited: 2020-05-02 Released: 2021-05-05 
• Deposition Author(s): Kim, B., Lee, S.H., Kim, K.-J.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.12 Å
• R-Value Free: 
  0.241 (Depositor), 0.248 (DCC) 
• R-Value Work: 
  0.185 (Depositor), 0.194 (DCC) 
• R-Value Observed: 
  0.187 (Depositor) 

Starting Model: experimental

Literature

Structural studies reveal the molecular mechanism of isocitrate lyase from Chloroflexus aurantiacus

Kim, B., Lee, S.H., Kim, K.-J.

To be published.

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: 201.63 kDa 
• Atom Count: 14,312 
• Modeled Residue Count: 1,848 
• Deposited Residue Count: 1,868 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Fumarate hydratase class II	A, B, C, D	467	[Mannheimia] succiniciproducens MBEL55E	Mutation(s): 1  Gene Names: fumC, MS0760 EC: 4.2.1.2
UniProt
Find proteins for Q65UJ3 (Mannheimia succiniciproducens (strain KCTC 0769BP / MBEL55E)) Explore Q65UJ3  Go to UniProtKB:  Q65UJ3

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
FUM (Subject of Investigation/LOI)	E [auth A], F [auth A], G [auth C], H [auth C]	FUMARIC ACID C4 H4 O4 VZCYOOQTPOCHFL-OWOJBTEDSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.12 Å
• R-Value Free:  0.241 (Depositor), 0.248 (DCC) 
• R-Value Work:  0.185 (Depositor), 0.194 (DCC) 
• R-Value Observed: 0.187 (Depositor) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 59.089	α = 90
b = 104.276	β = 94.1
c = 125.333	γ = 90

Software Package:

Software Name	Purpose
HKL-2000	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction
HKL-2000	data reduction
MOLREP	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2021-05-05 
Deposition Author(s): Kim, B., Lee, S.H., Kim, K.-J.

Revision History  

• Version 1.0: 2021-05-05
  Type: Initial release
  
• Version 2.0: 2023-11-15
  Changes: Atomic model, Data collection, Database references
• Version 2.1: 2023-11-29
  Changes: Refinement description