6QH4 | pdb_00006qh4

Crystal structure of human Methylmalonyl-CoA epimerase (MCEE) p.Arg143Cys variant

• PDB DOI: https://doi.org/10.2210/pdb6QH4/pdb

• Classification: ISOMERASE
• Organism(s): Homo sapiens
• Expression System: Escherichia coli K-12
• Mutation(s): Yes 


• Deposited: 2019-01-15 Released: 2019-02-27 
• Deposition Author(s): Bailey, H.J., Chaikuid, A., Krysztofinska, E., Froese, D.S., Sorrell, F.J., Diaz-Saez, L., Kennedy, E., Edwards, A.M., Bountra, C., Yue, W.W.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.92 Å
• R-Value Free: 
  0.276 (Depositor), 0.273 (DCC) 
• R-Value Work: 
  0.228 (Depositor), 0.227 (DCC) 
• R-Value Observed: 
  0.230 (Depositor) 

Starting Model: experimental

Literature

Crystal structure of human Methylmalonyl-CoA epimerase (MCEE) p.Arg143Cys variant

Bailey, H.J., Chaikuid, A., Krysztofinska, E., Froese, D.S., Sorrell, F.J., Diaz-Saez, L., Kennedy, E., Edwards, A.M., Bountra, C., Yue, W.W.

To be published.

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

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

Biological Assembly Evidence: gel filtration

Biological Assembly 2  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

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

Macromolecule Content 

• Total Structure Weight: 67.43 kDa 
• Atom Count: 3,949 
• Modeled Residue Count: 534 
• Deposited Residue Count: 620 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Methylmalonyl-CoA epimerase, mitochondrial	A [auth C], B [auth A], C [auth B], D	155	Homo sapiens	Mutation(s): 2  Gene Names: MCEE EC: 5.1.99.1
UniProt & NIH Common Fund Data Resources
Find proteins for Q96PE7 (Homo sapiens) Explore Q96PE7  Go to UniProtKB:  Q96PE7
PHAROS:  Q96PE7 GTEx:  ENSG00000124370

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
CO	E [auth C], F [auth A], G [auth B], H [auth D]	COBALT (II) ION Co XLJKHNWPARRRJB-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.92 Å
• R-Value Free:  0.276 (Depositor), 0.273 (DCC) 
• R-Value Work:  0.228 (Depositor), 0.227 (DCC) 
• R-Value Observed: 0.230 (Depositor) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 53.162	α = 90
b = 66.99	β = 90.02
c = 77.125	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
PDB_EXTRACT	data extraction
XDS	data reduction
STARANISO	data scaling
PHASER	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2019-02-27 
Deposition Author(s): Bailey, H.J., Chaikuid, A., Krysztofinska, E., Froese, D.S., Sorrell, F.J., Diaz-Saez, L., Kennedy, E., Edwards, A.M., Bountra, C., Yue, W.W.

Revision History  

• Version 1.0: 2019-02-27
  Type: Initial release
  
• Version 1.1: 2019-11-20
  Changes: Derived calculations
• Version 1.2: 2024-01-24
  Changes: Data collection, Database references, Derived calculations, Refinement description