5FCD

Crystal structure of MccD protein

• PDB DOI: https://doi.org/10.2210/pdb5FCD/pdb

• Classification: TRANSFERASE
• Organism(s): Escherichia coli
• Expression System: Escherichia coli 'BL21-Gold(DE3)pLysS AG
• Mutation(s): No 


• Deposited: 2015-12-15 Released: 2015-12-30 
• Deposition Author(s): Nocek, B., Jedrzejczak, R., Anderson, W.F., Severinov, K., Dubiley, S., Joachimiak, A., 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: 0.223 
• R-Value Work: 0.199 
• R-Value Observed: 0.200 

Literature

Crystal structure of MccD protein.

Nocek, B., Jedrzejczak, R., Anderson, W.F., Severinov, K., Dubiley, S., Joachimiak, A.

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 

Biological assembly 1 assigned by authors.

Biological Assembly 2  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 

Biological assembly 2 assigned by authors.

Biological Assembly 3  

Global Symmetry: Dihedral - D3  (Explore in 3D)
Global Stoichiometry: Hetero 12-mer - A6B6 Pseudo Symmetry: Asymmetric - C1 
Pseudo Stoichiometry: Hetero 12-mer - A6B1C1D1E1F1G1 

Biological assembly 3 generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 64.4 kDa 
• Atom Count: 3,973 
• Modelled Residue Count: 467 
• Deposited Residue Count: 545 
• Unique protein chains: 3

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
UNK-UNK-UNK-MSE-UNK	A [auth D]	5	Escherichia coli	Mutation(s): 0

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
UNK-UNK-UNK-UNK-MSE-UNK	B [auth E]	6	Escherichia coli	Mutation(s): 0

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
MccD	C [auth A], D [auth B]	267	Escherichia coli	Mutation(s): 0  Gene Names: mccD
UniProt
Find proteins for Q83Y56 (Escherichia coli) Explore Q83Y56  Go to UniProtKB:  Q83Y56

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
CL	E [auth A]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
MSE	A [auth D]	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: 0.223 
• R-Value Work: 0.199 
• R-Value Observed: 0.200 
• Space Group: P 6₃
• Diffraction Data: https://doi.org/10.18430/M35FCD

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 95.1	α = 90
b = 95.1	β = 90
c = 128.685	γ = 120

Software Package:

Software Name	Purpose
PHENIX	refinement
HKL-3000	data reduction
HKL-3000	data scaling
HKL-3000	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2015-12-30 
Deposition Author(s): Nocek, B., Jedrzejczak, R., Anderson, W.F., Severinov, K., Dubiley, S., Joachimiak, A., Center for Structural Genomics of Infectious Diseases (CSGID)

Revision History  

• Version 1.0: 2015-12-30
  Type: Initial release
  
• Version 1.1: 2017-02-08
  Changes: Structure summary