4E94

Crystal structure of MccF-like protein from Streptococcus pneumoniae

• PDB DOI: https://doi.org/10.2210/pdb4E94/pdb

• Classification: HYDROLASE
• Organism(s): Streptococcus pneumoniae TIGR4
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2012-03-20 Released: 2012-05-09 
• Deposition Author(s): Nocek, B., Tikhonov, A., Kwon, K., Severinov, K., Anderson, W.F., Joachimiak, A., Center for Structural Genomics of Infectious Diseases (CSGID)

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.65 Å
• R-Value Free: 
  0.175 (Depositor), 0.183 (DCC) 
• R-Value Work: 
  0.146 (Depositor), 0.154 (DCC) 
• R-Value Observed: 
  0.147 (Depositor) 

Literature

Crystal structure of MccF-like protein from Streptococcus pneumoniae

Nocek, B., Tikhonov, A., Kwon, K., Severinov, K., Anderson, W.F., Joachimiak, A., Center for Structural Genomics of Infectious Diseases (CSGID)

To be published.

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: 79.24 kDa 
• Atom Count: 6,309 
• Modelled Residue Count: 683 
• Deposited Residue Count: 692 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
MccC family protein	A, B	346	Streptococcus pneumoniae TIGR4	Mutation(s): 0  Gene Names: SP_0182
UniProt
Find proteins for A0A0H2UN46 (Streptococcus pneumoniae serotype 4 (strain ATCC BAA-334 / TIGR4)) Explore A0A0H2UN46  Go to UniProtKB:  A0A0H2UN46

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
SO4	C [auth A]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L
GOL	D [auth A], E [auth A], F [auth A]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N

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: 1.65 Å
• R-Value Free:  0.175 (Depositor), 0.183 (DCC) 
• R-Value Work:  0.146 (Depositor), 0.154 (DCC) 
• R-Value Observed: 0.147 (Depositor) 

Diffraction Data: https://doi.org/10.18430/m34e94

Space Group: P 2₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 108.323	α = 90
b = 118.912	β = 90
c = 51.737	γ = 90

Software Package:

Software Name	Purpose
SBC-Collect	data collection
HKL-3000	phasing
SHELX	model building
MLPHARE	phasing
ARP	model building
WARP	model building
PHENIX	refinement
HKL-3000	data reduction
HKL-3000	data scaling
SHELX	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2012-05-09 
Deposition Author(s): Nocek, B., Tikhonov, A., Kwon, K., Severinov, K., Anderson, W.F., Joachimiak, A., Center for Structural Genomics of Infectious Diseases (CSGID)

Revision History  

• Version 1.0: 2012-05-09
  Type: Initial release
  
• Version 1.1: 2017-11-15
  Changes: Refinement description
• Version 1.2: 2024-10-30
  Changes: Data collection, Database references, Derived calculations, Structure summary