4EYS

Crystal structure of MccF-like protein from Streptococcus pneumoniae in complex with AMP

• PDB DOI: https://doi.org/10.2210/pdb4EYS/pdb

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


• Deposited: 2012-05-01 Released: 2012-07-18 
• Deposition Author(s): Nocek, B., Anderson, W.F., Joachimiak, A., Center for Structural Genomics of Infectious Diseases (CSGID)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.58 Å
• R-Value Free: 
  0.198 (Depositor), 0.200 (DCC) 
• R-Value Work: 
  0.169 (Depositor), 0.180 (DCC) 
• R-Value Observed: 
  0.170 (Depositor) 

Starting Model: experimental

Literature

Crystal structure of MccF-like protein from Streptococcus pneumoniae in complex with AMP

Nocek, B., Tikhonov, A., 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.

Biological Assembly 2  

Global Symmetry: Cyclic - C3  (Explore in 3D)
Global Stoichiometry: Homo 3-mer - A3 

Biological assembly 2 generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 39.93 kDa 
• Atom Count: 3,086 
• Modelled Residue Count: 343 
• Deposited Residue Count: 346 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
MccC family protein	A	346	Streptococcus pneumoniae	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 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
AMP	B [auth A]	ADENOSINE MONOPHOSPHATE C10 H14 N5 O7 P UDMBCSSLTHHNCD-KQYNXXCUSA-N
SO4	D [auth A]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L
ACT	C [auth A]	ACETATE ION C2 H3 O2 QTBSBXVTEAMEQO-UHFFFAOYSA-M

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
MSE	A	L-PEPTIDE LINKING	C5 H11 N O2 Se		MET

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.58 Å
• R-Value Free:  0.198 (Depositor), 0.200 (DCC) 
• R-Value Work:  0.169 (Depositor), 0.180 (DCC) 
• R-Value Observed: 0.170 (Depositor) 

Diffraction Data: https://doi.org/10.18430/m34eys

Space Group: P 3 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 97.998	α = 90
b = 97.998	β = 90
c = 79.805	γ = 120

Software Package:

Software Name	Purpose
SBC-Collect	data collection
SHELX	model building
MOLREP	phasing
REFMAC	refinement
HKL-3000	data reduction
HKL-3000	data scaling
SHELX	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2012-07-18 
Deposition Author(s): Nocek, B., Anderson, W.F., Joachimiak, A., Center for Structural Genomics of Infectious Diseases (CSGID)

Revision History  

• Version 1.0: 2012-07-18
  Type: Initial release
  
• Version 1.1: 2023-09-13
  Changes: Data collection, Database references, Derived calculations, Refinement description
• Version 1.2: 2023-12-06
  Changes: Data collection
• Version 1.3: 2024-10-16
  Changes: Structure summary