1YXY

Crystal Structure of putative N-acetylmannosamine-6-P epimerase from Streptococcus pyogenes (APC29713) Structural genomics, MCSG

• PDB DOI: https://doi.org/10.2210/pdb1YXY/pdb

• Classification: ISOMERASE
• Organism(s): Streptococcus pyogenes
• Expression System: Escherichia coli BL21
• Mutation(s): No 


• Deposited: 2005-02-22 Released: 2005-04-05 
• Deposition Author(s): Rotella, F.J., Zhang, R.G., Lezondra, L.E.O., Collart, F.R., Joachimiak, A., Midwest Center for Structural Genomics (MCSG)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.60 Å
• R-Value Free: 0.207 
• R-Value Work: 0.193 
• R-Value Observed: 0.194 

Literature

The 1.6 A crystal structure of putative N-acetylmannosamine-6-P epimerase from Streptococcus pyogenes

Rotella, F.J., Zhang, R.G., Lezondra, L.E.O., Collart, F.R., Joachimiak, A.

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: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 2 assigned by authors.

Biological Assembly 3  

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

Biological assembly 3 generated by PISA (software)

Biological Assembly 4  

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

Biological assembly 4 generated by PQS (software)

Macromolecule Content

• Total Structure Weight: 50.19 kDa 
• Atom Count: 4,131 
• Modelled Residue Count: 460 
• Deposited Residue Count: 468 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Putative N-acetylmannosamine-6-phosphate 2-epimerase	A, B	234	Streptococcus pyogenes	Mutation(s): 0  Gene Names: nanE EC: 5.1.3.9
UniProt
Find proteins for P65522 (Streptococcus pyogenes serotype M1) Explore P65522  Go to UniProtKB:  P65522

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.60 Å
• R-Value Free: 0.207 
• R-Value Work: 0.193 
• R-Value Observed: 0.194 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 59.64	α = 90
b = 83.521	β = 90
c = 104.256	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
SBC-Collect	data collection
HKL-2000	data scaling
HKL-3000	phasing
SHELXD	phasing
SHELXE	model building
MLPHARE	phasing
DM	phasing
SOLVE	phasing
RESOLVE	phasing
O	model building
Coot	model building
CCP4	phasing
ARP/wARP	model building

Structure Validation

Entry History 

Deposition Data

• Released Date: 2005-04-05 
Deposition Author(s): Rotella, F.J., Zhang, R.G., Lezondra, L.E.O., Collart, F.R., Joachimiak, A., Midwest Center for Structural Genomics (MCSG)

Revision History  

• Version 1.0: 2005-04-05
  Type: Initial release
  
• Version 1.1: 2008-04-30
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Derived calculations, Version format compliance
• Version 1.3: 2024-02-14
  Changes: Data collection, Database references