1Y0E | pdb_00001y0e

Crystal structure of putative ManNAc-6-P epimerase from Staphylococcus aureus (strain N315)

• PDB DOI: https://doi.org/10.2210/pdb1Y0E/pdb

• Classification: ISOMERASE
• Organism(s): Staphylococcus aureus subsp. aureus N315
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2004-11-15 Released: 2004-12-28 
• Deposition Author(s): Chang, C., Joachimiak, A., Li, H., Midwest Center for Structural Genomics (MCSG)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.95 Å
• R-Value Free: 
  0.216 (Depositor), 0.210 (DCC) 
• R-Value Work: 
  0.177 (Depositor), 0.180 (DCC) 
• R-Value Observed: 
  0.179 (Depositor) 

Literature

Crystal structure of putative ManNAc-6-P epimerase from Staphylococcus aureus (strain N315)

Chang, C., Moy, S., Li, H., 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,PQS (software)

Macromolecule Content 

• Total Structure Weight: 50.2 kDa 
• Atom Count: 3,848 
• Modeled Residue Count: 444 
• Deposited Residue Count: 446 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Putative N-acetylmannosamine-6-phosphate 2-epimerase	A, B	223	Staphylococcus aureus subsp. aureus N315	Mutation(s): 8  Gene Names: nanE EC: 5.1.3.9
UniProt
Find proteins for P65517 (Staphylococcus aureus (strain N315)) Explore P65517  Go to UniProtKB:  P65517

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
PO4	C [auth A], D [auth A], E [auth B]	PHOSPHATE ION O4 P NBIIXXVUZAFLBC-UHFFFAOYSA-K

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: 1.95 Å
• R-Value Free:  0.216 (Depositor), 0.210 (DCC) 
• R-Value Work:  0.177 (Depositor), 0.180 (DCC) 
• R-Value Observed: 0.179 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 52.961	α = 90
b = 76.283	β = 90
c = 183.661	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
HKL-2000	data reduction
SCALEPACK	data scaling
SOLVE	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2004-12-28 
Deposition Author(s): Chang, C., Joachimiak, A., Li, H., Midwest Center for Structural Genomics (MCSG)

Revision History  

• Version 1.0: 2004-12-28
  Type: Initial release
  
• Version 1.1: 2008-04-30
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Advisory, Derived calculations, Source and taxonomy, Version format compliance
• Version 1.3: 2021-10-20
  Changes: Database references, Derived calculations
• Version 1.4: 2024-10-16
  Changes: Data collection, Structure summary