8BRZ

Room-temperature structure of Pedobacter heparinus N-acetylglucosamine 2-epimerase at 52 MPa helium gas pressure in a sapphire capillary

• PDB DOI: https://doi.org/10.2210/pdb8BRZ/pdb

• Classification: ISOMERASE
• Organism(s): Pedobacter heparinus
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2022-11-24 Released: 2023-12-13 
• Deposition Author(s): Lieske, J., Saouane, S., Assmann, M., Zaun, H., Kuballa, J., Meents, A.
• Funding Organization(s): German Federal Ministry for Education and Research

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.70 Å
• R-Value Free: 0.183 
• R-Value Work: 0.158 
• R-Value Observed: 0.158 

Literature

High-pressure macromolecular crystallography to explore the conformational space of proteins

Lieske, J., Saouane, S., Guenther, S., Reinke, P.Y.A., Falke, S., Ewert, W., Meyer, J., Pakendorf, T., Reime, B., Burkhardt, A., Crosas, E., Hakanpaeae, J., Stachnik, K., Sieg, J., Rarey, M., Assmann, M., Zaun, H., Kuballa, J., Chapman, H.N., Meents, A.

To be published.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 98 kDa 
• Atom Count: 7,120 
• Modelled Residue Count: 772 
• Deposited Residue Count: 836 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
N-acylglucosamine 2-epimerase	A, B	418	Pedobacter heparinus	Mutation(s): 0  Gene Names: Phep_3251
UniProt
Find proteins for C6Y403 (Pedobacter heparinus (strain ATCC 13125 / DSM 2366 / CIP 104194 / JCM 7457 / NBRC 12017 / NCIMB 9290 / NRRL B-14731 / HIM 762-3)) Explore C6Y403  Go to UniProtKB:  C6Y403

Small Molecules

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

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.70 Å
• R-Value Free: 0.183 
• R-Value Work: 0.158 
• R-Value Observed: 0.158 
• Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 56.41	α = 90
b = 94.08	β = 102.63
c = 81.71	γ = 90

Software Package:

Software Name	Purpose
Coot	model building
PHENIX	refinement
XDS	data reduction
XSCALE	data scaling
PHENIX	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2023-12-13 
Deposition Author(s): Lieske, J., Saouane, S., Assmann, M., Zaun, H., Kuballa, J., Meents, A.

---

Funding Organization	Location	Grant Number
German Federal Ministry for Education and Research	Germany	031B0405A

Revision History  

• Version 1.0: 2023-12-13
  Type: Initial release