8BS0 | pdb_00008bs0

Room-temperature structure of Pedobacter heparinus N-acetylglucosamine 2-epimerase at 80 MPa helium gas pressure in a sapphire capillary

PDB DOI: https://doi.org/10.2210/pdb8BS0/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:
0.181 (Depositor), 0.181 (DCC)
R-Value Work:
0.156 (Depositor), 0.157 (DCC)
R-Value Observed:
0.156 (Depositor)

Starting Model: experimental
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This is version 1.1 of the entry. See complete history.

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.

Macromolecule Content

Total Structure Weight: 98 kDa
Atom Count: 7,006
Modeled Residue Count: 772
Deposited Residue Count: 836
Unique protein chains: 1

Macromolecules

Find similar proteins by:

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 EC: 5.1.3.8
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
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	C6Y403
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
PO4 Query on PO4 Download:Ideal Coordinates CCD File SDF format, chain C [auth A] SDF format, chain E [auth B] MOL2 format, chain C [auth A] MOL2 format, chain E [auth B] mmCIF format, chain C [auth A] mmCIF format, chain E [auth B]	C [auth A], E [auth B]	PHOSPHATE ION O₄ P NBIIXXVUZAFLBC-UHFFFAOYSA-K		Interactions Focus chain C [auth A] Focus chain E [auth B] Interactions & Density Focus chain C [auth A] Focus chain E [auth B]
CL Query on CL Download:Ideal Coordinates CCD File SDF format, chain D [auth A] SDF format, chain F [auth B] MOL2 format, chain D [auth A] MOL2 format, chain F [auth B] mmCIF format, chain D [auth A] mmCIF format, chain F [auth B]	D [auth A], F [auth B]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain D [auth A] Focus chain F [auth B] Interactions & Density Focus chain D [auth A] Focus chain F [auth B]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.70 Å
R-Value Free: 0.181 (Depositor), 0.181 (DCC)
R-Value Work: 0.156 (Depositor), 0.157 (DCC)
R-Value Observed: 0.156 (Depositor)

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 56.35	α = 90
b = 93.98	β = 102.55
c = 81.52	γ = 90

Software Package:

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

Structure Validation

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Entry History

& Funding Information

Deposition Data

Released Date: 2023-12-13

Deposition Author(s):

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

Revision History (Full details and data files)

Version 1.0: 2023-12-13
Type: Initial release
Version 1.1: 2026-03-04
Changes: Refinement description, Structure summary

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RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.