8PMU

Crystal structure of the HC7 apo form

PDB DOI: https://doi.org/10.2210/pdb8PMU/pdb

Classification: LYASE
Organism(s): Bacillus cereus
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2023-06-29 Released: 2024-03-06
Deposition Author(s): Taleb, V., Hurtado-Guerrero, R.
Funding Organization(s): Spanish Ministry of Science, Innovation, and Universities

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.75 Å
R-Value Free: 0.231
R-Value Work: 0.191
R-Value Observed: 0.193

Starting Model: in silico
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wwPDB Validation 3D Report Full Report

This is version 1.0 of the entry. See complete history.

Literature

A family of di-glutamate mucin-degrading enzymes that bridges glycan hydrolases and peptidases

Narimatsu, Y., Bull, C., Taleb, V., Liao, Q., Companon, I., Sanchez-Navarro, D., Durbesson, F., Vincentelli, R., Hansen, L., Corzana, F., Rovira, C., Henrissat, B., Clausen, H., Joshi, H.J., Hurtado-Guerrero, R.

(2024) Nat Catal

DOI: https://doi.org/10.1038/s41929-024-01116-5

Macromolecule Content

Total Structure Weight: 74.31 kDa
Atom Count: 2,904
Modelled Residue Count: 340
Deposited Residue Count: 659
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
DUF3472 domain-containing protein	A	659	Bacillus cereus	Mutation(s): 0 Gene Names: GE376_31780
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
GOL Query on GOL Download Ideal Coordinates CCD File SDF format, chain B [auth A] MOL2 format, chain B [auth A] mmCIF format, chain B [auth A]	B [auth A]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain B [auth A] Interactions & Density Focus chain B [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.75 Å
R-Value Free: 0.231
R-Value Work: 0.191
R-Value Observed: 0.193
Space Group: P 4₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 93.854	α = 90
b = 93.854	β = 90
c = 87.287	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
XDS	data reduction
SCALA	data scaling
PHASER	phasing

Structure Validation

View Full Validation Report

Entry History & Funding Information

Deposition Data

Released Date: 2024-03-06

Deposition Author(s):

Hurtado-Guerrero, R.

Funding Organization	Location	Grant Number
Spanish Ministry of Science, Innovation, and Universities	Spain	--

Revision History (Full details and data files)

Version 1.0: 2024-03-06
Type: Initial release

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.