8PMU | pdb_00008pmu

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 (Depositor), 0.225 (DCC)
R-Value Work:
0.191 (Depositor)
R-Value Observed:
0.193 (Depositor)

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

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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
Modeled Residue Count: 340
Deposited Residue Count: 659
Unique protein chains: 1

Macromolecules

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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

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]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.75 Å
R-Value Free: 0.231 (Depositor), 0.225 (DCC)
R-Value Work: 0.191 (Depositor)
R-Value Observed: 0.193 (Depositor)

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

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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

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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.