7UFU | pdb_00007ufu

Cryo-EM Structure of Bl_Man38A nucleophile mutant in complex with mannose at 2.7 A

PDB DOI: https://doi.org/10.2210/pdb7UFU/pdb
EM Map EMD-26481: EMDB EMDataResource

Classification: HYDROLASE
Organism(s): Bifidobacterium longum
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2022-03-23 Released: 2022-11-16
Deposition Author(s): Santos, C.R., Cordeiro, R.L., Domingues, M.N., Borges, A.C., de Farias, M.A., Van Heel, M., Murakami, M.T., Portugal, R.V.
Funding Organization(s): Sao Paulo Research Foundation (FAPESP)

Experimental Data Snapshot

Method: ELECTRON MICROSCOPY
Resolution: 2.70 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

wwPDB Validation 3D Report Full Report

Validation slider image for 7UFU

This is version 1.1 of the entry. See complete history.

Literature

Cryo-EM Structure of Bl_Man38A nucleophile mutant in complex with mannose at 2.7 A

Santos, C.R., Cordeiro, R.L., Domingues, M.N., Borges, A.C., de Farias, M.A., Van Heel, M., Murakami, M.T., Portugal, R.V.

(2022) Nat Chem Biol

Macromolecule Content

Total Structure Weight: 472.75 kDa
Atom Count: 32,588
Modeled Residue Count: 4,152
Deposited Residue Count: 4,248
Unique protein chains: 1

Macromolecules

Find similar proteins by:

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Alpha-mannosidase	A, B, C, D	1,062	Bifidobacterium longum	Mutation(s): 0 Gene Names: BL1327
UniProt
Find proteins for Q8G4Q1 (Bifidobacterium longum (strain NCC 2705)) Explore Q8G4Q1 Go to UniProtKB: Q8G4Q1
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q8G4Q1
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
MAN (Subject of Investigation/LOI) Query on MAN Download:Ideal Coordinates CCD File SDF format, chain L [auth D] SDF format, chain J [auth C] SDF format, chain H [auth B] SDF format, chain F [auth A] MOL2 format, chain L [auth D] MOL2 format, chain J [auth C] MOL2 format, chain H [auth B] MOL2 format, chain F [auth A] mmCIF format, chain L [auth D] mmCIF format, chain J [auth C] mmCIF format, chain H [auth B] mmCIF format, chain F [auth A]	F [auth A], H [auth B], J [auth C], L [auth D]	alpha-D-mannopyranose C₆ H₁₂ O₆ WQZGKKKJIJFFOK-PQMKYFCFSA-N		Interactions Focus chain F [auth A] Focus chain H [auth B] Focus chain J [auth C] Focus chain L [auth D] Interactions & Density Focus chain F [auth A] Focus chain H [auth B] Focus chain J [auth C] Focus chain L [auth D]
ZN (Subject of Investigation/LOI) Query on ZN Download:Ideal Coordinates CCD File SDF format, chain K [auth D] SDF format, chain I [auth C] SDF format, chain G [auth B] SDF format, chain E [auth A] MOL2 format, chain K [auth D] MOL2 format, chain I [auth C] MOL2 format, chain G [auth B] MOL2 format, chain E [auth A] mmCIF format, chain K [auth D] mmCIF format, chain I [auth C] mmCIF format, chain G [auth B] mmCIF format, chain E [auth A]	E [auth A], G [auth B], I [auth C], K [auth D]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N		Interactions Focus chain E [auth A] Focus chain G [auth B] Focus chain I [auth C] Focus chain K [auth D] Interactions & Density Focus chain E [auth A] Focus chain G [auth B] Focus chain I [auth C] Focus chain K [auth D]

Experimental Data & Validation

Experimental Data

Method: ELECTRON MICROSCOPY
Resolution: 2.70 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

EM Software:

Task	Software Package	Version
MODEL REFINEMENT	PHENIX
RECONSTRUCTION	cisTEM

Structure Validation

View Full Validation Report

View more in-depth experimental data

Entry History

& Funding Information

Deposition Data

Released Date: 2022-11-16

Deposition Author(s):

Domingues, M.N.

de Farias, M.A.

Funding Organization	Location	Grant Number
Sao Paulo Research Foundation (FAPESP)	Brazil	2015/26982-0
Sao Paulo Research Foundation (FAPESP)	Brazil	2017/15340-2

Revision History (Full details and data files)

Version 1.0: 2022-11-16
Type: Initial release
Version 1.1: 2024-06-12
Changes: Data collection

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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.