6R8U | pdb_00006r8u

Escherichia coli AGPase in complex with AMP.

PDB DOI: https://doi.org/10.2210/pdb6R8U/pdb
EM Map EMD-4761: EMDB EMDataResource

Classification: TRANSFERASE
Organism(s): Escherichia coli
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2019-04-02 Released: 2020-02-05
Deposition Author(s): Cifuente, J.O., Comino, N., D'Angelo, C., Marina, A., Gil-Carton, D., Albesa-Jove, D., Guerin, M.E.
Funding Organization(s): Spanish Ministry of Economy and Competitiveness

Experimental Data Snapshot

Method: ELECTRON MICROSCOPY
Resolution: 3.00 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

Starting Model: experimental
View more details

wwPDB Validation 3D Report Full Report

Validation slider image for 6R8U

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

Literature

The allosteric control mechanism of bacterial glycogen biosynthesis disclosed by cryoEM

Cifuente, J.O., Comino, N., D'Angelo, C., Marina, A., Gil-Carton, D., Albesa-Jove, D., Guerin, M.E.

(2020) bioRxiv

DOI: https://doi.org/10.1101/2020.01.24.916759

Macromolecule Content

Total Structure Weight: 196.42 kDa
Atom Count: 13,536
Modeled Residue Count: 1,700
Deposited Residue Count: 1,724
Unique protein chains: 1

Macromolecules

Find similar proteins by:

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Glucose-1-phosphate adenylyltransferase	A, B, C [auth D], D [auth C]	431	Escherichia coli	Mutation(s): 0 Gene Names: glgC, b3430, JW3393 EC: 2.7.7.27
UniProt
Find proteins for P0A6V1 (Escherichia coli (strain K12)) Explore P0A6V1 Go to UniProtKB: P0A6V1
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P0A6V1
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
AMP Query on AMP Download:Ideal Coordinates CCD File SDF format, chain H [auth C] SDF format, chain G [auth D] SDF format, chain F [auth B] SDF format, chain E [auth A] MOL2 format, chain H [auth C] MOL2 format, chain G [auth D] MOL2 format, chain F [auth B] MOL2 format, chain E [auth A] mmCIF format, chain H [auth C] mmCIF format, chain G [auth D] mmCIF format, chain F [auth B] mmCIF format, chain E [auth A]	E [auth A], F [auth B], G [auth D], H [auth C]	ADENOSINE MONOPHOSPHATE C₁₀ H₁₄ N₅ O₇ P UDMBCSSLTHHNCD-KQYNXXCUSA-N		Interactions Focus chain E [auth A] Focus chain F [auth B] Focus chain G [auth D] Focus chain H [auth C] Interactions & Density Focus chain E [auth A] Focus chain F [auth B] Focus chain G [auth D] Focus chain H [auth C]

Experimental Data & Validation

Experimental Data

Method: ELECTRON MICROSCOPY
Resolution: 3.00 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

EM Software:

Task	Software Package	Version
RECONSTRUCTION	cryoSPARC	v2
MODEL REFINEMENT	PHENIX

Structure Validation

View Full Validation Report

View more in-depth experimental data

Entry History

& Funding Information

Deposition Data

Released Date: 2020-02-05

Deposition Author(s):

Albesa-Jove, D.

Funding Organization	Location	Grant Number
Spanish Ministry of Economy and Competitiveness	Spain	--

Revision History (Full details and data files)

Version 1.0: 2020-02-05
Type: Initial release
Version 1.1: 2024-05-22
Changes: Data collection, Database references, Refinement description

RCSB PDB is hosted by

RCSB PDB is a member of

RCSB Partners
Nucleic Acid Knowledgebase

CoreTrustSeal

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.