7XSY | pdb_00007xsy

Ligand free structure of branching enzyme isoform 3 (BE3) from Crocosphaera subtropica ATCC 51142

PDB DOI: https://doi.org/10.2210/pdb7XSY/pdb

Classification: TRANSFERASE
Organism(s): Crocosphaera subtropica ATCC 51142
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2022-05-15 Released: 2023-06-07
Deposition Author(s): Tamura, T., Suzuki, E., Suzuki, R.
Funding Organization(s): Japan Society for the Promotion of Science (JSPS)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.50 Å
R-Value Free:
0.261 (Depositor), 0.260 (DCC)
R-Value Work:
0.197 (Depositor), 0.202 (DCC)
R-Value Observed:
0.200 (Depositor)

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

Literature

Ligand free structure of branching enzyme isoform 3 (BE3) from Crocosphaera subtropica ATCC 51142

Tamura, T., Suzuki, E., Suzuki, R.

To be published.

Macromolecule Content

Total Structure Weight: 310.65 kDa
Atom Count: 21,274
Modeled Residue Count: 2,537
Deposited Residue Count: 2,668
Unique protein chains: 1

Macromolecules

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Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
1,4-alpha-glucan branching enzyme	A, B, C, D	667	Crocosphaera subtropica ATCC 51142	Mutation(s): 0 Gene Names: CP000806 EC: 2.4.1.18
UniProt
Find proteins for B1WZK4 (Crocosphaera subtropica (strain ATCC 51142 / BH68)) Explore B1WZK4 Go to UniProtKB: B1WZK4
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	B1WZK4
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 F [auth C] SDF format, chain E [auth A] MOL2 format, chain F [auth C] MOL2 format, chain E [auth A] mmCIF format, chain F [auth C] mmCIF format, chain E [auth A]	E [auth A], F [auth C]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain E [auth A] Focus chain F [auth C] Interactions & Density Focus chain E [auth A] Focus chain F [auth C]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.50 Å
R-Value Free: 0.261 (Depositor), 0.260 (DCC)
R-Value Work: 0.197 (Depositor), 0.202 (DCC)
R-Value Observed: 0.200 (Depositor)

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 148.05	α = 90
b = 149.91	β = 90
c = 162.01	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
iMOSFLM	data reduction
SCALA	data scaling
MOLREP	phasing

Structure Validation

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View more in-depth experimental data

Entry History

& Funding Information

Deposition Data

Released Date: 2023-06-07

Deposition Author(s):

Funding Organization	Location	Grant Number
Japan Society for the Promotion of Science (JSPS)	Japan	18K06135
Japan Society for the Promotion of Science (JSPS)	Japan	16K07467

Revision History (Full details and data files)

Version 1.0: 2023-06-07
Type: Initial release
Version 1.1: 2023-11-29
Changes: Data collection, Refinement description

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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.