5MB2 | pdb_00005mb2

Structure of sucrose phosphorylase from Bifidobacterium adolescentis bound to nigerose

PDB DOI: https://doi.org/10.2210/pdb5MB2/pdb

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

Deposited: 2016-11-07 Released: 2017-12-20
Deposition Author(s): Grimm, C., Kraus, M.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.75 Å
R-Value Free:
0.232 (Depositor), 0.230 (DCC)
R-Value Work:
0.197 (Depositor), 0.200 (DCC)
R-Value Observed:
0.199 (Depositor)

wwPDB Validation 3D Report Full Report

This is version 2.1 of the entry. See complete history.

Literature

Structure of sucrose phosphorylase from Bifidobacterium adolescentis bound to nigerose

Grimm, C.

To be published.

Macromolecule Content

Total Structure Weight: 56.36 kDa
Atom Count: 4,309
Modeled Residue Count: 504
Deposited Residue Count: 504
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Sucrose phosphorylase	A [auth B]	504	Bifidobacterium adolescentis	Mutation(s): 0 Gene Names: sucP EC: 2.4.1.7
UniProt
Find proteins for A0ZZH6 (Bifidobacterium adolescentis (strain ATCC 15703 / DSM 20083 / NCTC 11814 / E194a)) Explore A0ZZH6 Go to UniProtKB: A0ZZH6
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	A0ZZH6
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 MOL2 format, chain B mmCIF format, chain B	B	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain B Interactions & Density Focus chain B

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.75 Å
R-Value Free: 0.232 (Depositor), 0.230 (DCC)
R-Value Work: 0.197 (Depositor), 0.200 (DCC)
R-Value Observed: 0.199 (Depositor)

Space Group: P 4₃ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 82.915	α = 90
b = 82.915	β = 90
c = 153.644	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
PDB_EXTRACT	data extraction
XDS	data reduction
XSCALE	data scaling
PHASER	phasing

Structure Validation

View Full Validation Report

Entry History

Deposition Data

Released Date: 2017-12-20

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2017-12-20
Type: Initial release
Version 2.0: 2019-10-16
Changes: Advisory, Atomic model, Data collection
Version 2.1: 2024-05-08
Changes: Data collection, Database references

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.