7ZNP

Structure of AmedSP

PDB DOI: https://doi.org/10.2210/pdb7ZNP/pdb

Classification: HYDROLASE
Organism(s): Alteromonas mediterranea
Expression System: Escherichia coli BL21
Mutation(s): No

Deposited: 2022-04-21 Released: 2023-05-10
Deposition Author(s): Fredslund, F., Teze, D., Welner, D.H.
Funding Organization(s): Novo Nordisk Foundation

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.15 Å
R-Value Free: 0.229
R-Value Work: 0.185
R-Value Observed: 0.187

wwPDB Validation 3D Report Full Report

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

Literature

Structure of AmedSP

Fredslund, F., Teze, D., Welner, D.H.

To be published.

Macromolecule Content

Total Structure Weight: 55.72 kDa
Atom Count: 4,005
Modelled Residue Count: 502
Deposited Residue Count: 505
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	505	Alteromonas mediterranea	Mutation(s): 0 Gene Names: BM525_11180
UniProt
Find proteins for A0A1J0SGS2 (Alteromonas mediterranea) Explore A0A1J0SGS2 Go to UniProtKB: A0A1J0SGS2
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	A0A1J0SGS2
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
CL Query on CL Download Ideal Coordinates CCD File SDF format, chain C [auth A] MOL2 format, chain C [auth A]	C [auth A]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain C [auth A] Interactions & Density Focus chain C [auth A]
MG Query on MG Download Ideal Coordinates CCD File SDF format, chain B [auth A] MOL2 format, chain B [auth A]	B [auth A]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain B [auth A] Interactions & Density Focus chain B [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.15 Å
R-Value Free: 0.229
R-Value Work: 0.185
R-Value Observed: 0.187
Space Group: C 2 2 2
Diffraction Data: https://doi.org/10.15151/ESRF-DC-1114624654

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 132.456	α = 90
b = 143.558	β = 90
c = 72.797	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data reduction
XDS	data scaling
PHASER	phasing

Structure Validation

View Full Validation Report

Entry History & Funding Information

Deposition Data

Released Date: 2023-05-10

Deposition Author(s):

Funding Organization	Location	Grant Number
Novo Nordisk Foundation	Denmark	NNF20CC0035580

Revision History (Full details and data files)

Version 1.0: 2023-05-10
Type: Initial release
Version 1.1: 2024-02-07
Changes: Data collection, Refinement description

RCSB PDB Core Operations are funded by the National Science Foundation (DBI-1832184), 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 R01GM133198.