7QQJ | pdb_00007qqj

Sucrose phosphorylase from Jeotgalibaca ciconiae

PDB DOI: https://doi.org/10.2210/pdb7QQJ/pdb

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

Deposited: 2022-01-08 Released: 2023-01-18
Deposition Author(s): Ubiparip, Z., Capra, N., Rozeboom, H.J., Desmet, T., Thunnissen, A.M.W.H.
Funding Organization(s): European Commission

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.05 Å
R-Value Free:
0.254 (Depositor), 0.256 (DCC)
R-Value Work:
0.196 (Depositor), 0.196 (DCC)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

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

Literature

Sucrose phosphorylase from Jeotgalibaca ciconiae

Ubiparip, Z., Capra, N., Rozeboom, H.J., Thunnissen, A.M.W.H., Desmet, T.

To be published.

Macromolecule Content

Total Structure Weight: 112.03 kDa
Atom Count: 8,192
Modeled Residue Count: 946
Deposited Residue Count: 952
Unique protein chains: 1

Macromolecules

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Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Sucrose phosphorylase	A, B	476	Jeotgalibaca ciconiae	Mutation(s): 0 Gene Names: gtfA, EJN90_09285 EC: 2.4.1.7
UniProt
Find proteins for A0A3S9HEG3 (Jeotgalibaca ciconiae) Explore A0A3S9HEG3 Go to UniProtKB: A0A3S9HEG3
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	A0A3S9HEG3
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
TRS Query on TRS Download:Ideal Coordinates CCD File SDF format, chain C [auth B] MOL2 format, chain C [auth B] mmCIF format, chain C [auth B]	C [auth B]	2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL C₄ H₁₂ N O₃ LENZDBCJOHFCAS-UHFFFAOYSA-O		Interactions Focus chain C [auth B] Interactions & Density Focus chain C [auth B]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.05 Å
R-Value Free: 0.254 (Depositor), 0.256 (DCC)
R-Value Work: 0.196 (Depositor), 0.196 (DCC)

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 51.639	α = 90
b = 90.828	β = 92.832
c = 96.17	γ = 90

Software Package:

Software Name	Purpose
XDS	data scaling
Aimless	data scaling
PHASER	phasing
REFMAC	refinement

Structure Validation

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Entry History

& Funding Information

Deposition Data

Released Date: 2023-01-18

Deposition Author(s):

Thunnissen, A.M.W.H.

Funding Organization	Location	Grant Number
European Commission	European Union	761030

Revision History (Full details and data files)

Version 1.0: 2023-01-18
Type: Initial release
Version 1.1: 2024-01-31
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.