7UG8 | pdb_00007ug8

Crystal structure of a solute receptor from Synechococcus CC9311 in complex with alpha-ketovaleric and calcium

PDB DOI: https://doi.org/10.2210/pdb7UG8/pdb

Classification: TRANSPORT PROTEIN
Organism(s): Synechococcus sp. CC9311
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2022-03-24 Released: 2023-04-19
Deposition Author(s): Shah, B.S., Mikolajek, H., Orr, C.M., Mykhaylyk, V., Owens, R.J., Paulsen, I.T.
Funding Organization(s): Australian Research Council (ARC)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.80 Å
R-Value Free:
0.190 (Depositor), 0.190 (DCC)
R-Value Work:
0.169 (Depositor), 0.169 (DCC)

wwPDB Validation 3D Report Full Report

Validation slider image for 7UG8

Ligand Structure Quality Assessment

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

Literature

Crystal structure of a solute receptor from Synechococcus CC9311 in complex with alpha-ketovaleric and calcium

Shah, B.S., Mikolajek, H., Orr, C.M., Mykhaylyk, V., Owens, R., Paulsen, I.T.

To be published.

Macromolecule Content

Total Structure Weight: 77.36 kDa
Atom Count: 5,478
Modeled Residue Count: 659
Deposited Residue Count: 694
Unique protein chains: 1

Macromolecules

Find similar proteins by:

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Ketoacid-binding protein	A, B	347	Synechococcus sp. CC9311	Mutation(s): 0 Gene Names: sync_2776
UniProt
Find proteins for A0ACD6B8C3 (Synechococcus sp. (strain CC9311)) Explore A0ACD6B8C3 Go to UniProtKB: A0ACD6B8C3
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	A0ACD6B8C3
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
69O (Subject of Investigation/LOI) Query on 69O Download:Ideal Coordinates CCD File SDF format, chain G [auth B] SDF format, chain C [auth A] MOL2 format, chain G [auth B] MOL2 format, chain C [auth A] mmCIF format, chain G [auth B] mmCIF format, chain C [auth A]	C [auth A], G [auth B]	2-oxopentanoic acid C₅ H₈ O₃ KDVFRMMRZOCFLS-UHFFFAOYSA-N		Interactions Focus chain C [auth A] Focus chain G [auth B] Interactions & Density Focus chain C [auth A] Focus chain G [auth B]
EDO Query on EDO Download:Ideal Coordinates CCD File SDF format, chain F [auth B] SDF format, chain D [auth A] MOL2 format, chain F [auth B] MOL2 format, chain D [auth A] mmCIF format, chain F [auth B] mmCIF format, chain D [auth A]	D [auth A], F [auth B]	1,2-ETHANEDIOL C₂ H₆ O₂ LYCAIKOWRPUZTN-UHFFFAOYSA-N		Interactions Focus chain D [auth A] Focus chain F [auth B] Interactions & Density Focus chain D [auth A] Focus chain F [auth B]
CA Query on CA Download:Ideal Coordinates CCD File SDF format, chain H [auth B] SDF format, chain E [auth A] MOL2 format, chain H [auth B] MOL2 format, chain E [auth A] mmCIF format, chain H [auth B] mmCIF format, chain E [auth A]	E [auth A], H [auth B]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N		Interactions Focus chain E [auth A] Focus chain H [auth B] Interactions & Density Focus chain E [auth A] Focus chain H [auth B]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.80 Å
R-Value Free: 0.190 (Depositor), 0.190 (DCC)
R-Value Work: 0.169 (Depositor), 0.169 (DCC)

Space Group: P 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 54.68	α = 69.649
b = 54.75	β = 77.732
c = 61.15	γ = 67.267

Software Package:

Software Name	Purpose
REFMAC	refinement
XDS	data reduction
Aimless	data scaling
CRANK2	phasing
Coot	model building

Structure Validation

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Ligand Structure Quality Assessment

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Entry History

& Funding Information

Deposition Data

Released Date: 2023-04-19

Deposition Author(s):

Funding Organization	Location	Grant Number
Australian Research Council (ARC)	Australia	DP200102944
Australian Research Council (ARC)	Australia	CE200100029

Revision History (Full details and data files)

Version 1.0: 2023-04-19
Type: Initial release
Version 1.1: 2024-05-22
Changes: Data collection

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