7S6F | pdb_00007s6f

Crystal structure of UrtA1 from Synechococcus WH8102 in complex with urea and calcium

PDB DOI: https://doi.org/10.2210/pdb7S6F/pdb

Classification: TRANSPORT PROTEIN
Organism(s): Parasynechococcus marenigrum WH 8102
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2021-09-14 Released: 2021-10-20
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), 0.181 (DCC)
R-Value Work:
0.159 (Depositor), 0.156 (DCC)

wwPDB Validation 3D Report Full Report

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Ligand Structure Quality Assessment

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

Literature

Crystal structure of UrtA1 from Synechococcus WH8102 in complex with urea 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: 44.85 kDa
Atom Count: 3,344
Modeled Residue Count: 395
Deposited Residue Count: 406
Unique protein chains: 1

Macromolecules

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Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Putative urea ABC transporter, urea binding protein	A	406	Parasynechococcus marenigrum WH 8102	Mutation(s): 0 Gene Names: urtA1, SYNW2442
UniProt
Find proteins for Q7U3J0 (Parasynechococcus marenigrum (strain WH8102)) Explore Q7U3J0 Go to UniProtKB: Q7U3J0
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q7U3J0
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
EDO Query on EDO Download:Ideal Coordinates CCD File SDF format, chain D [auth A] SDF format, chain C [auth A] MOL2 format, chain D [auth A] MOL2 format, chain C [auth A] mmCIF format, chain D [auth A] mmCIF format, chain C [auth A]	C [auth A], D [auth A]	1,2-ETHANEDIOL C₂ H₆ O₂ LYCAIKOWRPUZTN-UHFFFAOYSA-N		Interactions Focus chain C [auth A] Focus chain D [auth A] Interactions & Density Focus chain C [auth A] Focus chain D [auth A]
URE (Subject of Investigation/LOI) Query on URE Download:Ideal Coordinates CCD File SDF format, chain B [auth A] MOL2 format, chain B [auth A] mmCIF format, chain B [auth A]	B [auth A]	UREA C H₄ N₂ O XSQUKJJJFZCRTK-UHFFFAOYSA-N		Interactions Focus chain B [auth A] Interactions & Density Focus chain B [auth A]
CA (Subject of Investigation/LOI) Query on CA Download:Ideal Coordinates CCD File SDF format, chain I [auth A] SDF format, chain H [auth A] SDF format, chain G [auth A] SDF format, chain F [auth A] SDF format, chain E [auth A] MOL2 format, chain I [auth A] MOL2 format, chain H [auth A] MOL2 format, chain G [auth A] MOL2 format, chain F [auth A] MOL2 format, chain E [auth A] mmCIF format, chain I [auth A] mmCIF format, chain H [auth A] mmCIF format, chain G [auth A] mmCIF format, chain F [auth A] mmCIF format, chain E [auth A]	E [auth A], F [auth A], G [auth A], H [auth A], I [auth A]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N		Interactions Focus chain E [auth A] Focus chain F [auth A] Focus chain G [auth A] Focus chain H [auth A] Focus chain I [auth A] Interactions & Density Focus chain E [auth A] Focus chain F [auth A] Focus chain G [auth A] Focus chain H [auth A] Focus chain I [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.80 Å
R-Value Free: 0.190 (Depositor), 0.181 (DCC)
R-Value Work: 0.159 (Depositor), 0.156 (DCC)

Space Group: P 2₁ 2 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 47.51	α = 90
b = 71.39	β = 90
c = 120.46	γ = 90

Software Package:

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

Structure Validation

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Entry History

& Funding Information

Deposition Data

Released Date: 2021-10-20

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: 2021-10-20
Type: Initial release
Version 1.1: 2024-10-23
Changes: Data collection, Structure summary

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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.