8HIC

Crystal structure of UrtA from Prochlorococcus marinus str. MIT 9313 in complex with urea and calcium

• PDB DOI: https://doi.org/10.2210/pdb8HIC/pdb

• Classification: TRANSPORT PROTEIN
• Organism(s): Prochlorococcus marinus str. MIT 9313
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2022-11-19 Released: 2023-11-22 
• Deposition Author(s): Zhang, Y.Z., Wang, P., Wang, C.
• Funding Organization(s): National Science Foundation (NSF, China)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.60 Å
• R-Value Free: 0.189 
• R-Value Work: 0.159 
• R-Value Observed: 0.161 

Literature

Crystal structure of UrtA from Prochlorococcus marinus str. MIT 9313 in complex with urea and calcium

Zhang, Y.Z., Wang, P., Wang, C.

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: gel filtration

Macromolecule Content

• Total Structure Weight: 45.87 kDa 
• Atom Count: 3,746 
• Modelled Residue Count: 395 
• Deposited Residue Count: 414 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Putative urea ABC transporter, substrate binding protein	A	414	Prochlorococcus marinus str. MIT 9313	Mutation(s): 0  Gene Names: urtA, PMT_2229
UniProt
Find proteins for Q7V3V9 (Prochlorococcus marinus (strain MIT 9313)) Explore Q7V3V9  Go to UniProtKB:  Q7V3V9

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
URE (Subject of Investigation/LOI)	B [auth A]	UREA C H4 N2 O XSQUKJJJFZCRTK-UHFFFAOYSA-N
CA	C [auth A], D [auth A], E [auth A], F [auth A]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.60 Å
• R-Value Free: 0.189 
• R-Value Work: 0.159 
• R-Value Observed: 0.161 
• Space Group: P 2₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 119.7	α = 90
b = 47.612	β = 90
c = 71.642	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
HKL-2000	data reduction
HKL-2000	data scaling
PHASER	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2023-11-22 
Deposition Author(s): Zhang, Y.Z., Wang, P., Wang, C.

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Funding Organization	Location	Grant Number
National Science Foundation (NSF, China)	China	2018YFC1406700

Revision History  

• Version 1.0: 2023-11-22
  Type: Initial release