9D8A | pdb_00009d8a

Structure of Rhizopus azygosporus Kinase in complex with GDP and MG

• PDB DOI: https://doi.org/10.2210/pdb9D8A/pdb

• Classification: TRANSFERASE
• Organism(s): Rhizopus azygosporus
• Expression System: Escherichia coli BL21
• Mutation(s): No 


• Deposited: 2024-08-19 Released: 2024-09-11 
• Deposition Author(s): Wimberly-Gard, G.M., Shuman, S.
• Funding Organization(s): National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.65 Å
• R-Value Free: 
  0.237 (Depositor), 0.243 (DCC) 
• R-Value Work: 
  0.169 (Depositor), 0.182 (DCC) 
• R-Value Observed: 
  0.173 (Depositor) 

Starting Model: in silico

Literature

Structure of Rhizopus azygosporus Kinase in complex with GDP and MG

Wimberly-Gard, G.M., Shuman, S.

To be published.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors and generated by (software)

Macromolecule Content 

• Total Structure Weight: 20.76 kDa 
• Atom Count: 1,478 
• Modeled Residue Count: 172 
• Deposited Residue Count: 176 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Rhizopus azygosporus Kinase	A	176	Rhizopus azygosporus	Mutation(s): 0  Gene Names: CU097_007847
UniProt
Find proteins for A0A367K070 (Rhizopus azygosporus) Explore A0A367K070  Go to UniProtKB:  A0A367K070

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
GDP (Subject of Investigation/LOI)	B [auth A]	GUANOSINE-5'-DIPHOSPHATE C10 H15 N5 O11 P2 QGWNDRXFNXRZMB-UUOKFMHZSA-N
MG (Subject of Investigation/LOI)	C [auth A]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.65 Å
• R-Value Free:  0.237 (Depositor), 0.243 (DCC) 
• R-Value Work:  0.169 (Depositor), 0.182 (DCC) 
• R-Value Observed: 0.173 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 39.417	α = 90
b = 66.46	β = 90
c = 73.703	γ = 90

Software Package:

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

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2024-09-11 
Deposition Author(s): Wimberly-Gard, G.M., Shuman, S.

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Funding Organization	Location	Grant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	R35-GM126945
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	GM134021

Revision History  

• Version 1.0: 2024-09-11
  Type: Initial release