8IYF

Structure of VldE-H182A in complex with GDP

• PDB DOI: https://doi.org/10.2210/pdb8IYF/pdb

• Classification: TRANSFERASE
• Organism(s): Streptomyces hygroscopicus subsp. limoneus
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2023-04-04 Released: 2024-04-10 
• Deposition Author(s): Wong, C.P., Mori, T., Mahmud, T., Abe, I.
• Funding Organization(s): Not funded

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.90 Å
• R-Value Free: 0.241 
• R-Value Work: 0.195 
• R-Value Observed: 0.197 

Literature

Structure of VldE-H182A in complex with GDP

Wong, C.P., Mori, T., Mahmud, T., Abe, I.

To be published.

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

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

Biological Assembly Evidence: gel filtration

Macromolecule Content

• Total Structure Weight: 110.77 kDa 
• Atom Count: 8,000 
• Modelled Residue Count: 950 
• Deposited Residue Count: 994 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Validamine 7-phosphate valienyltransferase	A, B	497	Streptomyces hygroscopicus subsp. limoneus	Mutation(s): 1  Gene Names: vldE, SHL15_8006 EC: 2.5.1.135
UniProt
Find proteins for Q15JG1 (Streptomyces hygroscopicus subsp. limoneus) Explore Q15JG1  Go to UniProtKB:  Q15JG1

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
GDP (Subject of Investigation/LOI)	C [auth A], D [auth B]	GUANOSINE-5'-DIPHOSPHATE C10 H15 N5 O11 P2 QGWNDRXFNXRZMB-UUOKFMHZSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.90 Å
• R-Value Free: 0.241 
• R-Value Work: 0.195 
• R-Value Observed: 0.197 
• Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 48.009	α = 90
b = 121.263	β = 90
c = 84.544	γ = 90

Software Package:

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

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2024-04-10 
Deposition Author(s): Wong, C.P., Mori, T., Mahmud, T., Abe, I.

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Funding Organization	Location	Grant Number
Not funded		--

Revision History  

• Version 1.0: 2024-04-10
  Type: Initial release