3T5T | pdb_00003t5t

Vall from streptomyces hygroscopicus in apo form

• PDB DOI: https://doi.org/10.2210/pdb3T5T/pdb

• Classification: TRANSFERASE
• Organism(s): Streptomyces hygroscopicus subsp. limoneus
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2011-07-28 Released: 2012-08-01 
• Deposition Author(s): Zhang, H., Zheng, L., Qian, H.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.70 Å
• R-Value Free: 
  0.209 (Depositor), 0.210 (DCC) 
• R-Value Work: 
  0.179 (Depositor), 0.180 (DCC) 
• R-Value Observed: 
  0.181 (Depositor) 

Starting Model: experimental

Literature

Structural basis for the substrate specificity of ValL

Zhang, H., Zheng, L., Qian, H.

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)

Macromolecule Content 

• Total Structure Weight: 110.08 kDa 
• Atom Count: 8,233 
• Modeled Residue Count: 945 
• Deposited Residue Count: 992 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Putative glycosyltransferase	A, B	496	Streptomyces hygroscopicus subsp. limoneus	Mutation(s): 0  Gene Names: vldE EC: 2.5.1.135
UniProt
Find proteins for Q15JG1 (Streptomyces hygroscopicus subsp. limoneus) Explore Q15JG1  Go to UniProtKB:  Q15JG1

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
IMD	H [auth A], L [auth B]	IMIDAZOLE C3 H5 N2 RAXXELZNTBOGNW-UHFFFAOYSA-O
MG	C [auth A], D [auth A], E [auth A], F [auth A], G [auth A], I [auth B], J [auth B], K [auth B]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.70 Å
• R-Value Free:  0.209 (Depositor), 0.210 (DCC) 
• R-Value Work:  0.179 (Depositor), 0.180 (DCC) 
• R-Value Observed: 0.181 (Depositor) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 80.671	α = 90
b = 46.693	β = 108.08
c = 123.879	γ = 90

Software Package:

Software Name	Purpose
HKL-2000	data collection
CNS	refinement
REFMAC	refinement
HKL-2000	data reduction
SCALA	data scaling
CNS	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2012-08-01 
Deposition Author(s): Zhang, H., Zheng, L., Qian, H.

Revision History  

• Version 1.0: 2012-08-01
  Type: Initial release
  
• Version 1.1: 2023-11-01
  Changes: Data collection, Database references, Derived calculations, Refinement description