6KVY | pdb_00006kvy

The structure of EanB/T414A complex with hercynine

• PDB DOI: https://doi.org/10.2210/pdb6KVY/pdb

• Classification: TRANSFERASE
• Organism(s): Chlorobium limicola
• Expression System: Escherichia coli K-12
• Mutation(s): Yes 


• Deposited: 2019-09-05 Released: 2020-09-09 
• Deposition Author(s): Wu, L., Liu, P.H., Zhou, J.H.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.78 Å
• R-Value Free: 
  0.183 (Depositor), 0.183 (DCC) 
• R-Value Work: 
  0.158 (Depositor), 0.159 (DCC) 
• R-Value Observed: 
  0.159 (Depositor) 

Literature

The structure of EanB/T414A complex with hercynine

Wu, L., Liu, P.H., Zhou, J.H.

To be published.

Biological Assembly 1  

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

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

Biological Assembly Evidence: gel filtration

Macromolecule Content 

• Total Structure Weight: 52.53 kDa 
• Atom Count: 4,063 
• Modeled Residue Count: 429 
• Deposited Residue Count: 460 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Sulfurtransferase	A	460	Chlorobium limicola	Mutation(s): 1  Gene Names: Clim_1149
UniProt
Find proteins for B3ECE3 (Chlorobium limicola (strain DSM 245 / NBRC 103803 / 6330)) Explore B3ECE3  Go to UniProtKB:  B3ECE3

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
AVJ (Subject of Investigation/LOI)	B [auth A]	N,N,N-trimethyl-histidine C9 H16 N3 O2 GPPYTCRVKHULJH-QMMMGPOBSA-O
CL	D [auth A], E [auth A]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M
MG	C [auth A]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
CSS	A	L-PEPTIDE LINKING	C3 H7 N O2 S2		CYS

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.78 Å
• R-Value Free:  0.183 (Depositor), 0.183 (DCC) 
• R-Value Work:  0.158 (Depositor), 0.159 (DCC) 
• R-Value Observed: 0.159 (Depositor) 

Space Group: P 2₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 87.876	α = 90
b = 111.072	β = 90
c = 60.378	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
HKL-3000	data reduction
HKL-3000	data scaling
PHENIX	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2020-09-09 
Deposition Author(s): Wu, L., Liu, P.H., Zhou, J.H.

Revision History  

• Version 1.0: 2020-09-09
  Type: Initial release
  
• Version 1.1: 2024-10-16
  Changes: Data collection, Database references, Derived calculations, Structure summary