6KSV | pdb_00006ksv

Crystal structure of SurE with D-Leu

• PDB DOI: https://doi.org/10.2210/pdb6KSV/pdb

• Classification: HYDROLASE
• Organism(s): Streptomyces albidoflavus
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2019-08-26 Released: 2020-06-24 
• Deposition Author(s): Zhai, R., Mori, T., Abe, I.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.42 Å
• R-Value Free: 
  0.279 (Depositor), 0.289 (DCC) 
• R-Value Work: 
  0.200 (Depositor) 
• R-Value Observed: 
  0.204 (Depositor) 

Starting Model: experimental

Literature

Heterochiral coupling in non-ribosomal peptide macrolactamization

Matsuda, K., Zhai, R., Mori, T., Kobayashi, M., Sano, A., Abe, I., Wakimoto, T.

(2020) Nat Catal 

• DOI: https://doi.org/10.1038/s41929-020-0456-7

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

Biological Assembly 2  

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

Biological assembly 2 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 100.4 kDa 
• Atom Count: 6,489 
• Modeled Residue Count: 853 
• Deposited Residue Count: 942 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Alpha/beta hydrolase	A, B	471	Streptomyces albidoflavus	Mutation(s): 0
UniProt
Find proteins for A0A679G4U8 (Streptomyces albidoflavus) Explore A0A679G4U8  Go to UniProtKB:  A0A679G4U8

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
E7L (Subject of Investigation/LOI)	I [auth B]	S-(2-acetamidoethyl) (2R)-2-azanyl-4-methyl-pentanethioate C10 H20 N2 O2 S FGUKBCKKFXHYHQ-SECBINFHSA-N
DLE (Subject of Investigation/LOI)	C [auth A]	D-LEUCINE C6 H13 N O2 ROHFNLRQFUQHCH-RXMQYKEDSA-N
SO4	D [auth A], E [auth A], F [auth A], J [auth B], K [auth B]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L
YT3	G [auth A], H [auth A], L [auth B]	YTTRIUM (III) ION Y GRTBAGCGDOYUBE-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.42 Å
• R-Value Free:  0.279 (Depositor), 0.289 (DCC) 
• R-Value Work:  0.200 (Depositor) 
• R-Value Observed: 0.204 (Depositor) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 48.37	α = 90
b = 152.06	β = 113.08
c = 64.54	γ = 90

Software Package:

Software Name	Purpose
XSCALE	data scaling
PHENIX	refinement
PDB_EXTRACT	data extraction
XDS	data reduction
PHASER	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2020-06-24 
Deposition Author(s): Zhai, R., Mori, T., Abe, I.

Revision History  

• Version 1.0: 2020-06-24
  Type: Initial release
  
• Version 1.1: 2023-11-22
  Changes: Data collection, Database references, Derived calculations, Refinement description
• Version 1.2: 2024-11-13
  Changes: Structure summary