5MRT | pdb_00005mrt

Crystal structure of L5 protease Lysobacter sp. XL1

• PDB DOI: https://doi.org/10.2210/pdb5MRT/pdb

• Classification: HYDROLASE
• Organism(s): Lysobacter sp. XL1
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2016-12-26 Released: 2018-01-17 
• Deposition Author(s): Gabdulkhakov, A., Tishchenko, S., Lisov, A., Leontievsky, A.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.60 Å
• R-Value Free: 
  0.227 (Depositor), 0.226 (DCC) 
• R-Value Work: 
  0.168 (Depositor), 0.167 (DCC) 
• R-Value Observed: 
  0.170 (Depositor) 

Starting Model: experimental

Literature

Crystal structure of L5 protease Lysobacter sp. XL1

Gabdulkhakov, A., Tishchenko, S., Lisov, A., Leontievsky, A.

To be published.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Biological Assembly 2  

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

Biological assembly 2 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 42.05 kDa 
• Atom Count: 3,242 
• Modeled Residue Count: 388 
• Deposited Residue Count: 410 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Lytic endopeptidase preproenzyme	A, B	205	Lysobacter sp. XL1	Mutation(s): 0  Gene Names: alpB
UniProt
Find proteins for D2K8B4 (Lysobacter sp. (strain XL1)) Explore D2K8B4  Go to UniProtKB:  D2K8B4

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
GOL	I [auth B]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N
FMT	C [auth A], D [auth A], E [auth A], F [auth A], K [auth B], L [auth B]	FORMIC ACID C H2 O2 BDAGIHXWWSANSR-UHFFFAOYSA-N
CL	J [auth B]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M
NA	G [auth A], H [auth A]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.60 Å
• R-Value Free:  0.227 (Depositor), 0.226 (DCC) 
• R-Value Work:  0.168 (Depositor), 0.167 (DCC) 
• R-Value Observed: 0.170 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 62.549	α = 90
b = 66.668	β = 90
c = 96.642	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
PROTEUM PLUS	data reduction
PROTEUM PLUS	data scaling
PHASER	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2018-01-17 
Deposition Author(s): Gabdulkhakov, A., Tishchenko, S., Lisov, A., Leontievsky, A.

Revision History  

• Version 1.0: 2018-01-17
  Type: Initial release
  
• Version 1.1: 2024-01-17
  Changes: Data collection, Database references, Derived calculations, Refinement description
• Version 1.2: 2024-11-13
  Changes: Structure summary