4K7C | pdb_00004k7c

Crystal structure of pepw from lactobacillus rhamnosis hn001 (dr20) determined as the selenomet derivative

• PDB DOI: https://doi.org/10.2210/pdb4K7C/pdb

• Classification: HYDROLASE
• Organism(s): Lacticaseibacillus rhamnosus HN001
• Expression System: Lactococcus cremoris subsp. cremoris NZ9000
• Mutation(s): No 


• Deposited: 2013-04-16 Released: 2013-06-19 
• Deposition Author(s): Webby, C., Knapp, K.M., Anderson, B.F., Norris, G.E.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.66 Å
• R-Value Free: 
  0.210 (Depositor), 0.216 (DCC) 
• R-Value Work: 
  0.177 (Depositor), 0.187 (DCC) 
• R-Value Observed: 
  0.179 (Depositor) 

Starting Model: experimental

Literature

Crystal structure of pepw from lactobacillus rhamnosis hn001 (dr20) determined as the selenomet derivative

Webby, C., Knapp, K.M., Anderson, B.F., Norris, G.E.

To be published.

Biological Assembly 1  

Global Symmetry: Dihedral - D3  (Explore in 3D)
Global Stoichiometry: Homo 6-mer - A6 

Biological assembly 1 generated by PISA (software)

Biological Assembly 2  

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

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

Macromolecule Content 

• Total Structure Weight: 51.89 kDa 
• Atom Count: 4,219 
• Modeled Residue Count: 446 
• Deposited Residue Count: 446 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Aminopeptidase C	A	446	Lacticaseibacillus rhamnosus HN001	Mutation(s): 0  Gene Names: LRH 13711, LRH_13711 EC: 3.4.22

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
GOL	B [auth A], C [auth A], D [auth A], E [auth A], F [auth A], G [auth A], H [auth A], I [auth A]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
MSE	A	L-PEPTIDE LINKING	C5 H11 N O2 Se		MET

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.66 Å
• R-Value Free:  0.210 (Depositor), 0.216 (DCC) 
• R-Value Work:  0.177 (Depositor), 0.187 (DCC) 
• R-Value Observed: 0.179 (Depositor) 

Space Group: P 6₃ 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 143.432	α = 90
b = 143.432	β = 90
c = 97.17	γ = 120

Software Package:

Software Name	Purpose
CrystalClear	data collection
PHASER	phasing
REFMAC	refinement
CrystalClear	data reduction
CrystalClear	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2013-06-19 
Deposition Author(s): Webby, C., Knapp, K.M., Anderson, B.F., Norris, G.E.

Revision History  

• Version 1.0: 2013-06-19
  Type: Initial release
  
• Version 1.1: 2017-11-15
  Changes: Advisory, Refinement description
• Version 1.2: 2023-09-20
  Changes: Advisory, Data collection, Database references, Derived calculations, Refinement description
• Version 1.3: 2023-12-06
  Changes: Data collection
• Version 1.4: 2024-11-27
  Changes: Structure summary