7YX7 | pdb_00007yx7

Modified oligopeptidase B from S. proteomaculans in intermediate conformation with 1 spermine molecule at 1.72 A resolution

• PDB DOI: https://doi.org/10.2210/pdb7YX7/pdb

• Classification: HYDROLASE
• Organism(s): Serratia proteamaculans
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2022-02-15 Released: 2023-01-18 
• Deposition Author(s): Petrenko, D.E., Boyko, K.M., Nikolaeva, A.Y., Vlaskina, A.V., Mikhailova, A.G., Timofeev, V.I., Rakitina, T.V.
• Funding Organization(s): Not funded

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.72 Å
• R-Value Free: 
  0.239 (Depositor) 
• R-Value Work: 
  0.199 (Depositor) 
• R-Value Observed: 
  0.201 (Depositor) 

Starting Model: experimental

Literature

Elucidation of the Conformational Transition of Oligopeptidase B by an Integrative Approach Based on the Combination of X-ray, SAXS, and Essential Dynamics Sampling Simulation

Britikov, V.V., Timofeev, V.I., Petrenko, D.E., Britikova, E.V., Nikolaeva, A.Y., Vlaskina, A.V., Boyko, K.M., Mikhailova, A.G., Rakitina, T.V.

(2022) Crystals (Basel) 12

• DOI: https://doi.org/10.3390/cryst12050712

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 78.66 kDa 
• Atom Count: 6,201 
• Modeled Residue Count: 677 
• Deposited Residue Count: 677 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Oligopeptidase B	A	677	Serratia proteamaculans	Mutation(s): 6  Gene Names: opdB
UniProt
Find proteins for B3VI58 (Serratia proteamaculans) Explore B3VI58  Go to UniProtKB:  B3VI58

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
SPM	B [auth A]	SPERMINE C10 H26 N4 PFNFFQXMRSDOHW-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.72 Å
• R-Value Free:  0.239 (Depositor) 
• R-Value Work:  0.199 (Depositor) 
• R-Value Observed: 0.201 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 72.95	α = 90
b = 100.53	β = 90
c = 108.88	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
PDB_EXTRACT	data extraction
iMOSFLM	data reduction
SCALA	data scaling
PHASER	phasing

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2023-01-18 
Deposition Author(s): Petrenko, D.E., Boyko, K.M., Nikolaeva, A.Y., Vlaskina, A.V., Mikhailova, A.G., Timofeev, V.I., Rakitina, T.V.

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Funding Organization	Location	Grant Number
Not funded		--

Revision History  

• Version 1.0: 2023-01-18
  Type: Initial release
  
• Version 1.1: 2024-01-31
  Changes: Data collection, Refinement description