7YX7

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

Experimental Data Snapshot

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

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.1 of the entry. See complete history.

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

Macromolecule Content

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

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

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
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	B3VI58
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
SPM Query on SPM Download Ideal Coordinates CCD File SDF format, chain B [auth A] MOL2 format, chain B [auth A]	B [auth A]	SPERMINE C₁₀ H₂₆ N₄ PFNFFQXMRSDOHW-UHFFFAOYSA-N		Interactions Focus chain B [auth A] Interactions & Density Focus chain B [auth A]

Experimental Data & Validation

Experimental Data

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

View Full Validation Report

Ligand Structure Quality Assessment

Entry History & Funding Information

Deposition Data

Released Date: 2023-01-18

Deposition Author(s):

Nikolaeva, A.Y.

Mikhailova, A.G.

Funding Organization	Location	Grant Number
Not funded		--

Revision History (Full details and data files)

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

RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM133198.