7RXK

Multi-conformer model of Apo Ketosteroid Isomerase Y32F/Y57F mutant from Pseudomonas Putida (pKSI) at 250 K

PDB DOI: https://doi.org/10.2210/pdb7RXK/pdb

Classification: ISOMERASE
Organism(s): Pseudomonas putida
Expression System: Escherichia coli
Mutation(s): Yes

Deposited: 2021-08-23 Released: 2022-11-09
Deposition Author(s): Yabukarski, F., Doukov, T., Herschlag, D.
Funding Organization(s): National Science Foundation (NSF, United States)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.10 Å
R-Value Free: 0.166
R-Value Work: 0.153
R-Value Observed: 0.154

wwPDB Validation 3D Report Full Report

This is version 1.0 of the entry. See complete history.

Literature

Ensemble-function relationships to evaluate catalysis in the ketosteroid isomerase oxyanion hole

Yabukarski, F., Doukov, T., Pinney, M., Biel, J., Fraser, J., Herschlag, D.

To be published.

Macromolecule Content

Total Structure Weight: 29.15 kDa
Atom Count: 5,199
Modelled Residue Count: 257
Deposited Residue Count: 262
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Steroid Delta-isomerase	A, B	131	Pseudomonas putida	Mutation(s): 2 Gene Names: ksi EC: 5.3.3.1
UniProt
Find proteins for P07445 (Pseudomonas putida) Explore P07445 Go to UniProtKB: P07445
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P07445
Protein Feature View Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
CL Query on CL Download Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain F [auth B] MOL2 format, chain E [auth A] MOL2 format, chain F [auth B]	E [auth A], F [auth B]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Ligand Interaction
MG Query on MG Download Ideal Coordinates CCD File SDF format, chain C [auth A] SDF format, chain D [auth A] MOL2 format, chain C [auth A] MOL2 format, chain D [auth A]	C [auth A], D [auth A]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Ligand Interaction

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.10 Å
R-Value Free: 0.166
R-Value Work: 0.153
R-Value Observed: 0.154
Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 36.266	α = 90
b = 74.059	β = 90
c = 96.229	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data reduction
Aimless	data scaling
PHASER	phasing

Structure Validation

View Full Validation Report

Entry History & Funding Information

Deposition Data

Released Date: 2022-11-09

Deposition Author(s):

Funding Organization	Location	Grant Number
National Science Foundation (NSF, United States)	United States	MCB-1714723

Revision History (Full details and data files)

Version 1.0: 2022-11-09
Type: Initial release

RCSB PDB Core Operations are funded by the National Science Foundation (DBI-1832184), 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.