1GS3 | pdb_00001gs3

High resolution crystal structure of PI delta-5-3-Ketosteroid Isomerase mutants Y30F/Y55F/Y115F/D38N (Y32F/Y57F/Y119F/D40N, PI numbering)complexed with equilenin at 2.1 A resolution

PDB DOI: https://doi.org/10.2210/pdb1GS3/pdb

Classification: ISOMERASE
Organism(s): Pseudomonas putida
Expression System: Escherichia coli BL21(DE3)
Mutation(s): Yes

Deposited: 2001-12-27 Released: 2003-01-23
Deposition Author(s): Shin, S., Ha, N.-C., Oh, B.-H.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.10 Å
R-Value Free:
0.275 (Depositor)
R-Value Work:
0.213 (Depositor)
R-Value Observed:
0.213 (Depositor)

Starting Model: experimental
View more details

wwPDB Validation 3D Report Full Report

This is version 1.4 of the entry. See complete history.

Literature

Contribution of a Low-Barrier Hydrogen Bond to Catalysis by Delta-5-3-Ketosteroid Isomerase is not Extremely High Compared to that of an Ordinary Hydrogen Bond. Low-Barrier Hydrogen Bond of Pi Ksi

Choi, G., Shin, S., Yun, S.-G., Jang, D.S., Nam, G.H., Hong, B.-H., Lee, H.-C., Oh, B.-H., Choi, K.Y.

To be published.

Macromolecule Content

Total Structure Weight: 14.77 kDa
Atom Count: 1,015
Modelled Residue Count: 123
Deposited Residue Count: 131
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	131	Pseudomonas putida	Mutation(s): 4 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
Sequence Annotations Expand
Reference Sequence LOADING

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
EQU Query on EQU Download Ideal Coordinates CCD File SDF format, chain B [auth A] MOL2 format, chain B [auth A] mmCIF format, chain B [auth A]	B [auth A]	EQUILENIN C₁₈ H₁₈ O₂ PDRGHUMCVRDZLQ-WMZOPIPTSA-N		Interactions Focus chain B [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.10 Å
R-Value Free: 0.275 (Depositor)
R-Value Work: 0.213 (Depositor)
R-Value Observed: 0.213 (Depositor)

Space Group: C 2 2 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 36.319	α = 90
b = 96.237	β = 90
c = 74.431	γ = 90

Software Package:

Software Name	Purpose
CNS	refinement
DENZO	data reduction
SCALEPACK	data scaling
AMoRE	phasing

Structure Validation

View Full Validation Report

Entry History

Deposition Data

Released Date: 2003-01-23

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2003-01-23
Type: Initial release
Version 1.1: 2011-05-08
Changes: Version format compliance
Version 1.2: 2011-07-13
Changes: Version format compliance
Version 1.3: 2018-04-04
Changes: Data collection
Version 1.4: 2023-12-13
Changes: Data collection, Database references, Derived calculations, 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 R01GM157729.