4HU9

E. coli thioredoxin variant with (4S)-FluoroPro76 as single proline residue

PDB DOI: https://doi.org/10.2210/pdb4HU9/pdb

Classification: OXIDOREDUCTASE
Organism(s): Escherichia coli K-12
Expression System: Escherichia coli
Mutation(s): Yes

Deposited: 2012-11-02 Released: 2013-05-29
Deposition Author(s): Scharer, M.A., Rubini, M., Capitani, G., Glockshuber, R.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.55 Å
R-Value Free: 0.210
R-Value Work: 0.173
R-Value Observed: 0.175

wwPDB Validation 3D Report Full Report

This is version 1.3 of the entry. See complete history.

Literature

(4R)- and (4S)-Fluoroproline in the Conserved cis-Prolyl Peptide Bond of the Thioredoxin Fold: Tertiary Structure Context Dictates Ring Puckering.

Rubini, M., Scharer, M.A., Capitani, G., Glockshuber, R.

(2013) Chembiochem 14: 1053-1057

PubMed: 23712956 Search on PubMed
DOI: https://doi.org/10.1002/cbic.201300178
Primary Citation of Related Structures:
4HU7, 4HU9, 4HUA

PubMed Abstract:
Fine-tuning protein stability: The non-natural amino acids (2S,4R)- and (2S,4S)-fluoroproline modulate protein stability by biasing the proline ring pucker and the cis/trans equilibrium of prolyl peptide bonds. We incorporated both fluoroproline stereoisomers at the invariant cis-proline residue of the thioredoxin fold. The results show that tertiary structure context overrules the conformational preferences of fluoroprolines.

Organizational Affiliation

Department of Organic Chemistry/Cellular Chemistry, University of Konstanz, Universitätsstrasse 10, 78464 Konstanz, Germany. marina.rubini@uni-konstanz.de

Macromolecule Content

Total Structure Weight: 11.66 kDa
Atom Count: 1,010
Modelled Residue Count: 108
Deposited Residue Count: 108
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Thioredoxin-1	A	108	Escherichia coli K-12	Mutation(s): 4 Gene Names: trxA
UniProt
Find proteins for P0AA25 (Escherichia coli (strain K12)) Explore P0AA25 Go to UniProtKB: P0AA25
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P0AA25
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
CU Query on CU 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]	COPPER (II) ION Cu JPVYNHNXODAKFH-UHFFFAOYSA-N		Interactions Focus chain B [auth A] Interactions & Density Focus chain B [auth A]

Modified Residues 1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
4FB Query on 4FB	A	L-PEPTIDE LINKING	C₅ H₈ F N O₂		PRO

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.55 Å
R-Value Free: 0.210
R-Value Work: 0.173
R-Value Observed: 0.175
Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 88.27	α = 90
b = 48.76	β = 101.94
c = 31.57	γ = 90

Software Package:

Software Name	Purpose
XSCALE	data scaling
PHASER	phasing
PHENIX	refinement
PDB_EXTRACT	data extraction
RemDAq	data collection
XDS	data reduction

Structure Validation

View Full Validation Report

Entry History

Deposition Data

Released Date: 2013-05-29

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2013-05-29
Type: Initial release
Version 1.1: 2013-07-03
Changes: Database references
Version 1.2: 2017-09-20
Changes: Advisory, Refinement description
Version 1.3: 2024-11-20
Changes: Advisory, Data collection, Database references, Derived calculations, Structure summary