4HU7

E. coli thioredoxin variant with Pro76 as single proline residue

PDB DOI: https://doi.org/10.2210/pdb4HU7/pdb

Classification: OXIDOREDUCTASE
Organism(s): Escherichia coli K-12
Expression System: Escherichia coli BL21(DE3)
Mutation(s): Yes

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

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.40 Å
R-Value Free: 0.198
R-Value Work: 0.162
R-Value Observed: 0.163

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: 23.32 kDa
Atom Count: 1,855
Modelled Residue Count: 211
Deposited Residue Count: 216
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, B	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 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
CU Query on CU Download Ideal Coordinates CCD File SDF format, chain C [auth A] SDF format, chain E [auth B] MOL2 format, chain C [auth A] MOL2 format, chain E [auth B]	C [auth A], E [auth B]	COPPER (II) ION Cu JPVYNHNXODAKFH-UHFFFAOYSA-N		Interactions Focus chain C [auth A] Focus chain E [auth B] Interactions & Density Focus chain C [auth A] Focus chain E [auth B]
NA Query on NA Download Ideal Coordinates CCD File SDF format, chain D [auth A] MOL2 format, chain D [auth A]	D [auth A]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N		Interactions Focus chain D [auth A] Interactions & Density Focus chain D [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.40 Å
R-Value Free: 0.198
R-Value Work: 0.162
R-Value Observed: 0.163
Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 33.85	α = 90
b = 60.88	β = 100.38
c = 45.33	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: 2017-11-15
Changes: Advisory, Refinement description
Version 1.3: 2023-09-20
Changes: Advisory, Data collection, Database references, Derived calculations, Refinement description