1NW2

The crystal structure of the mutant R82E of Thioredoxin from Alicyclobacillus acidocaldarius

PDB DOI: https://doi.org/10.2210/pdb1NW2/pdb

Classification: ELECTRON TRANSPORT
Organism(s): Alicyclobacillus acidocaldarius
Expression System: Escherichia coli
Mutation(s): Yes

Deposited: 2003-02-05 Released: 2003-08-05
Deposition Author(s): Bartolucci, S., De Simone, G., Galdiero, S., Improta, R., Menchise, V., Pedone, C., Pedone, E., Saviano, M.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.90 Å
R-Value Free: 0.255
R-Value Work: 0.212
R-Value Observed: 0.228

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

This is version 1.5 of the entry. See complete history.

Literature

An integrated structural and computational study of the thermostability of two thioredoxin mutants from Alicyclobacillus acidocaldarius

Bartolucci, S., De Simone, G., Galdiero, S., Improta, R., Menchise, V., Pedone, C., Pedone, E., Saviano, M.

(2003) J Bacteriol 185: 4285-4289

PubMed: 12837806 Search on PubMedSearch on PubMed Central
DOI: https://doi.org/10.1128/JB.185.14.4285-4289.2003
Primary Citation of Related Structures:
1NSW, 1NW2

PubMed Abstract:
We report a crystallographic and computational analysis of two mutant forms of the Alicyclobacillus acidocaldarius thioredoxin (BacTrx) done in order to evaluate the contribution of two specific amino acids to the thermostability of BacTrx. Our results suggest that the thermostability of BacTrx may be modulated by mutations affecting the overall electrostatic energy of the protein.

Organizational Affiliation

Dipartimento di Chimica Biologica, University of Naples Federico II, Istituto di Biostrutture e Bioimmagini-CNR, 80134 Naples, Italy.

Macromolecule Content

Total Structure Weight: 93.85 kDa
Atom Count: 7,202
Modelled Residue Count: 840
Deposited Residue Count: 840
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	A, B, C, D, E A, B, C, D, E, F, G, H	105	Alicyclobacillus acidocaldarius	Mutation(s): 1 EC: 1.8.1.9
UniProt
Find proteins for P80579 (Alicyclobacillus acidocaldarius subsp. acidocaldarius) Explore P80579 Go to UniProtKB: P80579
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P80579
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
CAC Query on CAC Download Ideal Coordinates CCD File SDF format, chain Q [auth D] SDF format, chain R [auth D] MOL2 format, chain Q [auth D] MOL2 format, chain R [auth D] mmCIF format, chain Q [auth D] mmCIF format, chain R [auth D]	Q [auth D], R [auth D]	CACODYLATE ION C₂ H₆ As O₂ OGGXGZAMXPVRFZ-UHFFFAOYSA-M		Interactions Focus chain Q [auth D] Focus chain R [auth D] Interactions & Density Focus chain Q [auth D] Focus chain R [auth D]
ZN Query on ZN Download Ideal Coordinates CCD File SDF format, chain AA [auth H] SDF format, chain I [auth A] SDF format, chain L [auth B] SDF format, chain O [auth C] SDF format, chain S [auth D] SDF format, chain T [auth D] SDF format, chain U [auth E] SDF format, chain W [auth F] SDF format, chain Y [auth G] MOL2 format, chain AA [auth H] MOL2 format, chain I [auth A] MOL2 format, chain L [auth B] MOL2 format, chain O [auth C] MOL2 format, chain S [auth D] MOL2 format, chain T [auth D] MOL2 format, chain U [auth E] MOL2 format, chain W [auth F] MOL2 format, chain Y [auth G] mmCIF format, chain AA [auth H] mmCIF format, chain I [auth A] mmCIF format, chain L [auth B] mmCIF format, chain O [auth C] mmCIF format, chain S [auth D] mmCIF format, chain T [auth D] mmCIF format, chain U [auth E] mmCIF format, chain W [auth F] mmCIF format, chain Y [auth G]	AA [auth H] I [auth A] L [auth B] O [auth C] S [auth D] AA [auth H], I [auth A], L [auth B], O [auth C], S [auth D], T [auth D], U [auth E], W [auth F], Y [auth G]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N		Interactions Focus chain AA [auth H] Focus chain I [auth A] Focus chain L [auth B] Focus chain O [auth C] Focus chain S [auth D] Focus chain T [auth D] Focus chain U [auth E] Focus chain W [auth F] Focus chain Y [auth G] Interactions & Density Focus chain AA [auth H] Focus chain I [auth A] Focus chain L [auth B] Focus chain O [auth C] Focus chain S [auth D] Focus chain T [auth D] Focus chain U [auth E] Focus chain W [auth F] Focus chain Y [auth G]
ACT Query on ACT Download Ideal Coordinates CCD File SDF format, chain BA [auth H] SDF format, chain J [auth A] SDF format, chain K [auth A] SDF format, chain M [auth B] SDF format, chain N [auth B] SDF format, chain P [auth C] SDF format, chain V [auth E] SDF format, chain X [auth F] SDF format, chain Z [auth G] MOL2 format, chain BA [auth H] MOL2 format, chain J [auth A] MOL2 format, chain K [auth A] MOL2 format, chain M [auth B] MOL2 format, chain N [auth B] MOL2 format, chain P [auth C] MOL2 format, chain V [auth E] MOL2 format, chain X [auth F] MOL2 format, chain Z [auth G] mmCIF format, chain BA [auth H] mmCIF format, chain J [auth A] mmCIF format, chain K [auth A] mmCIF format, chain M [auth B] mmCIF format, chain N [auth B] mmCIF format, chain P [auth C] mmCIF format, chain V [auth E] mmCIF format, chain X [auth F] mmCIF format, chain Z [auth G]	BA [auth H] J [auth A] K [auth A] M [auth B] N [auth B] BA [auth H], J [auth A], K [auth A], M [auth B], N [auth B], P [auth C], V [auth E], X [auth F], Z [auth G]	ACETATE ION C₂ H₃ O₂ QTBSBXVTEAMEQO-UHFFFAOYSA-M		Interactions Focus chain BA [auth H] Focus chain J [auth A] Focus chain K [auth A] Focus chain M [auth B] Focus chain N [auth B] Focus chain P [auth C] Focus chain V [auth E] Focus chain X [auth F] Focus chain Z [auth G] Interactions & Density Focus chain BA [auth H] Focus chain J [auth A] Focus chain K [auth A] Focus chain M [auth B] Focus chain N [auth B] Focus chain P [auth C] Focus chain V [auth E] Focus chain X [auth F] Focus chain Z [auth G]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.90 Å
R-Value Free: 0.255
R-Value Work: 0.212
R-Value Observed: 0.228
Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 79.61	α = 90
b = 60.21	β = 93.3
c = 82.95	γ = 90

Software Package:

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

Structure Validation

View Full Validation Report

Entry History

Deposition Data

Released Date: 2003-08-05

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2003-08-05
Type: Initial release
Version 1.1: 2008-04-29
Changes: Version format compliance
Version 1.2: 2011-07-13
Changes: Non-polymer description, Version format compliance
Version 1.3: 2021-10-27
Changes: Data collection, Database references, Derived calculations
Version 1.4: 2023-08-16
Changes: Data collection, Refinement description
Version 1.5: 2024-10-30
Changes: Structure summary