5J60 | pdb_00005j60

Structure of a thioredoxin reductase from Gloeobacter violaceus

PDB DOI: https://doi.org/10.2210/pdb5J60/pdb

Classification: OXIDOREDUCTASE
Organism(s): Gloeobacter violaceus PCC 7421
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2016-04-04 Released: 2016-07-27
Deposition Author(s): Buey, R.M., de Pereda, J.M., Balsera, M.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.90 Å
R-Value Free:
0.202 (Depositor), 0.207 (DCC)
R-Value Work:
0.177 (Depositor), 0.183 (DCC)
R-Value Observed:
0.178 (Depositor)

Starting Model: experimental
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Ligand Structure Quality Assessment

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

Literature

A New Member of the Thioredoxin Reductase Family from Early Oxygenic Photosynthetic Organisms.

Buey, R.M., Galindo-Trigo, S., Lopez-Maury, L., Velazquez-Campoy, A., Revuelta, J.L., Florencio, F.J., de Pereda, J.M., Schurmann, P., Buchanan, B.B., Balsera, M.

(2017) Mol Plant 10: 212-215

PubMed: 27418374 Search on PubMed
DOI: https://doi.org/10.1016/j.molp.2016.06.019
Primary Citation Related Structures:
5J60

Organizational Affiliation

Department Microbiología y Genética, Universidad de Salamanca, Salamanca 37007, Spain.

Macromolecule Content

Total Structure Weight: 141.62 kDa
Atom Count: 9,822
Modeled Residue Count: 1,225
Deposited Residue Count: 1,280
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Thioredoxin reductase	A, B, C, D	320	Gloeobacter violaceus PCC 7421	Mutation(s): 0 Gene Names: glr0719
UniProt
Find proteins for Q7NMP6 (Gloeobacter violaceus (strain ATCC 29082 / PCC 7421)) Explore Q7NMP6 Go to UniProtKB: Q7NMP6
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q7NMP6
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
FAD Query on FAD Download:Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain H [auth B] SDF format, chain K [auth C] SDF format, chain L [auth D] MOL2 format, chain E [auth A] MOL2 format, chain H [auth B] MOL2 format, chain K [auth C] MOL2 format, chain L [auth D] mmCIF format, chain E [auth A] mmCIF format, chain H [auth B] mmCIF format, chain K [auth C] mmCIF format, chain L [auth D]	E [auth A], H [auth B], K [auth C], L [auth D]	FLAVIN-ADENINE DINUCLEOTIDE C₂₇ H₃₃ N₉ O₁₅ P₂ VWWQXMAJTJZDQX-UYBVJOGSSA-N		Interactions Focus chain E [auth A] Focus chain H [auth B] Focus chain K [auth C] Focus chain L [auth D] Interactions & Density Focus chain E [auth A] Focus chain H [auth B] Focus chain K [auth C] Focus chain L [auth D]
PG4 Query on PG4 Download:Ideal Coordinates CCD File SDF format, chain G [auth A] SDF format, chain I [auth B] MOL2 format, chain G [auth A] MOL2 format, chain I [auth B] mmCIF format, chain G [auth A] mmCIF format, chain I [auth B]	G [auth A], I [auth B]	TETRAETHYLENE GLYCOL C₈ H₁₈ O₅ UWHCKJMYHZGTIT-UHFFFAOYSA-N		Interactions Focus chain G [auth A] Focus chain I [auth B] Interactions & Density Focus chain G [auth A] Focus chain I [auth B]
CA Query on CA Download:Ideal Coordinates CCD File SDF format, chain F [auth A] SDF format, chain J [auth B] MOL2 format, chain F [auth A] MOL2 format, chain J [auth B] mmCIF format, chain F [auth A] mmCIF format, chain J [auth B]	F [auth A], J [auth B]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N		Interactions Focus chain F [auth A] Focus chain J [auth B] Interactions & Density Focus chain F [auth A] Focus chain J [auth B]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.90 Å
R-Value Free: 0.202 (Depositor), 0.207 (DCC)
R-Value Work: 0.177 (Depositor), 0.183 (DCC)
R-Value Observed: 0.178 (Depositor)

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 83.278	α = 90
b = 122.042	β = 90
c = 139.153	γ = 90

Software Package:

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

Structure Validation

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Ligand Structure Quality Assessment

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Entry History

Deposition Data

Released Date: 2016-07-27

Deposition Author(s):

Buey, R.M.

de Pereda, J.M.

Balsera, M.

Revision History (Full details and data files)

Version 1.0: 2016-07-27
Type: Initial release
Version 1.1: 2017-01-18
Changes: Database references
Version 1.2: 2018-01-24
Changes: Source and taxonomy
Version 1.3: 2024-01-10
Changes: Data collection, Database references, Derived calculations, Refinement description