6NUP | pdb_00006nup

Structure of thioredoxin (trxA) from Rickettsia prowazekii str. Madrid E.

PDB DOI: https://doi.org/10.2210/pdb6NUP/pdb

Classification: OXIDOREDUCTASE
Organism(s): Rickettsia prowazekii str. Madrid E
Expression System: Escherichia coli 'BL21-Gold(DE3)pLysS AG
Mutation(s): No

Deposited: 2019-02-01 Released: 2019-02-20
Deposition Author(s): Seattle Structural Genomics Center for Infectious Disease (SSGCID)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.60 Å
R-Value Free:
0.206 (Depositor), 0.207 (DCC)
R-Value Work:
0.163 (Depositor), 0.164 (DCC)
R-Value Observed:
0.167 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

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This is version 1.2 of the entry. See complete history.

Literature

Structure of thioredoxin (trxA) from Rickettsia prowazekii str. Madrid E.

Abendroth, J., Buchko, G.W., Davies, D.R., Lorimer, D.D., Horanyi, P.S., Edwards, T.E.

To be published.

Macromolecule Content

Total Structure Weight: 15.67 kDa
Atom Count: 1,047
Modeled Residue Count: 113
Deposited Residue Count: 134
Unique protein chains: 1

Macromolecules

Find similar proteins by:

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Thioredoxin	A	134	Rickettsia prowazekii str. Madrid E	Mutation(s): 0 Gene Names: trxA, RP002
UniProt
Find proteins for Q9ZEE0 (Rickettsia prowazekii (strain Madrid E)) Explore Q9ZEE0 Go to UniProtKB: Q9ZEE0
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q9ZEE0
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
CIT Query on CIT Download:Ideal Coordinates CCD File SDF format, chain B [auth A] SDF format, chain C [auth A] MOL2 format, chain B [auth A] MOL2 format, chain C [auth A] mmCIF format, chain B [auth A] mmCIF format, chain C [auth A]	B [auth A], C [auth A]	CITRIC ACID C₆ H₈ O₇ KRKNYBCHXYNGOX-UHFFFAOYSA-N		Interactions Focus chain B [auth A] Focus chain C [auth A] Interactions & Density Focus chain B [auth A] Focus chain C [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.60 Å
R-Value Free: 0.206 (Depositor), 0.207 (DCC)
R-Value Work: 0.163 (Depositor), 0.164 (DCC)
R-Value Observed: 0.167 (Depositor)

Diffraction Data:

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 32.74	α = 90
b = 45.16	β = 90
c = 60.93	γ = 90

Software Package:

Software Name	Purpose
XDS	data reduction
XSCALE	data scaling
PHENIX	refinement
PDB_EXTRACT	data extraction
MoRDa	phasing
Coot	model building

Structure Validation

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Entry History

Deposition Data

Released Date: 2019-02-20

Deposition Author(s):

Seattle Structural Genomics Center for Infectious Disease (SSGCID)

Revision History (Full details and data files)

Version 1.0: 2019-02-20
Type: Initial release
Version 1.1: 2024-04-03
Changes: Data collection, Database references, Refinement description
Version 1.2: 2024-10-16
Changes: Structure summary

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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. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.