3VFI | pdb_00003vfi

Crystal Structure of a Metagenomic Thioredoxin

PDB DOI: https://doi.org/10.2210/pdb3VFI/pdb

Classification: ELECTRON TRANSPORT
Organism(s): Silicibacter phage DSS3phi2
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2012-01-09 Released: 2013-01-23
Deposition Author(s): Craig, T.K., Gardberg, A., Lorimer, D.D., Burgin Jr., A.B., Segall, A., Rohwer, F.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.75 Å
R-Value Free:
0.233 (Depositor), 0.240 (DCC)
R-Value Work:
0.201 (Depositor), 0.210 (DCC)

wwPDB Validation 3D Report Full Report

This is version 1.1 of the entry. See complete history.

Literature

Structure of a Metagenomic Thioredoxin

Craig, T.K., Gardberg, A., Lorimer, D.D., Burgin Jr., A.B., Segall, A., Rohwer, F.

To be published.

Macromolecule Content

Total Structure Weight: 12.07 kDa
Atom Count: 889
Modeled Residue Count: 104
Deposited Residue Count: 104
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	104	Silicibacter phage DSS3phi2	Mutation(s): 0
UniProt
Find proteins for C4NT42 (Silicibacter phage DSS3phi2) Explore C4NT42 Go to UniProtKB: C4NT42
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	C4NT42
Sequence Annotations Expand
Reference Sequence

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.75 Å
R-Value Free: 0.233 (Depositor), 0.240 (DCC)
R-Value Work: 0.201 (Depositor), 0.210 (DCC)

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 30.219	α = 90
b = 55.364	β = 90
c = 54.435	γ = 90

Software Package:

Software Name	Purpose
SCALEPACK	data scaling
PHASER	phasing
PHENIX	refinement
PDB_EXTRACT	data extraction
HKL-2000	data reduction
HKL-2000	data scaling

Structure Validation

View Full Validation Report

Entry History

Deposition Data

Released Date: 2013-01-23

Deposition Author(s):

Burgin Jr., A.B.

Revision History (Full details and data files)

Version 1.0: 2013-01-23
Type: Initial release
Version 1.1: 2024-11-06
Changes: Data collection, Database references, Structure summary

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.