3HA9 | pdb_00003ha9

The 1.7A Crystal Structure of a Thioredoxin-like Protein from Aeropyrum pernix

PDB DOI: https://doi.org/10.2210/pdb3HA9/pdb

Classification: structural genomics, unknown function
Organism(s): Aeropyrum pernix
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2009-05-01 Released: 2009-05-19
Deposition Author(s): Stein, A.J., Cuff, M.E., Sather, A., Hendricks, R., Freeman, L., Joachimiak, A., Midwest Center for Structural Genomics (MCSG)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.70 Å
R-Value Free:
0.232 (Depositor), 0.250 (DCC)
R-Value Work:
0.194 (Depositor), 0.220 (DCC)
R-Value Observed:
0.196 (Depositor)

wwPDB Validation 3D Report Full Report

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

Literature

The 1.7A Crystal Structure of a Thioredoxin-like Protein from Aeropyrum pernix

Stein, A.J., Cuff, M.E., Sather, A., Hendricks, R., Freeman, L., Joachimiak, A.

To be published.

Macromolecule Content

Total Structure Weight: 18.17 kDa
Atom Count: 1,385
Modeled Residue Count: 161
Deposited Residue Count: 165
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
uncharacterized Thioredoxin-like protein	A	165	Aeropyrum pernix	Mutation(s): 0 Gene Names: APE2568, APE_2568.1
UniProt
Find proteins for Q9Y8R5 (Aeropyrum pernix (strain ATCC 700893 / DSM 11879 / JCM 9820 / NBRC 100138 / K1)) Explore Q9Y8R5 Go to UniProtKB: Q9Y8R5
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q9Y8R5
Sequence Annotations Expand
Reference Sequence

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.70 Å
R-Value Free: 0.232 (Depositor), 0.250 (DCC)
R-Value Work: 0.194 (Depositor), 0.220 (DCC)
R-Value Observed: 0.196 (Depositor)

Space Group: P 4₃ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 74.742	α = 90
b = 74.742	β = 90
c = 59.451	γ = 90

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction
SBC-Collect	data collection
HKL-3000	data reduction
HKL-3000	data scaling
HKL-3000	phasing
SHELX	phasing
MLPHARE	phasing
DM	phasing
ARP/wARP	model building
Coot	model building

Structure Validation

View Full Validation Report

Entry History

Deposition Data

Released Date: 2009-05-19

Deposition Author(s):

Midwest Center for Structural Genomics (MCSG)

Revision History (Full details and data files)

Version 1.0: 2009-05-19
Type: Initial release
Version 1.1: 2011-07-13
Changes: Advisory, Version format compliance
Version 1.2: 2017-11-01
Changes: Refinement description
Version 1.3: 2024-10-09
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.