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), 0.289 (DCC)
R-Value Work:
0.194 (Depositor)
R-Value Observed:
0.196 (Depositor)

wwPDB Validation 3D Report Full Report

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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

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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% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% 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), 0.289 (DCC)
R-Value Work: 0.194 (Depositor)
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

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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

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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.