3DA5 | pdb_00003da5

Crystal Structure of Piwi/Argonaute/Zwille(PAZ) domain from Thermococcus thioreducens

PDB DOI: https://doi.org/10.2210/pdb3DA5/pdb

Classification: RNA BINDING PROTEIN
Organism(s): Thermococcus thioreducens
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2008-05-28 Released: 2008-07-29
Deposition Author(s): Hughes, R.C., Ng, J.D.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.94 Å
R-Value Free:
0.267 (Depositor), 0.260 (DCC)
R-Value Work:
0.216 (Depositor), 0.220 (DCC)
R-Value Observed:
0.218 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

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

Literature

Crystal Structure of Piwi/Argonaute/Zwille(PAZ) domain from Thermococcus thioreducens

Hughes, R.C., Ng, J.D.

To be published.

Macromolecule Content

Total Structure Weight: 30.87 kDa
Atom Count: 2,037
Modeled Residue Count: 242
Deposited Residue Count: 256
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Argonaute	A, B	128	Thermococcus thioreducens	Mutation(s): 0 Gene Names: Ago-PAZ
UniProt
Find proteins for D0VWU1 (Thermococcus thioreducens) Explore D0VWU1 Go to UniProtKB: D0VWU1
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	D0VWU1
Sequence Annotations Expand
Reference Sequence

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.94 Å
R-Value Free: 0.267 (Depositor), 0.260 (DCC)
R-Value Work: 0.216 (Depositor), 0.220 (DCC)
R-Value Observed: 0.218 (Depositor)

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 57.392	α = 90
b = 60.896	β = 90
c = 66.447	γ = 90

Software Package:

Software Name	Purpose
MOLREP	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction
HKL-2000	data collection
DENZO	data reduction
SCALEPACK	data scaling

Structure Validation

View Full Validation Report

Entry History

Deposition Data

Released Date: 2008-07-29

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2008-07-29
Type: Initial release
Version 1.1: 2011-07-13
Changes: Version format compliance
Version 1.2: 2017-10-25
Changes: Refinement description
Version 1.3: 2023-08-30
Changes: Data collection, Database references, Refinement description

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.