3V85 | pdb_00003v85

1.9 Angstrom resolution crystal structure of the protein Q9SIY3 from Arabidopsis thaliana

PDB DOI: https://doi.org/10.2210/pdb3V85/pdb

Classification: HYDROLASE
Organism(s): Arabidopsis thaliana
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2011-12-22 Released: 2012-11-07
Deposition Author(s): Garcia, C., Fucile, G., Petit, P., Christendat, D.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.90 Å
R-Value Free:
0.230 (Depositor), 0.231 (DCC)
R-Value Work:
0.172 (Depositor)
R-Value Observed:
0.175 (Depositor)

wwPDB Validation 3D Report Full Report

Validation slider image for 3V85

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

Literature

A yeast-like mRNA triphosphatase from Arabidopsis thaliana

Garcia, C., Fucile, G., Moeder, W., Christendat, D., Yoshioka, K.

To be published.

Macromolecule Content

Total Structure Weight: 24.39 kDa
Atom Count: 1,811
Modeled Residue Count: 204
Deposited Residue Count: 210
Unique protein chains: 1

Macromolecules

Find similar proteins by:

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
CYTH-like phosphatase	A	210	Arabidopsis thaliana	Mutation(s): 0 Gene Names: At2g11890 EC: 3.6.1 (UniProt), 3.6.1.25 (UniProt)
UniProt
Find proteins for Q9SIY3 (Arabidopsis thaliana) Explore Q9SIY3 Go to UniProtKB: Q9SIY3
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q9SIY3
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] MOL2 format, chain B [auth A] mmCIF format, chain B [auth A]	B [auth A]	CITRIC ACID C₆ H₈ O₇ KRKNYBCHXYNGOX-UHFFFAOYSA-N		Interactions Focus chain B [auth A] Interactions & Density Focus chain B [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.90 Å
R-Value Free: 0.230 (Depositor), 0.231 (DCC)
R-Value Work: 0.172 (Depositor)
R-Value Observed: 0.175 (Depositor)

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 44.776	α = 90
b = 33.952	β = 95.23
c = 71.596	γ = 90

Software Package:

Software Name	Purpose
ADSC	data collection
SOLVE	phasing
PHENIX	refinement
XDS	data reduction
SCALA	data scaling

Structure Validation

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Entry History

Deposition Data

Released Date: 2012-11-07

Deposition Author(s):

Christendat, D.

Revision History (Full details and data files)

Version 1.0: 2012-11-07
Type: Initial release
Version 1.1: 2024-02-28
Changes: Data collection, Database references, Derived calculations

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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.