5Y09 | pdb_00005y09

Crystal structure of Deg9 at 295 K

PDB DOI: https://doi.org/10.2210/pdb5Y09/pdb

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

Deposited: 2017-07-15 Released: 2017-10-18
Deposition Author(s): Ouyang, M., Li, X.Y., Liu, L., Zhang, L.X.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.45 Å
R-Value Free:
0.253 (Depositor), 0.256 (DCC)
R-Value Work:
0.206 (Depositor), 0.209 (DCC)
R-Value Observed:
0.208 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Validation slider image for 5Y09

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

Literature

Crystal structure of Deg9 at 295 K

Ouyang, M., Li, X.Y., Zhao, S., Zhang, L.X.

To be published.

Macromolecule Content

Total Structure Weight: 124.76 kDa
Atom Count: 6,685
Modeled Residue Count: 834
Deposited Residue Count: 1,132
Unique protein chains: 1

Macromolecules

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Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Protease Do-like 9	A, B	566	Arabidopsis thaliana	Mutation(s): 0 Gene Names: Deg9, DEGP9, At5g40200, MSN9.10, MSN9.100 EC: 3.4.21
UniProt
Find proteins for Q9FL12 (Arabidopsis thaliana) Explore Q9FL12 Go to UniProtKB: Q9FL12
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q9FL12
Sequence Annotations Expand
Reference Sequence

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.45 Å
R-Value Free: 0.253 (Depositor), 0.256 (DCC)
R-Value Work: 0.206 (Depositor), 0.209 (DCC)
R-Value Observed: 0.208 (Depositor)

Space Group: I 4

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 132.372	α = 90
b = 132.372	β = 90
c = 154.73	γ = 90

Software Package:

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

Structure Validation

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Entry History

Deposition Data

Released Date: 2017-10-18

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2017-10-18
Type: Initial release
Version 1.1: 2023-11-22
Changes: Data collection, Database references, Refinement description

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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.