7T34 | pdb_00007t34

Crystal structure of AtDHDPR1 from Arabidopsis thaliana

PDB DOI: https://doi.org/10.2210/pdb7T34/pdb

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

Deposited: 2021-12-06 Released: 2022-12-14
Deposition Author(s): Mackie, E.R.R., Panjikar, S., Soares da Costa, T.P.
Funding Organization(s): Australian Research Council (ARC)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.89 Å
R-Value Free:
0.220 (Depositor), 0.213 (DCC)
R-Value Work:
0.188 (Depositor), 0.199 (DCC)
R-Value Observed:
0.191 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

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

Literature

From bacteria to plants: a repurposing strategy in the pursuit for novel herbicides

Mackie, E.R.R., Barrow, A.S., Giel, M.C., Hulett, M.D., Gendall, A.R., Panjikar, S., Soares da Costa, T.P.

To be published.

Macromolecule Content

Total Structure Weight: 32.27 kDa
Atom Count: 1,793
Modeled Residue Count: 235
Deposited Residue Count: 299
Unique protein chains: 1

Macromolecules

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Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
4-hydroxy-tetrahydrodipicolinate reductase 1, chloroplastic	A	299	Arabidopsis thaliana	Mutation(s): 0 Gene Names: DAPB1, At2g44040, F6E13.17 EC: 1.17.1.8
UniProt
Find proteins for O80574 (Arabidopsis thaliana) Explore O80574 Go to UniProtKB: O80574
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	O80574
Sequence Annotations Expand
Reference Sequence

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.89 Å
R-Value Free: 0.220 (Depositor), 0.213 (DCC)
R-Value Work: 0.188 (Depositor), 0.199 (DCC)
R-Value Observed: 0.191 (Depositor)

Space Group: I 4₁ 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 118.84	α = 90
b = 118.84	β = 90
c = 127.44	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
PHENIX	refinement
XDS	data reduction
Aimless	data scaling
Auto-Rickshaw	phasing

Structure Validation

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Entry History

& Funding Information

Deposition Data

Released Date: 2022-12-14

Deposition Author(s):

Soares da Costa, T.P.

Funding Organization	Location	Grant Number
Australian Research Council (ARC)	Australia	IH180100006

Revision History (Full details and data files)

Version 1.0: 2022-12-14
Type: Initial release
Version 1.1: 2023-10-25
Changes: Data collection, 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.