5YM0 | pdb_00005ym0

The crystal structure of DHAD

PDB DOI: https://doi.org/10.2210/pdb5YM0/pdb

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

Deposited: 2017-10-20 Released: 2018-10-24
Deposition Author(s): Zang, X., Huang, W.X., Cheng, R., Wu, L., Zhou, J.H., Tang, Y., Yan, Y.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.84 Å
R-Value Free:
0.197 (Depositor), 0.174 (DCC)
R-Value Work:
0.170 (Depositor), 0.171 (DCC)
R-Value Observed:
0.171 (Depositor)

wwPDB Validation 3D Report Full Report

Validation slider image for 5YM0

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

Literature

The crystal structure of DHAD

Zang, X., Huang, W.X., Cheng, R., Wu, L., Zhou, J.H.

To be published.

Macromolecule Content

Total Structure Weight: 68.26 kDa
Atom Count: 4,285
Modeled Residue Count: 520
Deposited Residue Count: 633
Unique protein chains: 1

Macromolecules

Find similar proteins by:

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Dihydroxy-acid dehydratase, chloroplastic	A	633	Arabidopsis thaliana	Mutation(s): 0 Gene Names: DHAD, ILVD, At3g23940, F14O13.13 EC: 4.2.1.9
UniProt
Find proteins for Q9LIR4 (Arabidopsis thaliana) Explore Q9LIR4 Go to UniProtKB: Q9LIR4
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q9LIR4
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
SO4 Query on SO4 Download:Ideal Coordinates CCD File SDF format, chain B [auth A] SDF format, chain C [auth A] SDF format, chain D [auth A] MOL2 format, chain B [auth A] MOL2 format, chain C [auth A] MOL2 format, chain D [auth A] mmCIF format, chain B [auth A] mmCIF format, chain C [auth A] mmCIF format, chain D [auth A]	B [auth A], C [auth A], D [auth A]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain B [auth A] Focus chain C [auth A] Focus chain D [auth A] Interactions & Density Focus chain B [auth A] Focus chain C [auth A] Focus chain D [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.84 Å
R-Value Free: 0.197 (Depositor), 0.174 (DCC)
R-Value Work: 0.170 (Depositor), 0.171 (DCC)
R-Value Observed: 0.171 (Depositor)

Space Group: P 4₂ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 135.472	α = 90
b = 135.472	β = 90
c = 67.963	γ = 90

Software Package:

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

Structure Validation

View Full Validation Report

View more in-depth experimental data

Entry History

Deposition Data

Released Date: 2018-10-24

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2018-10-24
Type: Initial release
Version 1.1: 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.