5DY3 | pdb_00005dy3

Crystal structure of Dbr2

PDB DOI: https://doi.org/10.2210/pdb5DY3/pdb

Classification: OXIDOREDUCTASE
Organism(s): Artemisia annua
Expression System: Escherichia coli
Mutation(s): Yes

Deposited: 2015-09-24 Released: 2016-10-05
Deposition Author(s): Li, L., Chen, T.T., Xu, Y.C.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.82 Å
R-Value Free:
0.189 (Depositor)
R-Value Work:
0.153 (Depositor), 0.157 (DCC)
R-Value Observed:
0.155 (Depositor)

wwPDB Validation 3D Report Full Report

Validation slider image for 5DY3

Ligand Structure Quality Assessment

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

Literature

The Crystal structure of Dbr2

Li, L.

To be published.

Macromolecule Content

Total Structure Weight: 43.16 kDa
Atom Count: 3,291
Modeled Residue Count: 374
Deposited Residue Count: 387
Unique protein chains: 1

Macromolecules

Find similar proteins by:

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Artemisinic aldehyde Delta(11(13)) reductase	A	387	Artemisia annua	Mutation(s): 1 Gene Names: DBR2 EC: 1.3.1.92
UniProt
Find proteins for C5H429 (Artemisia annua) Explore C5H429 Go to UniProtKB: C5H429
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	C5H429
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
FMN Query on FMN 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]	FLAVIN MONONUCLEOTIDE C₁₇ H₂₁ N₄ O₉ P FVTCRASFADXXNN-SCRDCRAPSA-N		Interactions Focus chain B [auth A] Interactions & Density Focus chain B [auth A]
HBA Query on HBA Download:Ideal Coordinates CCD File SDF format, chain C [auth A] MOL2 format, chain C [auth A] mmCIF format, chain C [auth A]	C [auth A]	P-HYDROXYBENZALDEHYDE C₇ H₆ O₂ RGHHSNMVTDWUBI-UHFFFAOYSA-N		Interactions Focus chain C [auth A] Interactions & Density Focus chain C [auth A]
PEG Query on PEG Download:Ideal Coordinates CCD File SDF format, chain D [auth A] MOL2 format, chain D [auth A] mmCIF format, chain D [auth A]	D [auth A]	DI(HYDROXYETHYL)ETHER C₄ H₁₀ O₃ MTHSVFCYNBDYFN-UHFFFAOYSA-N		Interactions Focus chain D [auth A] Interactions & Density Focus chain D [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.82 Å
R-Value Free: 0.189 (Depositor)
R-Value Work: 0.153 (Depositor), 0.157 (DCC)
R-Value Observed: 0.155 (Depositor)

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 51.893	α = 90
b = 80.797	β = 90
c = 84.303	γ = 90

Software Package:

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

Structure Validation

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Ligand Structure Quality Assessment

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Entry History

Deposition Data

Released Date: 2016-10-05

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2016-10-05
Type: Initial release
Version 1.1: 2024-03-20
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.