4V37 | pdb_00004v37

Crystal structure of betaine aldehyde dehydrogenase from spinach showing a thiohemiacetal with 3-aminopropionaldehyde

PDB DOI: https://doi.org/10.2210/pdb4V37/pdb

Classification: OXIDOREDUCTASE
Organism(s): Spinacia oleracea
Expression System: Escherichia coli BL21
Mutation(s): Yes

Deposited: 2014-10-16 Released: 2016-01-20
Deposition Author(s): Zarate-Romero, A., Munoz-Clares, R.A.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.10 Å
R-Value Free:
0.209 (Depositor), 0.210 (DCC)
R-Value Work:
0.167 (Depositor), 0.170 (DCC)
R-Value Observed:
0.169 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.2 of the entry. See complete history.

Literature

Identification of a Stable Thiohemiacetal Involving a Conserved Cysteine in the Substrate Inactivation of S. Oleracea Betaine Aldehyde Dehydrogenase

Zarate-Romero, A., Mujica-Jimenez, C., Murillo-Melo, D.S., Montiel, C., Munoz-Clares, R.A.

To be published.

Macromolecule Content

Total Structure Weight: 221.07 kDa
Atom Count: 16,821
Modeled Residue Count: 1,977
Deposited Residue Count: 1,988
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
BETAINE ALDEHYDE DEHYDROGENASE, CHLOROPLASTIC	A, B, C, D	497	Spinacia oleracea	Mutation(s): 1 EC: 1.2.1.8 (PDB Primary Data), 1.2.1 (UniProt), 1.2.1.19 (UniProt), 1.2.1.47 (UniProt)
UniProt
Find proteins for P17202 (Spinacia oleracea) Explore P17202 Go to UniProtKB: P17202
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P17202
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 6 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
NAD Query on NAD Download:Ideal Coordinates CCD File SDF format, chain U [auth D] SDF format, chain O [auth C] SDF format, chain J [auth B] SDF format, chain E [auth A] MOL2 format, chain U [auth D] MOL2 format, chain O [auth C] MOL2 format, chain J [auth B] MOL2 format, chain E [auth A] mmCIF format, chain U [auth D] mmCIF format, chain O [auth C] mmCIF format, chain J [auth B] mmCIF format, chain E [auth A]	E [auth A], J [auth B], O [auth C], U [auth D]	NICOTINAMIDE-ADENINE-DINUCLEOTIDE C₂₁ H₂₇ N₇ O₁₄ P₂ BAWFJGJZGIEFAR-NNYOXOHSSA-N		Interactions Focus chain E [auth A] Focus chain J [auth B] Focus chain O [auth C] Focus chain U [auth D] Interactions & Density Focus chain E [auth A] Focus chain J [auth B] Focus chain O [auth C] Focus chain U [auth D]
PG4 Query on PG4 Download:Ideal Coordinates CCD File SDF format, chain S [auth C] SDF format, chain H [auth A] MOL2 format, chain S [auth C] MOL2 format, chain H [auth A] mmCIF format, chain S [auth C] mmCIF format, chain H [auth A]	H [auth A], S [auth C]	TETRAETHYLENE GLYCOL C₈ H₁₈ O₅ UWHCKJMYHZGTIT-UHFFFAOYSA-N		Interactions Focus chain H [auth A] Focus chain S [auth C] Interactions & Density Focus chain H [auth A] Focus chain S [auth C]
AE3 Query on AE3 Download:Ideal Coordinates CCD File SDF format, chain M [auth B] MOL2 format, chain M [auth B] mmCIF format, chain M [auth B]	M [auth B]	2-(2-ETHOXYETHOXY)ETHANOL C₆ H₁₄ O₃ XXJWXESWEXIICW-UHFFFAOYSA-N		Interactions Focus chain M [auth B] Interactions & Density Focus chain M [auth B]
0D8 Query on 0D8 Download:Ideal Coordinates CCD File SDF format, chain V [auth D] SDF format, chain Q [auth C] SDF format, chain P [auth C] SDF format, chain K [auth B] SDF format, chain F [auth A] MOL2 format, chain V [auth D] MOL2 format, chain Q [auth C] MOL2 format, chain P [auth C] MOL2 format, chain K [auth B] MOL2 format, chain F [auth A] mmCIF format, chain V [auth D] mmCIF format, chain Q [auth C] mmCIF format, chain P [auth C] mmCIF format, chain K [auth B] mmCIF format, chain F [auth A]	F [auth A], K [auth B], P [auth C], Q [auth C], V [auth D]	3-aminopropan-1-ol C₃ H₉ N O WUGQZFFCHPXWKQ-UHFFFAOYSA-N		Interactions Focus chain F [auth A] Focus chain K [auth B] Focus chain P [auth C] Focus chain Q [auth C] Focus chain V [auth D] Interactions & Density Focus chain F [auth A] Focus chain K [auth B] Focus chain P [auth C] Focus chain Q [auth C] Focus chain V [auth D]
FMT Query on FMT Download:Ideal Coordinates CCD File SDF format, chain W [auth D] SDF format, chain R [auth C] SDF format, chain L [auth B] SDF format, chain G [auth A] MOL2 format, chain W [auth D] MOL2 format, chain R [auth C] MOL2 format, chain L [auth B] MOL2 format, chain G [auth A] mmCIF format, chain W [auth D] mmCIF format, chain R [auth C] mmCIF format, chain L [auth B] mmCIF format, chain G [auth A]	G [auth A], L [auth B], R [auth C], W [auth D]	FORMIC ACID C H₂ O₂ BDAGIHXWWSANSR-UHFFFAOYSA-N		Interactions Focus chain G [auth A] Focus chain L [auth B] Focus chain R [auth C] Focus chain W [auth D] Interactions & Density Focus chain G [auth A] Focus chain L [auth B] Focus chain R [auth C] Focus chain W [auth D]
K Query on K Download:Ideal Coordinates CCD File SDF format, chain X [auth D] SDF format, chain T [auth C] SDF format, chain N [auth B] SDF format, chain I [auth A] MOL2 format, chain X [auth D] MOL2 format, chain T [auth C] MOL2 format, chain N [auth B] MOL2 format, chain I [auth A] mmCIF format, chain X [auth D] mmCIF format, chain T [auth C] mmCIF format, chain N [auth B] mmCIF format, chain I [auth A]	I [auth A], N [auth B], T [auth C], X [auth D]	POTASSIUM ION K NPYPAHLBTDXSSS-UHFFFAOYSA-N		Interactions Focus chain I [auth A] Focus chain N [auth B] Focus chain T [auth C] Focus chain X [auth D] Interactions & Density Focus chain I [auth A] Focus chain N [auth B] Focus chain T [auth C] Focus chain X [auth D]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.10 Å
R-Value Free: 0.209 (Depositor), 0.210 (DCC)
R-Value Work: 0.167 (Depositor), 0.170 (DCC)
R-Value Observed: 0.169 (Depositor)

Space Group: P 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 68.296	α = 82.07
b = 80.372	β = 86.4
c = 85.833	γ = 79.06

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data reduction
SCALA	data scaling
PHASER	phasing

Structure Validation

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Ligand Structure Quality Assessment

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Entry History

Deposition Data

Released Date: 2016-01-20

Deposition Author(s):

Zarate-Romero, A.

Munoz-Clares, R.A.

Revision History (Full details and data files)

Version 1.0: 2016-01-20
Type: Initial release
Version 1.1: 2024-01-10
Changes: Data collection, Database references, Derived calculations, Other, Refinement description
Version 1.2: 2024-11-20
Changes: Structure summary