4LRT

Crystal and solution structures of the bifunctional enzyme (Aldolase/Aldehyde dehydrogenase) from Thermomonospora curvata, reveal a cofactor-binding domain motion during NAD+ and CoA accommodation whithin the shared cofactor-binding site

PDB DOI: https://doi.org/10.2210/pdb4LRT/pdb

Classification: Lyase/OXIDOREDUCTASE
Organism(s): Thermomonospora curvata DSM 43183
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2013-07-20 Released: 2013-09-04
Deposition Author(s): Fischer, B., Branlant, G., Talfournier, F., Gruez, A.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.50 Å
R-Value Free: 0.170
R-Value Work: 0.151
R-Value Observed: 0.152

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 2.1 of the entry. See complete history.

Literature

Crystal and solution structures of the bifunctional enzyme (Aldolase/Aldehyde dehydrogenase) from Thermomonospora curvata, reveal a cofactor-binding domain motion during NAD+ and CoA accommodation whithin the shared cofactor-binding site

Fischer, B., Branlant, G., Talfournier, F., Gruez, A.

To be published.

Macromolecule Content

Total Structure Weight: 145.23 kDa
Atom Count: 12,212
Modelled Residue Count: 1,257
Deposited Residue Count: 1,356
Unique protein chains: 2

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
4-hydroxy-2-oxovalerate aldolase	A, C	355	Thermomonospora curvata DSM 43183	Mutation(s): 0 Gene Names: Tcur_0536 EC: 4.1.3.39
UniProt
Find proteins for D1A3K8 (Thermomonospora curvata (strain ATCC 19995 / DSM 43183 / JCM 3096 / KCTC 9072 / NBRC 15933 / NCIMB 10081 / Henssen B9)) Explore D1A3K8 Go to UniProtKB: D1A3K8
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	D1A3K8
Sequence Annotations Expand
Reference Sequence

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(by identity cutoff) | 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Acetaldehyde dehydrogenase	B, D	323	Thermomonospora curvata DSM 43183	Mutation(s): 0 Gene Names: Tcur_0535 EC: 1.2.1.10
UniProt
Find proteins for D1A3K7 (Thermomonospora curvata (strain ATCC 19995 / DSM 43183 / JCM 3096 / KCTC 9072 / NBRC 15933 / NCIMB 10081 / Henssen B9)) Explore D1A3K7 Go to UniProtKB: D1A3K7
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	D1A3K7
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 6 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
COA Query on COA Download Ideal Coordinates CCD File SDF format, chain L [auth B] SDF format, chain S [auth D] MOL2 format, chain L [auth B] MOL2 format, chain S [auth D] mmCIF format, chain L [auth B] mmCIF format, chain S [auth D]	L [auth B], S [auth D]	COENZYME A C₂₁ H₃₆ N₇ O₁₆ P₃ S RGJOEKWQDUBAIZ-IBOSZNHHSA-N		Interactions Focus chain L [auth B] Focus chain S [auth D] Interactions & Density Focus chain L [auth B] Focus chain S [auth D]
SO4 Query on SO4 Download Ideal Coordinates CCD File SDF format, chain H [auth B] SDF format, chain Q [auth D] MOL2 format, chain H [auth B] MOL2 format, chain Q [auth D] mmCIF format, chain H [auth B] mmCIF format, chain Q [auth D]	H [auth B], Q [auth D]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain H [auth B] Focus chain Q [auth D] Interactions & Density Focus chain H [auth B] Focus chain Q [auth D]
GOL Query on GOL Download Ideal Coordinates CCD File SDF format, chain K [auth B] SDF format, chain N [auth C] SDF format, chain O [auth C] MOL2 format, chain K [auth B] MOL2 format, chain N [auth C] MOL2 format, chain O [auth C] mmCIF format, chain K [auth B] mmCIF format, chain N [auth C] mmCIF format, chain O [auth C]	K [auth B], N [auth C], O [auth C]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain K [auth B] Focus chain N [auth C] Focus chain O [auth C] Interactions & Density Focus chain K [auth B] Focus chain N [auth C] Focus chain O [auth C]
PYR Query on PYR Download Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain M [auth C] MOL2 format, chain E [auth A] MOL2 format, chain M [auth C] mmCIF format, chain E [auth A] mmCIF format, chain M [auth C]	E [auth A], M [auth C]	PYRUVIC ACID C₃ H₄ O₃ LCTONWCANYUPML-UHFFFAOYSA-N		Interactions Focus chain E [auth A] Focus chain M [auth C] Interactions & Density Focus chain E [auth A] Focus chain M [auth C]
MG Query on MG Download Ideal Coordinates CCD File SDF format, chain G [auth A] SDF format, chain P [auth C] MOL2 format, chain G [auth A] MOL2 format, chain P [auth C] mmCIF format, chain G [auth A] mmCIF format, chain P [auth C]	G [auth A], P [auth C]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain G [auth A] Focus chain P [auth C] Interactions & Density Focus chain G [auth A] Focus chain P [auth C]
NA Query on NA Download Ideal Coordinates CCD File SDF format, chain F [auth A] SDF format, chain I [auth B] SDF format, chain J [auth B] SDF format, chain R [auth D] MOL2 format, chain F [auth A] MOL2 format, chain I [auth B] MOL2 format, chain J [auth B] MOL2 format, chain R [auth D] mmCIF format, chain F [auth A] mmCIF format, chain I [auth B] mmCIF format, chain J [auth B] mmCIF format, chain R [auth D]	F [auth A], I [auth B], J [auth B], R [auth D]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N		Interactions Focus chain F [auth A] Focus chain I [auth B] Focus chain J [auth B] Focus chain R [auth D] Interactions & Density Focus chain F [auth A] Focus chain I [auth B] Focus chain J [auth B] Focus chain R [auth D]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.50 Å
R-Value Free: 0.170
R-Value Work: 0.151
R-Value Observed: 0.152
Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 94.5	α = 90
b = 116.7	β = 90
c = 131.5	γ = 90

Software Package:

Software Name	Purpose
XDS	data scaling
MOLREP	phasing
REFMAC	refinement
XDS	data reduction
XSCALE	data scaling

Structure Validation

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Entry History

Deposition Data

Released Date: 2013-09-04

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2013-09-04
Type: Initial release
Version 1.1: 2023-09-20
Changes: Data collection, Database references, Derived calculations, Refinement description
Version 2.0: 2023-11-15
Changes: Atomic model, Data collection, Derived calculations
Version 2.1: 2024-11-06
Changes: Structure summary

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4LRT

Crystal and solution structures of the bifunctional enzyme (Aldolase/Aldehyde dehydrogenase) from Thermomonospora curvata, reveal a cofactor-binding domain motion during NAD+ and CoA accommodation whithin the shared cofactor-binding site

Crystal and solution structures of the bifunctional enzyme (Aldolase/Aldehyde dehydrogenase) from Thermomonospora curvata, reveal a cofactor-binding domain motion during NAD+ and CoA accommodation whithin the shared cofactor-binding site

Entity ID: 1

UniProt

Entity Groups

Sequence Annotations

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Entity ID: 2

UniProt

Entity Groups

Sequence Annotations

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Experimental Data

Structure Validation

Ligand Structure Quality Assessment

Deposition Data

Revision History (Full details and data files)