8QMS

Succinic semialdehyde dehydrogenase from E. coli with Q262R substitution and bound NAD+

PDB DOI: https://doi.org/10.2210/pdb8QMS/pdb

Classification: OXIDOREDUCTASE
Organism(s): Escherichia coli K-12
Expression System: Escherichia coli BL21(DE3)
Mutation(s): Yes

Deposited: 2023-09-25 Released: 2024-10-02
Deposition Author(s): He, H., Zarzycki, J., Erb, T.J.
Funding Organization(s): Max Planck Society

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.90 Å
R-Value Free: 0.213
R-Value Work: 0.181
R-Value Observed: 0.182

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.0 of the entry. See complete history.

Literature

Adaptive laboratory evolution recruits the promiscuity of succinate semialdehyde dehydrogenase to repair different metabolic deficiencies

He, H., Gomez-Coronado, P.A., Zarzycki, J., Barthel, S., Kahnt, J., Claus, P., Klein, M., Klose, M., de Crecy-Lagard, V., Schindler, D., Paczia, N., Glatter, T., Erb, T.J.

(2024) Nat Commun

Macromolecule Content

Total Structure Weight: 201.85 kDa
Atom Count: 15,217
Modelled Residue Count: 1,840
Deposited Residue Count: 1,848
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Succinate semialdehyde dehydrogenase [NAD(P)+] Sad	A, B, C, D	462	Escherichia coli K-12	Mutation(s): 1 Gene Names: sad, yneI, b1525, JW5247 EC: 1.2.1.16
UniProt
Find proteins for P76149 (Escherichia coli (strain K12)) Explore P76149 Go to UniProtKB: P76149
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P76149
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
NAD (Subject of Investigation/LOI) Query on NAD Download Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain F [auth B] SDF format, chain G [auth C] SDF format, chain H [auth D] MOL2 format, chain E [auth A] MOL2 format, chain F [auth B] MOL2 format, chain G [auth C] MOL2 format, chain H [auth D]	E [auth A], F [auth B], G [auth C], H [auth D]	NICOTINAMIDE-ADENINE-DINUCLEOTIDE C₂₁ H₂₇ N₇ O₁₄ P₂ BAWFJGJZGIEFAR-NNYOXOHSSA-N		Interactions Focus chain E [auth A] Focus chain F [auth B] Focus chain G [auth C] Focus chain H [auth D]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.90 Å
R-Value Free: 0.213
R-Value Work: 0.181
R-Value Observed: 0.182
Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 91.3	α = 90
b = 115.69	β = 90
c = 179.61	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
XSCALE	data scaling
XDS	data reduction
PHENIX	phasing

Structure Validation

View Full Validation Report

Ligand Structure Quality Assessment

Entry History & Funding Information

Deposition Data

Released Date: 2024-10-02

Deposition Author(s):

Funding Organization	Location	Grant Number
Max Planck Society	Germany	--

Revision History (Full details and data files)

Version 1.0: 2024-10-02
Type: Initial release

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.