8WHG | pdb_00008whg

imine reductase mutant - M3

• PDB DOI: https://doi.org/10.2210/pdb8WHG/pdb

• Classification: OXIDOREDUCTASE
• Organism(s): Streptomyces viridochromogenes
• Expression System: Escherichia coli 'BL21-Gold(DE3)pLysS AG
• Mutation(s): Yes 


• Deposited: 2023-09-23 Released: 2024-09-25 
• Deposition Author(s): Zhu, X.X., Chen, X.R., Zheng, G.W.
• Funding Organization(s): National Natural Science Foundation of China (NSFC)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.71 Å
• R-Value Free: 
  0.271 (Depositor), 0.272 (DCC) 
• R-Value Work: 
  0.230 (Depositor), 0.232 (DCC) 
• R-Value Observed: 
  0.231 (Depositor) 

Starting Model: in silico

Literature

A structure of imine reductase mutant at 2.7 Angstroms resolution.

Zhu, X.X., Chen, X.R., Zheng, G.W.

To be published.

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly Evidence: gel filtration

Biological Assembly 2  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 2 assigned by authors and generated by PISA (software)

Biological Assembly 3  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 3 assigned by authors and generated by PISA (software)

Biological Assembly 4  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 Pseudo Symmetry: Cyclic - C2  (Explore in 3D)
Pseudo Stoichiometry: Homo 2-mer - A2 

Biological assembly 4 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 249.67 kDa 
• Atom Count: 16,316 
• Modeled Residue Count: 2,172 
• Deposited Residue Count: 2,376 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
6-phosphogluconate dehydrogenase NAD-binding protein	A, B, C, D, E, F, G, H	297	Streptomyces viridochromogenes	Mutation(s): 12  Gene Names: SSQG_04344
UniProt
Find proteins for D9X416 (Streptomyces viridochromogenes (strain DSM 40736 / JCM 4977 / BCRC 1201 / Tue 494)) Explore D9X416  Go to UniProtKB:  D9X416

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NAP (Subject of Investigation/LOI)	I [auth B], J [auth E]	NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE C21 H28 N7 O17 P3 XJLXINKUBYWONI-NNYOXOHSSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.71 Å
• R-Value Free:  0.271 (Depositor), 0.272 (DCC) 
• R-Value Work:  0.230 (Depositor), 0.232 (DCC) 
• R-Value Observed: 0.231 (Depositor) 

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 335.102	α = 90
b = 96.071	β = 100.48
c = 103.79	γ = 90

Software Package:

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

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2024-09-25 
Deposition Author(s): Zhu, X.X., Chen, X.R., Zheng, G.W.

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Funding Organization	Location	Grant Number
National Natural Science Foundation of China (NSFC)	China	--

Revision History  

• Version 1.0: 2024-09-25
  Type: Initial release