6JIT | pdb_00006jit

Complex structure of an imine reductase at 2.05 Angstrom resolution

• PDB DOI: https://doi.org/10.2210/pdb6JIT/pdb

• Classification: OXIDOREDUCTASE
• Organism(s): Stackebrandtia nassauensis DSM 44728
• Expression System: Escherichia coli K-12
• Mutation(s): Yes 


• Deposited: 2019-02-23 Released: 2020-02-26 
• Deposition Author(s): Li, H., Wu, L., Zheng, G.W., Zhou, J.H.
• Funding Organization(s): National Natural Science Foundation of China

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.05 Å
• R-Value Free: 
  0.219 (Depositor), 0.220 (DCC) 
• R-Value Work: 
  0.190 (Depositor), 0.190 (DCC) 
• R-Value Observed: 
  0.191 (Depositor) 

Starting Model: experimental

Literature

Complex structure of an imine reductase at 2.05 Angstrom resolution

Li, H., Wu, L., Zheng, G.W., Zhou, J.H.

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)

Macromolecule Content 

• Total Structure Weight: 94.41 kDa 
• Atom Count: 7,060 
• Modeled Residue Count: 863 
• Deposited Residue Count: 897 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
6-phosphogluconate dehydrogenase NAD-binding protein	A, B, C	299	Stackebrandtia nassauensis DSM 44728	Mutation(s): 3  Gene Names: Snas_4330
UniProt
Find proteins for D3Q3R0 (Stackebrandtia nassauensis (strain DSM 44728 / CIP 108903 / NRRL B-16338 / NBRC 102104 / LLR-40K-21)) Explore D3Q3R0  Go to UniProtKB:  D3Q3R0

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NAP	F [auth C]	NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE C21 H28 N7 O17 P3 XJLXINKUBYWONI-NNYOXOHSSA-N
LW7	E [auth B]	1-(2-phenylethyl)-3,4-dihydroisoquinoline C17 H17 N GDEYQNLNJXESFX-UHFFFAOYSA-N
CL	D [auth A]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.05 Å
• R-Value Free:  0.219 (Depositor), 0.220 (DCC) 
• R-Value Work:  0.190 (Depositor), 0.190 (DCC) 
• R-Value Observed: 0.191 (Depositor) 

Space Group: P 3₁ 1 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 106.598	α = 90
b = 106.598	β = 90
c = 168.343	γ = 120

Software Package:

Software Name	Purpose
PHENIX	refinement
HKL-3000	data reduction
HKL-3000	data scaling
PHENIX	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2020-02-26 
Deposition Author(s): Li, H., Wu, L., Zheng, G.W., Zhou, J.H.

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Funding Organization	Location	Grant Number
National Natural Science Foundation of China	China	21878085
National Natural Science Foundation of China	China	21536004

Revision History  

• Version 1.0: 2020-02-26
  Type: Initial release
  
• Version 1.1: 2023-11-22
  Changes: Data collection, Database references, Refinement description