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

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), 0.191 (DCC)
R-Value Observed:
0.191 (Depositor)

Starting Model: experimental
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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.

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

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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
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	D3Q3R0
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
NAP Query on NAP Download:Ideal Coordinates CCD File SDF format, chain F [auth C] MOL2 format, chain F [auth C] mmCIF format, chain F [auth C]	F [auth C]	NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE C₂₁ H₂₈ N₇ O₁₇ P₃ XJLXINKUBYWONI-NNYOXOHSSA-N		Interactions Focus chain F [auth C] Interactions & Density Focus chain F [auth C]
LW7 Query on LW7 Download:Ideal Coordinates CCD File SDF format, chain E [auth B] MOL2 format, chain E [auth B] mmCIF format, chain E [auth B]	E [auth B]	1-(2-phenylethyl)-3,4-dihydroisoquinoline C₁₇ H₁₇ N GDEYQNLNJXESFX-UHFFFAOYSA-N		Interactions Focus chain E [auth B] Interactions & Density Focus chain E [auth B]
CL Query on CL Download:Ideal Coordinates CCD File SDF format, chain D [auth A] MOL2 format, chain D [auth A] mmCIF format, chain D [auth A]	D [auth A]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain D [auth A] Interactions & Density Focus chain D [auth A]

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), 0.191 (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

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Entry History

& Funding Information

Deposition Data

Released Date: 2020-02-26

Deposition Author(s):

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

Revision History (Full details and data files)

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

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