6JIZ | pdb_00006jiz

Apo structure of an imine reductase at 1.76 Angstrom resolution

PDB DOI: https://doi.org/10.2210/pdb6JIZ/pdb

Classification: OXIDOREDUCTASE
Organism(s): Stackebrandtia nassauensis DSM 44728
Expression System: Escherichia coli K-12
Mutation(s): No

Deposited: 2019-02-24 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: 1.76 Å
R-Value Free:
0.192 (Depositor), 0.195 (DCC)
R-Value Work:
0.164 (Depositor), 0.167 (DCC)
R-Value Observed:
0.165 (Depositor)

wwPDB Validation 3D Report Full Report

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Ligand Structure Quality Assessment

This is version 1.1 of the entry. See complete history.

Literature

Apo structure of an imine reductase at 1.76 Angstrom resolution

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

To be published.

Macromolecule Content

Total Structure Weight: 95.07 kDa
Atom Count: 7,657
Modeled Residue Count: 881
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): 0 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 7 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
NAP Query on NAP Download:Ideal Coordinates CCD File SDF format, chain Q [auth C] MOL2 format, chain Q [auth C] mmCIF format, chain Q [auth C]	Q [auth C]	NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE C₂₁ H₂₈ N₇ O₁₇ P₃ XJLXINKUBYWONI-NNYOXOHSSA-N		Interactions Focus chain Q [auth C] Interactions & Density Focus chain Q [auth C]
LW9 Query on LW9 Download:Ideal Coordinates CCD File SDF format, chain O [auth B] MOL2 format, chain O [auth B] mmCIF format, chain O [auth B]	O [auth B]	3-ethylheptane C₉ H₂₀ PSVQKOKKLWHNRP-UHFFFAOYSA-N		Interactions Focus chain O [auth B] Interactions & Density Focus chain O [auth B]
EDO Query on EDO Download:Ideal Coordinates CCD File SDF format, chain V [auth C] SDF format, chain U [auth C] MOL2 format, chain V [auth C] MOL2 format, chain U [auth C] mmCIF format, chain V [auth C] mmCIF format, chain U [auth C]	U [auth C], V [auth C]	1,2-ETHANEDIOL C₂ H₆ O₂ LYCAIKOWRPUZTN-UHFFFAOYSA-N		Interactions Focus chain U [auth C] Focus chain V [auth C] Interactions & Density Focus chain U [auth C] Focus chain V [auth C]
ACT Query on ACT Download:Ideal Coordinates CCD File SDF format, chain R [auth C] SDF format, chain L [auth B] SDF format, chain K [auth B] SDF format, chain J [auth B] SDF format, chain F [auth A] SDF format, chain E [auth A] SDF format, chain D [auth A] MOL2 format, chain R [auth C] MOL2 format, chain L [auth B] MOL2 format, chain K [auth B] MOL2 format, chain J [auth B] MOL2 format, chain F [auth A] MOL2 format, chain E [auth A] MOL2 format, chain D [auth A] mmCIF format, chain R [auth C] mmCIF format, chain L [auth B] mmCIF format, chain K [auth B] mmCIF format, chain J [auth B] mmCIF format, chain F [auth A] mmCIF format, chain E [auth A] mmCIF format, chain D [auth A]	D [auth A] E [auth A] F [auth A] J [auth B] K [auth B] D [auth A], E [auth A], F [auth A], J [auth B], K [auth B], L [auth B], R [auth C]	ACETATE ION C₂ H₃ O₂ QTBSBXVTEAMEQO-UHFFFAOYSA-M		Interactions Focus chain D [auth A] Focus chain E [auth A] Focus chain F [auth A] Focus chain J [auth B] Focus chain K [auth B] Focus chain L [auth B] Focus chain R [auth C] Interactions & Density Focus chain D [auth A] Focus chain E [auth A] Focus chain F [auth A] Focus chain J [auth B] Focus chain K [auth B] Focus chain L [auth B] Focus chain R [auth C]
CL Query on CL Download:Ideal Coordinates CCD File SDF format, chain T [auth C] SDF format, chain S [auth C] SDF format, chain N [auth B] SDF format, chain M [auth B] SDF format, chain G [auth A] MOL2 format, chain T [auth C] MOL2 format, chain S [auth C] MOL2 format, chain N [auth B] MOL2 format, chain M [auth B] MOL2 format, chain G [auth A] mmCIF format, chain T [auth C] mmCIF format, chain S [auth C] mmCIF format, chain N [auth B] mmCIF format, chain M [auth B] mmCIF format, chain G [auth A]	G [auth A], M [auth B], N [auth B], S [auth C], T [auth C]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain G [auth A] Focus chain M [auth B] Focus chain N [auth B] Focus chain S [auth C] Focus chain T [auth C] Interactions & Density Focus chain G [auth A] Focus chain M [auth B] Focus chain N [auth B] Focus chain S [auth C] Focus chain T [auth C]
NA Query on NA Download:Ideal Coordinates CCD File SDF format, chain P [auth C] SDF format, chain I [auth A] MOL2 format, chain P [auth C] MOL2 format, chain I [auth A] mmCIF format, chain P [auth C] mmCIF format, chain I [auth A]	I [auth A], P [auth C]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N		Interactions Focus chain I [auth A] Focus chain P [auth C] Interactions & Density Focus chain I [auth A] Focus chain P [auth C]
NH4 Query on NH4 Download:Ideal Coordinates CCD File SDF format, chain H [auth A] MOL2 format, chain H [auth A] mmCIF format, chain H [auth A]	H [auth A]	AMMONIUM ION H₄ N QGZKDVFQNNGYKY-UHFFFAOYSA-O		Interactions Focus chain H [auth A] Interactions & Density Focus chain H [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.76 Å
R-Value Free: 0.192 (Depositor), 0.195 (DCC)
R-Value Work: 0.164 (Depositor), 0.167 (DCC)
R-Value Observed: 0.165 (Depositor)

Space Group: P 3₁ 1 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 106.659	α = 90
b = 106.659	β = 90
c = 168.557	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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Ligand Structure Quality Assessment

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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: 2024-03-27
Changes: Data collection, Database references, Derived calculations

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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. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.