6TOE | pdb_00006toe

Imine Reductase from Myxococcus stipitatus V8 variant in complex with NAD+

PDB DOI: https://doi.org/10.2210/pdb6TOE/pdb

Classification: OXIDOREDUCTASE
Organism(s): Myxococcus stipitatus
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2019-12-11 Released: 2020-12-09
Deposition Author(s): Sharma, M., Nestl, B., Grogan, G.
Funding Organization(s): Biotechnology and Biological Sciences Research Council (BBSRC)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.78 Å
R-Value Free:
0.228 (Depositor), 0.228 (DCC)
R-Value Work:
0.192 (Depositor), 0.195 (DCC)
R-Value Observed:
0.194 (Depositor)

Starting Model: experimental
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Ligand Structure Quality Assessment

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Literature

Inverting the Stereoselectivity of an NADH-Dependent Imine-Reductase Variant

Stockinger, P., Borlinghaus, N., Sharma, M., Aberle, B., Grogan, G., Pleiss, J., Nestl, B.

(2021) ChemCatChem

DOI: https://doi.org/10.1002/cctc.202101057

Macromolecule Content

Total Structure Weight: 205.29 kDa
Atom Count: 13,254
Modeled Residue Count: 1,743
Deposited Residue Count: 1,866
Unique protein chains: 1

Macromolecules

Find similar proteins by:

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Coenzyme F420-dependent NADP oxidoreductase	A, B, C, D, E A, B, C, D, E, F	311	Myxococcus stipitatus	Mutation(s): 0 Gene Names: MYSTI_01767
UniProt
Find proteins for L7U9F5 (Myxococcus stipitatus (strain DSM 14675 / JCM 12634 / Mx s8)) Explore L7U9F5 Go to UniProtKB: L7U9F5
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	L7U9F5
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 J [auth F] SDF format, chain I [auth C] SDF format, chain H [auth B] SDF format, chain G [auth A] MOL2 format, chain J [auth F] MOL2 format, chain I [auth C] MOL2 format, chain H [auth B] MOL2 format, chain G [auth A] mmCIF format, chain J [auth F] mmCIF format, chain I [auth C] mmCIF format, chain H [auth B] mmCIF format, chain G [auth A]	G [auth A], H [auth B], I [auth C], J [auth F]	NICOTINAMIDE-ADENINE-DINUCLEOTIDE C₂₁ H₂₇ N₇ O₁₄ P₂ BAWFJGJZGIEFAR-NNYOXOHSSA-N		Interactions Focus chain G [auth A] Focus chain H [auth B] Focus chain I [auth C] Focus chain J [auth F] Interactions & Density Focus chain G [auth A] Focus chain H [auth B] Focus chain I [auth C] Focus chain J [auth F]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.78 Å
R-Value Free: 0.228 (Depositor), 0.228 (DCC)
R-Value Work: 0.192 (Depositor), 0.195 (DCC)
R-Value Observed: 0.194 (Depositor)

Space Group: P 6₅

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 199.412	α = 90
b = 199.412	β = 90
c = 97.94	γ = 120

Software Package:

Software Name	Purpose
REFMAC	refinement
PDB_EXTRACT	data extraction
XDS	data reduction
SCALA	data scaling
MOLREP	phasing

Structure Validation

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Ligand Structure Quality Assessment

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Entry History

& Funding Information

Deposition Data

Released Date: 2020-12-09

Deposition Author(s):

Funding Organization	Location	Grant Number
Biotechnology and Biological Sciences Research Council (BBSRC)	United Kingdom	BB/M006832/1

Revision History (Full details and data files)

Version 1.0: 2020-12-09
Type: Initial release
Version 1.1: 2021-12-22
Changes: Database references
Version 1.2: 2024-01-24
Changes: Data collection, Refinement description

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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.