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)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.71 Å
R-Value Free:
0.271 (Depositor), 0.273 (DCC)
R-Value Work:
0.230 (Depositor), 0.233 (DCC)
R-Value Observed:
0.231 (Depositor)

Starting Model: in silico
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Ligand Structure Quality Assessment

This is version 1.0 of the entry. See complete history.

Literature

A structure of imine reductase mutant at 2.7 Angstroms resolution.

Zhu, X.X., Chen, X.R., Zheng, G.W.

To be published.

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

Find similar proteins by:

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
6-phosphogluconate dehydrogenase NAD-binding protein	A, B, C, D, E 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
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	D9X416
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
NAP (Subject of Investigation/LOI) Query on NAP Download:Ideal Coordinates CCD File SDF format, chain I [auth B] SDF format, chain J [auth E] MOL2 format, chain I [auth B] MOL2 format, chain J [auth E] mmCIF format, chain I [auth B] mmCIF format, chain J [auth E]	I [auth B], J [auth E]	NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE C₂₁ H₂₈ N₇ O₁₇ P₃ XJLXINKUBYWONI-NNYOXOHSSA-N		Interactions Focus chain I [auth B] Focus chain J [auth E] Interactions & Density Focus chain I [auth B] Focus chain J [auth E]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.71 Å
R-Value Free: 0.271 (Depositor), 0.273 (DCC)
R-Value Work: 0.230 (Depositor), 0.233 (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

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Ligand Structure Quality Assessment

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Entry History

& Funding Information

Deposition Data

Released Date: 2024-09-25

Deposition Author(s):

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

Revision History (Full details and data files)

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

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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.