8ZAV | pdb_00008zav

alcohol dehydrogenases KpADH mutant - S9Y/F161K

PDB DOI: https://doi.org/10.2210/pdb8ZAV/pdb

Classification: STRUCTURAL PROTEIN
Organism(s): Vanderwaltozyma polyspora DSM 70294
Expression System: Escherichia coli BL21(DE3)
Mutation(s): Yes

Deposited: 2024-04-25 Released: 2024-06-26
Deposition Author(s): Zhang, L., Ni, Y., Xu, G.C.
Funding Organization(s): Other government

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.90 Å
R-Value Free:
0.288 (Depositor), 0.283 (DCC)
R-Value Work:
0.239 (Depositor), 0.240 (DCC)
R-Value Observed:
0.242 (Depositor)

Starting Model: experimental
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Ligand Structure Quality Assessment

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Literature

Engineering alcohol dehydrogenases KpADH for enhanced organic-solvent tolerance and its molecular mechanisms

Zhang, L., Ni, Y., Xu, G.C.

To be published.

Macromolecule Content

Total Structure Weight: 79.63 kDa
Atom Count: 5,608
Modeled Residue Count: 684
Deposited Residue Count: 684
Unique protein chains: 1

Macromolecules

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Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
NAD-dependent epimerase/dehydratase domain-containing protein	A, B	342	Vanderwaltozyma polyspora DSM 70294	Mutation(s): 2 Gene Names: Kpol_529p27
UniProt
Find proteins for A7TM80 (Vanderwaltozyma polyspora (strain ATCC 22028 / DSM 70294 / BCRC 21397 / CBS 2163 / NBRC 10782 / NRRL Y-8283 / UCD 57-17)) Explore A7TM80 Go to UniProtKB: A7TM80
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	A7TM80
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 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 E [auth B] SDF format, chain C [auth A] MOL2 format, chain E [auth B] MOL2 format, chain C [auth A] mmCIF format, chain E [auth B] mmCIF format, chain C [auth A]	C [auth A], E [auth B]	NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE C₂₁ H₂₈ N₇ O₁₇ P₃ XJLXINKUBYWONI-NNYOXOHSSA-N		Interactions Focus chain C [auth A] Focus chain E [auth B] Interactions & Density Focus chain C [auth A] Focus chain E [auth B]
EDO (Subject of Investigation/LOI) Query on EDO Download:Ideal Coordinates CCD File SDF format, chain F [auth B] SDF format, chain D [auth A] MOL2 format, chain F [auth B] MOL2 format, chain D [auth A] mmCIF format, chain F [auth B] mmCIF format, chain D [auth A]	D [auth A], F [auth B]	1,2-ETHANEDIOL C₂ H₆ O₂ LYCAIKOWRPUZTN-UHFFFAOYSA-N		Interactions Focus chain D [auth A] Focus chain F [auth B] Interactions & Density Focus chain D [auth A] Focus chain F [auth B]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.90 Å
R-Value Free: 0.288 (Depositor), 0.283 (DCC)
R-Value Work: 0.239 (Depositor), 0.240 (DCC)
R-Value Observed: 0.242 (Depositor)

Space Group: P 6₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 103.44	α = 90
b = 103.44	β = 90
c = 134.95	γ = 120

Software Package:

Software Name	Purpose
REFMAC	refinement
HKL-2000	data scaling

Structure Validation

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Ligand Structure Quality Assessment

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Entry History

& Funding Information

Deposition Data

Released Date: 2024-06-26

Deposition Author(s):

Funding Organization	Location	Grant Number
Other government		--

Revision History (Full details and data files)

Version 1.0: 2024-06-26
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.