8K1G | pdb_00008k1g

Crystal structure of ethylene glycol-bound glycerol dehydrogenase from Klebsiella pneumoniae

PDB DOI: https://doi.org/10.2210/pdb8K1G/pdb

Classification: OXIDOREDUCTASE
Organism(s): Klebsiella pneumoniae
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2023-07-10 Released: 2024-05-29
Deposition Author(s): Kang, W.
Funding Organization(s): National Research Foundation (NRF, Korea)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.09 Å
R-Value Free:
0.207 (Depositor), 0.206 (DCC)
R-Value Work:
0.186 (Depositor), 0.186 (DCC)
R-Value Observed:
0.187 (Depositor)

Starting Model: experimental
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Ligand Structure Quality Assessment

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

Literature

Crystal Structure of Glycerol Dehydrogenase from Klebsiella pneumoniae

Ko, G.S., Nguyen, T.Q., Kho, S., Kang, W.

(2024) J Korean Chem Soc 68: 32-39

DOI: https://doi.org/10.5012/jkcs.2024.68.1.32

Macromolecule Content

Total Structure Weight: 39.25 kDa
Atom Count: 2,913
Modeled Residue Count: 367
Deposited Residue Count: 367
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Glycerol dehydrogenase	A	367	Klebsiella pneumoniae	Mutation(s): 0 Gene Names: gldA EC: 1.1.1.6
UniProt
Find proteins for A6TGD6 (Klebsiella pneumoniae subsp. pneumoniae (strain ATCC 700721 / MGH 78578)) Explore A6TGD6 Go to UniProtKB: A6TGD6
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	A6TGD6
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
GOL (Subject of Investigation/LOI) Query on GOL Download:Ideal Coordinates CCD File SDF format, chain F [auth A] MOL2 format, chain F [auth A] mmCIF format, chain F [auth A]	F [auth A]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain F [auth A] Interactions & Density Focus chain F [auth A]
ZN (Subject of Investigation/LOI) Query on ZN Download:Ideal Coordinates CCD File SDF format, chain B [auth A] MOL2 format, chain B [auth A] mmCIF format, chain B [auth A]	B [auth A]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N		Interactions Focus chain B [auth A] Interactions & Density Focus chain B [auth A]
EDO (Subject of Investigation/LOI) Query on EDO Download:Ideal Coordinates CCD File SDF format, chain H [auth A] SDF format, chain G [auth A] SDF format, chain E [auth A] SDF format, chain D [auth A] SDF format, chain C [auth A] MOL2 format, chain H [auth A] MOL2 format, chain G [auth A] MOL2 format, chain E [auth A] MOL2 format, chain D [auth A] MOL2 format, chain C [auth A] mmCIF format, chain H [auth A] mmCIF format, chain G [auth A] mmCIF format, chain E [auth A] mmCIF format, chain D [auth A] mmCIF format, chain C [auth A]	C [auth A], D [auth A], E [auth A], G [auth A], H [auth A]	1,2-ETHANEDIOL C₂ H₆ O₂ LYCAIKOWRPUZTN-UHFFFAOYSA-N		Interactions Focus chain C [auth A] Focus chain D [auth A] Focus chain E [auth A] Focus chain G [auth A] Focus chain H [auth A] Interactions & Density Focus chain C [auth A] Focus chain D [auth A] Focus chain E [auth A] Focus chain G [auth A] Focus chain H [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.09 Å
R-Value Free: 0.207 (Depositor), 0.206 (DCC)
R-Value Work: 0.186 (Depositor), 0.186 (DCC)
R-Value Observed: 0.187 (Depositor)

Diffraction Data:

Space Group: I 4 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 182.014	α = 90
b = 182.014	β = 90
c = 80.707	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
DENZO	data reduction
SCALEPACK	data scaling
PHASER	phasing

Structure Validation

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Ligand Structure Quality Assessment

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Entry History

& Funding Information

Deposition Data

Released Date: 2024-05-29

Deposition Author(s):

Kang, W.

Funding Organization	Location	Grant Number
National Research Foundation (NRF, Korea)	Korea, Republic Of	2021R1A6A1A10044154
National Research Foundation (NRF, Korea)	Korea, Republic Of	2022R1C1C1004221