6K0Z | pdb_00006k0z

Substrate bound state of Staphylococcus Aureus AldH

PDB DOI: https://doi.org/10.2210/pdb6K0Z/pdb

Classification: OXIDOREDUCTASE
Organism(s): Staphylococcus aureus
Expression System: Escherichia coli
Mutation(s): Yes

Deposited: 2019-05-08 Released: 2020-05-20
Deposition Author(s): Zhang, Z., Tao, X.
Funding Organization(s): National Science Foundation (China)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.50 Å
R-Value Free:
0.261 (Depositor), 0.261 (DCC)
R-Value Work:
0.235 (Depositor), 0.235 (DCC)
R-Value Observed:
0.237 (Depositor)

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This is version 1.2 of the entry. See complete history.

Literature

Structural Insight into the Substrate Gating Mechanism by Staphylococcus aureus Aldehyde Dehydrogenase

Tao, X., Zhang, Z., Zhang, X., Li, H., Sun, H., Mao, Z., Xia, W.

(2020) Ccs Chemistry 2: 946-954

DOI: https://doi.org/10.31635/ccschem.020.202000219

Macromolecule Content

Total Structure Weight: 52.78 kDa
Atom Count: 3,610
Modeled Residue Count: 458
Deposited Residue Count: 466
Unique protein chains: 1

Macromolecules

Find similar proteins by:

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Aldehyde dehydrogenase	A	466	Staphylococcus aureus	Mutation(s): 1 EC: 1.2.1
UniProt
Find proteins for Q2FWX9 (Staphylococcus aureus (strain NCTC 8325 / PS 47)) Explore Q2FWX9 Go to UniProtKB: Q2FWX9
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q2FWX9
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
GOL Query on GOL 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]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain B [auth A] Interactions & Density Focus chain B [auth A]
EDO Query on EDO Download:Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain D [auth A] SDF format, chain C [auth A] MOL2 format, chain E [auth A] MOL2 format, chain D [auth A] MOL2 format, chain C [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]	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] Interactions & Density Focus chain C [auth A] Focus chain D [auth A] Focus chain E [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.50 Å
R-Value Free: 0.261 (Depositor), 0.261 (DCC)
R-Value Work: 0.235 (Depositor), 0.235 (DCC)
R-Value Observed: 0.237 (Depositor)

Space Group: I 4 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 176.444	α = 90
b = 176.444	β = 90
c = 95.755	γ = 90

Software Package:

Software Name	Purpose
PHENIX	phasing
PHENIX	refinement
HKL-2000	data reduction
HKL-2000	data scaling

Structure Validation

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Entry History

& Funding Information

Deposition Data

Released Date: 2020-05-20

Deposition Author(s):

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

Revision History (Full details and data files)

Version 1.0: 2020-05-20
Type: Initial release
Version 1.1: 2021-06-02
Changes: Database references
Version 1.2: 2024-03-27
Changes: Data collection, Database references

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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.