9FE6 | pdb_00009fe6

Short-chain dehydrogenase/reductase (SDR) from Thermus caliditerrae

PDB DOI: https://doi.org/10.2210/pdb9FE6/pdb

Classification: OXIDOREDUCTASE
Organism(s): Thermus caliditerrae
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2024-05-17 Released: 2024-06-26
Deposition Author(s): Kapur, B., Nar, H.
Funding Organization(s): Not funded

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.88 Å
R-Value Free:
0.245 (Depositor), 0.233 (DCC)
R-Value Work:
0.217 (Depositor), 0.208 (DCC)
R-Value Observed:
0.219 (Depositor)

Starting Model: in silico
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This is version 1.0 of the entry. See complete history.

Literature

In silico enzyme screening identifies an SDR ketoreductase from Thermus caliditerrae as an attractive biocatalyst and promising candidate for protein engineering

Sosa, Y., Kapur, B., Hurtak, J., Kingsley, L., Wu, H., Gruber, S., Nar, H., Khattabi, S., Moral, J., Lucas, M., Martin, C., Loncar, N., Buono, F., Pefaur, N., Nixon, A.E., Song, J.

(2024) Front Chem Biol

Macromolecule Content

Total Structure Weight: 150.98 kDa
Atom Count: 8,205
Modeled Residue Count: 1,048
Deposited Residue Count: 1,410
Unique protein chains: 1

Macromolecules

Find similar proteins by:

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
SDR family oxidoreductase	A, B, C, D, E	282	Thermus caliditerrae	Mutation(s): 0 Gene Names: ENM28_03685
UniProt
Find proteins for A0A7C5VFX3 (Thermus caliditerrae) Explore A0A7C5VFX3 Go to UniProtKB: A0A7C5VFX3
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	A0A7C5VFX3
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
MG Query on MG Download:Ideal Coordinates CCD File SDF format, chain G [auth B] SDF format, chain F [auth A] MOL2 format, chain G [auth B] MOL2 format, chain F [auth A] mmCIF format, chain G [auth B] mmCIF format, chain F [auth A]	F [auth A], G [auth B]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain F [auth A] Focus chain G [auth B] Interactions & Density Focus chain F [auth A] Focus chain G [auth B]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.88 Å
R-Value Free: 0.245 (Depositor), 0.233 (DCC)
R-Value Work: 0.217 (Depositor), 0.208 (DCC)
R-Value Observed: 0.219 (Depositor)

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 56.673	α = 90
b = 122.989	β = 90
c = 163.347	γ = 90

Software Package:

Software Name	Purpose
BUSTER	refinement
autoPROC	data reduction
autoPROC	data scaling
PHASER	phasing

Structure Validation

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Entry History

& Funding Information

Deposition Data

Released Date: 2024-06-26

Deposition Author(s):

Funding Organization	Location	Grant Number
Not funded		--

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.