9FEB | pdb_00009feb

Short-chain dehydrogenase/reductase (SDR) from Thermus caliditerrae in complex with NADP

• PDB DOI: https://doi.org/10.2210/pdb9FEB/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

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.70 Å
• R-Value Free: 
  0.198 (Depositor), 0.192 (DCC) 
• R-Value Work: 
  0.176 (Depositor), 0.168 (DCC) 
• R-Value Observed: 
  0.177 (Depositor) 

Starting Model: in silico

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 

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 5-mer - A4B1 Local Symmetry: Dihedral - D2  (Explore in 3D)
Local Stoichiometry: Homo 4-mer - A4 

Local Symmetry: Dihedral - D2  (Explore in 3D)
Local Stoichiometry: Homo 4-mer - A4 

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly Evidence: gel filtration

Macromolecule Content 

• Total Structure Weight: 153.96 kDa 
• Atom Count: 8,926 
• Modeled Residue Count: 1,049 
• Deposited Residue Count: 1,410 
• Unique protein chains: 1

Macromolecules

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

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NAP (Subject of Investigation/LOI)	F [auth A], H [auth B], J [auth C], K [auth D]	NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE C21 H28 N7 O17 P3 XJLXINKUBYWONI-NNYOXOHSSA-N
MG	G [auth A], I [auth B]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.70 Å
• R-Value Free:  0.198 (Depositor), 0.192 (DCC) 
• R-Value Work:  0.176 (Depositor), 0.168 (DCC) 
• R-Value Observed: 0.177 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 56.621	α = 90
b = 121.862	β = 90
c = 162.91	γ = 90

Software Package:

Software Name	Purpose
autoPROC	data processing
autoPROC	data reduction
XDS	data reduction
Aimless	data scaling
STARANISO	data scaling
autoPROC	data scaling
PHASER	phasing
Coot	model building
BUSTER	refinement

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2024-06-26 
Deposition Author(s): Kapur, B., Nar, H.

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Funding Organization	Location	Grant Number
Not funded		--

Revision History  

• Version 1.0: 2024-06-26
  Type: Initial release