8I4R | pdb_00008i4r

Crystal structure of Acyl-CoA dehydrogenase complexed with Acetyl-CoA from Thermobifida fusca

PDB DOI: https://doi.org/10.2210/pdb8I4R/pdb

Classification: OXIDOREDUCTASE
Organism(s): Thermobifida fusca
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2023-01-20 Released: 2024-01-24
Deposition Author(s): Choi, M., Seok, J., Kim, K.-J.
Funding Organization(s): Not funded

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.51 Å
R-Value Free:
0.195 (Depositor), 0.210 (DCC)
R-Value Work:
0.166 (Depositor), 0.180 (DCC)
R-Value Observed:
0.167 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

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

Literature

Crystal structure of Acyl-CoA dehydrogenase complexed with Acetyl-CoA from Thermobifida fusca

Choi, M., Kim, K.-J.

To be published.

Macromolecule Content

Total Structure Weight: 44.91 kDa
Atom Count: 3,107
Modeled Residue Count: 381
Deposited Residue Count: 393
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Acyl-CoA dehydrogenase	A	393	Thermobifida fusca	Mutation(s): 0 Gene Names: Tfu_1647 EC: 6.2.1.5
UniProt
Find proteins for A0A4D5XMK4 (Thermobifida fusca (strain YX)) Explore A0A4D5XMK4 Go to UniProtKB: A0A4D5XMK4
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	A0A4D5XMK4
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
ACO (Subject of Investigation/LOI) Query on ACO Download Ideal Coordinates CCD File SDF format, chain C [auth A] MOL2 format, chain C [auth A] mmCIF format, chain C [auth A]	C [auth A]	*ACETYL COENZYME A** C₂₃ H₃₈ N₇ O₁₇ P₃ S ZSLZBFCDCINBPY-ZSJPKINUSA-N		Interactions Focus chain C [auth A] Interactions & Density Focus chain C [auth A]
FAD (Subject of Investigation/LOI) Query on FAD 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]	FLAVIN-ADENINE DINUCLEOTIDE C₂₇ H₃₃ N₉ O₁₅ P₂ VWWQXMAJTJZDQX-UYBVJOGSSA-N		Interactions Focus chain B [auth A] Interactions & Density Focus chain B [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.51 Å
R-Value Free: 0.195 (Depositor), 0.210 (DCC)
R-Value Work: 0.166 (Depositor), 0.180 (DCC)
R-Value Observed: 0.167 (Depositor)

Space Group: I 4₁ 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 102.143	α = 90
b = 102.143	β = 90
c = 312.183	γ = 90

Software Package:

Software Name	Purpose
HKL-2000	data scaling
MOLREP	phasing
REFMAC	refinement
MOLREP	phasing
HKL-2000	data reduction

Structure Validation

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Ligand Structure Quality Assessment

Entry History & Funding Information

Deposition Data

Released Date: 2024-01-24

Deposition Author(s):

Funding Organization	Location	Grant Number
Not funded		--

Revision History (Full details and data files)

Version 1.0: 2024-01-24
Type: Initial release

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.