7W0J | pdb_00007w0j

Acyl-CoA dehydrogenase, Tfu_1647

PDB DOI: https://doi.org/10.2210/pdb7W0J/pdb

Classification: FLAVOPROTEIN
Organism(s): Thermobifida fusca YX
Expression System: Escherichia coli BL21
Mutation(s): No

Deposited: 2021-11-18 Released: 2022-11-23
Deposition Author(s): Liu, L.X., Zhou, S.H., Deng, Y.
Funding Organization(s): Not funded

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 3.13 Å
R-Value Free:
0.270 (Depositor), 0.268 (DCC)
R-Value Work:
0.215 (Depositor), 0.216 (DCC)
R-Value Observed:
0.217 (Depositor)

Starting Model: experimental
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Ligand Structure Quality Assessment

This is version 1.1 of the entry. See complete history.

Literature

Crystal structure of an Acyl-CoA dehydrogenase Tfu_1647

Liu, L.X., Zhou, S.H., Deng, Y.

To be published.

Macromolecule Content

Total Structure Weight: 339.66 kDa
Atom Count: 23,345
Modeled Residue Count: 3,026
Deposited Residue Count: 3,080
Unique protein chains: 1

Macromolecules

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Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Acyl-CoA dehydrogenase	A B [auth D] C [auth G] D [auth F] E [auth B] A, B [auth D], C [auth G], D [auth F], E [auth B], F [auth C], G [auth E], H	385	Thermobifida fusca YX	Mutation(s): 0 Gene Names: Tfu_1647 EC: 1.3.8 (PDB Primary Data), 6.2.1.5 (UniProt)
UniProt
Find proteins for A0A4D5XMK4 (Thermobifida fusca (strain YX)) Explore A0A4D5XMK4 Go to UniProtKB: A0A4D5XMK4
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	A0A4D5XMK4
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
875 Query on 875 Download:Ideal Coordinates CCD File SDF format, chain K [auth H] SDF format, chain J [auth E] SDF format, chain I [auth E] MOL2 format, chain K [auth H] MOL2 format, chain J [auth E] MOL2 format, chain I [auth E] mmCIF format, chain K [auth H] mmCIF format, chain J [auth E] mmCIF format, chain I [auth E]	I [auth E], J [auth E], K [auth H]	[[(2R,3S,4R,5R)-5-(6-aminopurin-9-yl)-3,4-bis(oxidanyl)oxolan-2-yl]methoxy-oxidanyl-phosphoryl] [(2R,3S,4S)-5-azanyl-2,3,4-tris(oxidanyl)pentyl] hydrogen phosphate C₁₅ H₂₆ N₆ O₁₃ P₂ JFHZDRWPWXRIBP-AOOZFPJJSA-N		Interactions Focus chain I [auth E] Focus chain J [auth E] Focus chain K [auth H] Interactions & Density Focus chain I [auth E] Focus chain J [auth E] Focus chain K [auth H]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 3.13 Å
R-Value Free: 0.270 (Depositor), 0.268 (DCC)
R-Value Work: 0.215 (Depositor), 0.216 (DCC)
R-Value Observed: 0.217 (Depositor)

Space Group: P 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 85.124	α = 90.19
b = 88.908	β = 91.93
c = 97.178	γ = 112.09

Software Package:

Software Name	Purpose
PHENIX	refinement
HKL-2000	data reduction
PDB_EXTRACT	data extraction
HKL-3000	data scaling
HKL-3000	phasing

Structure Validation

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Ligand Structure Quality Assessment

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Entry History

& Funding Information

Deposition Data

Released Date: 2022-11-23

Deposition Author(s):

Funding Organization	Location	Grant Number
Not funded		--

Revision History (Full details and data files)

Version 1.0: 2022-11-23
Type: Initial release
Version 1.1: 2023-11-29
Changes: Data collection, Refinement description

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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.