6SDA | pdb_00006sda

Bd2924 C10 acyl-coenzymeA bound form

• PDB DOI: https://doi.org/10.2210/pdb6SDA/pdb

• Classification: OXIDOREDUCTASE
• Organism(s): Bdellovibrio bacteriovorus HD100
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2019-07-26 Released: 2019-09-11 
• Deposition Author(s): Lovering, A.L., Harding, C.J.
• Funding Organization(s): Biotechnology and Biological Sciences Research Council

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.87 Å
• R-Value Free: 
  0.191 (Depositor), 0.190 (DCC) 
• R-Value Work: 
  0.161 (Depositor), 0.170 (DCC) 
• R-Value Observed: 
  0.163 (Depositor) 

Literature

Target highlights in CASP13: Experimental target structures through the eyes of their authors.

Lepore, R., Kryshtafovych, A., Alahuhta, M., Veraszto, H.A., Bomble, Y.J., Bufton, J.C., Bullock, A.N., Caba, C., Cao, H., Davies, O.R., Desfosses, A., Dunne, M., Fidelis, K., Goulding, C.W., Gurusaran, M., Gutsche, I., Harding, C.J., Hartmann, M.D., Hayes, C.S., Joachimiak, A., Leiman, P.G., Loppnau, P., Lovering, A.L., Lunin, V.V., Michalska, K., Mir-Sanchis, I., Mitra, A.K., Moult, J., Phillips Jr., G.N., Pinkas, D.M., Rice, P.A., Tong, Y., Topf, M., Walton, J.D., Schwede, T.

(2019) Proteins 87: 1037-1057

• PubMed: 31442339 
• DOI: https://doi.org/10.1002/prot.25805
• Primary Citation of Related Structures:  
  6CVZ, 6SD8, 6SDA


• PubMed Abstract: 
  

  The functional and biological significance of selected CASP13 targets are described by the authors of the structures. The structural biologists discuss the most interesting structural features of the target proteins and assess whether these features were correctly reproduced in the predictions submitted to the CASP13 experiment.

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Organizational Affiliation: 
• BSC-CNS Barcelona Supercomputing Center, Barcelona, Spain.
Genome Center, University of California, Davis, California.
Biosciences Center, National Renewable Energy Laboratory, Golden, Colorado.
Department of Protein Evolution, Max Planck Institute for Developmental Biology, Tübingen, Germany.
Nuffield Department of Medicine; Structural Genomics Consortium, University of Oxford, Oxford, UK.
School of Biochemistry, University of Bristol, Bristol, UK.
Department of Chemistry and Biochemistry, University of Windsor, Windsor, Ontario, Canada.
Department of BioSciences, Rice University, Houston, Texas.
Great Lakes Bioenergy Research Center, University of Wisconsin, Madison, Wisconsin.
Institute for Cell and Molecular Biosciences, Faculty of Medical Sciences, Newcastle University, Newcastle upon Tyne, UK.
School of Biological Sciences, University of Auckland, Auckland, New Zealand.
Institut de Biologie Structurale, Université Grenoble Alpes, CEA, CNRS, Grenoble, France.
Institute of Food, Nutrition and Health, Zurich, Switzerland.
Department of Molecular Biology and Biochemistry; Pharmaceutical Sciences, University of California Irvine, Irvine, California.
School of Biosciences, University of Birmingham, Birmingham, UK.
Department of Molecular, Cellular and Developmental Biology, Biomolecular Science and Engineering Program, University of California, Santa Barbara, California.
Structural Biology Center, Biosciences Division, Midwest Center for Structural Genomics, Argonne.
Department of Biochemistry and Molecular Biology, University of Chicago, Chicago, Illinois.
Department of Biochemistry and Molecular Biology, Sealy Center for Structural Biology and Molecular Biophysics, University of Texas Medical Branch, Galveston, Texas.
Structural Genomics Consortium, University of Toronto, Toronto, Ontario, Canada.
Department of Biochemistry and Molecular Biology, The University of Chicago, Chicago, Illinois.
Institute for Bioscience and Biotechnology Research, Department of Cell Biology and Molecular genetics, University of Maryland, Rockville, Maryland, USA.
Institute of Structural and Molecular Biology, Birkbeck, University College London, London, UK.
Great Lakes Bioenergy Research Center and Department of Plant Biology, Michigan State University, East Lansing, Michigan.
Biozentrum University of Basel, Basel, Switzerland.
SIB Swiss Institute of Bioinformatics, Biozentrum University of Basel, Basel, Switzerland.

Biological Assembly 1  

Global Symmetry: Dihedral - D2  (Explore in 3D)
Global 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: 113.82 kDa 
• Atom Count: 8,651 
• Modeled Residue Count: 1,006 
• Deposited Residue Count: 1,010 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Probable acyl-CoA dehydrogenase	A, B	505	Bdellovibrio bacteriovorus HD100	Mutation(s): 0  Gene Names: Bd2924 EC: 1.3.99
UniProt
Find proteins for Q6MJ59 (Bdellovibrio bacteriovorus (strain ATCC 15356 / DSM 50701 / NCIMB 9529 / HD100)) Explore Q6MJ59  Go to UniProtKB:  Q6MJ59

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
MFK	D [auth B]	decanoyl-CoA C31 H54 N7 O17 P3 S CNKJPHSEFDPYDB-HSJNEKGZSA-N
FAD	C [auth A], E [auth B]	FLAVIN-ADENINE DINUCLEOTIDE C27 H33 N9 O15 P2 VWWQXMAJTJZDQX-UYBVJOGSSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.87 Å
• R-Value Free:  0.191 (Depositor), 0.190 (DCC) 
• R-Value Work:  0.161 (Depositor), 0.170 (DCC) 
• R-Value Observed: 0.163 (Depositor) 

Space Group: C 2 2 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 126.266	α = 90
b = 134.647	β = 90
c = 133.179	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data reduction
Aimless	data scaling
PHASER	phasing
PDB_EXTRACT	data extraction

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2019-09-11 
Deposition Author(s): Lovering, A.L., Harding, C.J.

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Funding Organization	Location	Grant Number
Biotechnology and Biological Sciences Research Council	United Kingdom	studentship

Revision History  

• Version 1.0: 2019-09-11
  Type: Initial release
  
• Version 1.1: 2020-03-25
  Changes: Database references
• Version 1.2: 2024-05-15
  Changes: Data collection, Database references, Refinement description