6SD8

Bd2924 apo-form

PDB DOI: https://doi.org/10.2210/pdb6SD8/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

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.51 Å
R-Value Free: 0.193
R-Value Work: 0.174
R-Value Observed: 0.175

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.2 of the entry. See complete history.

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 Search on PubMedSearch on PubMed Central
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.

Organizational Affiliation

BSC-CNS Barcelona Supercomputing Center, Barcelona, Spain.

Macromolecule Content

Total Structure Weight: 112.9 kDa
Atom Count: 8,715
Modelled Residue Count: 1,006
Deposited Residue Count: 1,010
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Probable acyl-CoA dehydrogenase	A [auth X], B [auth A]	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
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q6MJ59
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
FAD Query on FAD Download Ideal Coordinates CCD File SDF format, chain C [auth X] SDF format, chain D [auth A] MOL2 format, chain C [auth X] MOL2 format, chain D [auth A]	C [auth X], D [auth A]	FLAVIN-ADENINE DINUCLEOTIDE C₂₇ H₃₃ N₉ O₁₅ P₂ VWWQXMAJTJZDQX-UYBVJOGSSA-N		Interactions Focus chain C [auth X] Focus chain D [auth A] Interactions & Density Focus chain C [auth X] Focus chain D [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.51 Å
R-Value Free: 0.193
R-Value Work: 0.174
R-Value Observed: 0.175
Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 137.75	α = 90
b = 113.012	β = 120.84
c = 89.044	γ = 90

Software Package:

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

Structure Validation

View Full Validation Report

Ligand Structure Quality Assessment

Entry History & Funding Information

Deposition Data

Released Date: 2019-09-11

Deposition Author(s):

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

Revision History (Full details and data files)

Version 1.0: 2019-09-11
Type: Initial release
Version 1.1: 2019-11-06
Changes: Data collection, Database references
Version 1.2: 2019-11-20
Changes: Database references

RCSB PDB Core Operations are funded by the National Science Foundation (DBI-1832184), 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 R01GM133198.