3OWA | pdb_00003owa

Crystal Structure of Acyl-CoA Dehydrogenase complexed with FAD from Bacillus anthracis

PDB DOI: https://doi.org/10.2210/pdb3OWA/pdb

Classification: OXIDOREDUCTASE
Organism(s): Bacillus anthracis str. 'Ames Ancestor
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2010-09-17 Released: 2010-10-13
Deposition Author(s): Kim, Y., Maltseva, N., Kwon, K., Anderson, W.F., Joachimiak, A., Center for Structural Genomics of Infectious Diseases (CSGID)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.97 Å
R-Value Free:
0.201 (Depositor), 0.202 (DCC)
R-Value Work:
0.162 (Depositor), 0.164 (DCC)
R-Value Observed:
0.164 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.5 of the entry. See complete history.

Literature

Crystal Structure of Acyl-CoA Dehydrogenase complexed with FAD from Bacillus anthracis

Kim, Y., Maltseva, N., Kwon, K., Anderson, W.F., Joachimiak, A., Center for Structural Genomics of Infectious Diseases (CSGID)

To be published.

Macromolecule Content

Total Structure Weight: 272.59 kDa
Atom Count: 20,926
Modeled Residue Count: 2,325
Deposited Residue Count: 2,388
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Acyl-CoA dehydrogenase	A, B, C, D	597	Bacillus anthracis str. 'Ames Ancestor	Mutation(s): 0 Gene Names: BAS4875, BA_5246, GBAA5246, GBAA_5246 EC: 1.3.99
UniProt
Find proteins for A0A6H3ADM7 (Bacillus anthracis) Explore A0A6H3ADM7 Go to UniProtKB: A0A6H3ADM7
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	A0A6H3ADM7
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 5 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
FAD Query on FAD Download:Ideal Coordinates CCD File SDF format, chain Y [auth D] SDF format, chain R [auth C] SDF format, chain J [auth B] SDF format, chain E [auth A] MOL2 format, chain Y [auth D] MOL2 format, chain R [auth C] MOL2 format, chain J [auth B] MOL2 format, chain E [auth A] mmCIF format, chain Y [auth D] mmCIF format, chain R [auth C] mmCIF format, chain J [auth B] mmCIF format, chain E [auth A]	E [auth A], J [auth B], R [auth C], Y [auth D]	FLAVIN-ADENINE DINUCLEOTIDE C₂₇ H₃₃ N₉ O₁₅ P₂ VWWQXMAJTJZDQX-UYBVJOGSSA-N		Interactions Focus chain E [auth A] Focus chain J [auth B] Focus chain R [auth C] Focus chain Y [auth D] Interactions & Density Focus chain E [auth A] Focus chain J [auth B] Focus chain R [auth C] Focus chain Y [auth D]
1PE Query on 1PE Download:Ideal Coordinates CCD File SDF format, chain Z [auth D] SDF format, chain U [auth C] SDF format, chain M [auth B] SDF format, chain F [auth A] MOL2 format, chain Z [auth D] MOL2 format, chain U [auth C] MOL2 format, chain M [auth B] MOL2 format, chain F [auth A] mmCIF format, chain Z [auth D] mmCIF format, chain U [auth C] mmCIF format, chain M [auth B] mmCIF format, chain F [auth A]	F [auth A], M [auth B], U [auth C], Z [auth D]	PENTAETHYLENE GLYCOL C₁₀ H₂₂ O₆ JLFNLZLINWHATN-UHFFFAOYSA-N		Interactions Focus chain F [auth A] Focus chain M [auth B] Focus chain U [auth C] Focus chain Z [auth D] Interactions & Density Focus chain F [auth A] Focus chain M [auth B] Focus chain U [auth C] Focus chain Z [auth D]
PEG Query on PEG Download:Ideal Coordinates CCD File SDF format, chain X [auth D] SDF format, chain W [auth C] SDF format, chain N [auth B] SDF format, chain G [auth A] MOL2 format, chain X [auth D] MOL2 format, chain W [auth C] MOL2 format, chain N [auth B] MOL2 format, chain G [auth A] mmCIF format, chain X [auth D] mmCIF format, chain W [auth C] mmCIF format, chain N [auth B] mmCIF format, chain G [auth A]	G [auth A], N [auth B], W [auth C], X [auth D]	DI(HYDROXYETHYL)ETHER C₄ H₁₀ O₃ MTHSVFCYNBDYFN-UHFFFAOYSA-N		Interactions Focus chain G [auth A] Focus chain N [auth B] Focus chain W [auth C] Focus chain X [auth D] Interactions & Density Focus chain G [auth A] Focus chain N [auth B] Focus chain W [auth C] Focus chain X [auth D]
SO4 Query on SO4 Download:Ideal Coordinates CCD File SDF format, chain O [auth B] SDF format, chain I [auth A] MOL2 format, chain O [auth B] MOL2 format, chain I [auth A] mmCIF format, chain O [auth B] mmCIF format, chain I [auth A]	I [auth A], O [auth B]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain I [auth A] Focus chain O [auth B] Interactions & Density Focus chain I [auth A] Focus chain O [auth B]
GOL Query on GOL Download:Ideal Coordinates CCD File SDF format, chain V [auth C] SDF format, chain T [auth C] SDF format, chain S [auth C] SDF format, chain Q [auth B] SDF format, chain P [auth B] SDF format, chain L [auth B] SDF format, chain K [auth B] SDF format, chain H [auth A] MOL2 format, chain V [auth C] MOL2 format, chain T [auth C] MOL2 format, chain S [auth C] MOL2 format, chain Q [auth B] MOL2 format, chain P [auth B] MOL2 format, chain L [auth B] MOL2 format, chain K [auth B] MOL2 format, chain H [auth A] mmCIF format, chain V [auth C] mmCIF format, chain T [auth C] mmCIF format, chain S [auth C] mmCIF format, chain Q [auth B] mmCIF format, chain P [auth B] mmCIF format, chain L [auth B] mmCIF format, chain K [auth B] mmCIF format, chain H [auth A]	H [auth A] K [auth B] L [auth B] P [auth B] Q [auth B] H [auth A], K [auth B], L [auth B], P [auth B], Q [auth B], S [auth C], T [auth C], V [auth C]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain H [auth A] Focus chain K [auth B] Focus chain L [auth B] Focus chain P [auth B] Focus chain Q [auth B] Focus chain S [auth C] Focus chain T [auth C] Focus chain V [auth C] Interactions & Density Focus chain H [auth A] Focus chain K [auth B] Focus chain L [auth B] Focus chain P [auth B] Focus chain Q [auth B] Focus chain S [auth C] Focus chain T [auth C] Focus chain V [auth C]

Modified Residues 1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
MSE Query on MSE	A, B, C, D	L-PEPTIDE LINKING	C₅ H₁₁ N O₂ Se		MET

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.97 Å
R-Value Free: 0.201 (Depositor), 0.202 (DCC)
R-Value Work: 0.162 (Depositor), 0.164 (DCC)
R-Value Observed: 0.164 (Depositor)

Diffraction Data:

Space Group: P 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 75.613	α = 92.8
b = 98.028	β = 106.63
c = 107.743	γ = 105.3

Software Package:

Software Name	Purpose
REFMAC	refinement
HKL-3000	data collection
BALBES	phasing
PHENIX	refinement
SBC-Collect	data collection
HKL-3000	data reduction
HKL-3000	data scaling

Structure Validation

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Ligand Structure Quality Assessment

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Entry History

Deposition Data

Released Date: 2010-10-13

Deposition Author(s):

Center for Structural Genomics of Infectious Diseases (CSGID)

Revision History (Full details and data files)

Version 1.0: 2010-10-13
Type: Initial release
Version 1.1: 2011-07-13
Changes: Version format compliance
Version 1.2: 2019-07-17
Changes: Data collection, Derived calculations, Refinement description
Version 1.3: 2023-09-06
Changes: Data collection, Database references, Derived calculations, Refinement description
Version 1.4: 2023-12-06
Changes: Data collection
Version 1.5: 2024-10-30
Changes: Structure summary