5K7Z | pdb_00005k7z

Crystal structure of AibR in complex with isovaleryl coenzyme A and operator DNA

• PDB DOI: https://doi.org/10.2210/pdb5K7Z/pdb
• NAKB: 5K7Z

• Classification: TRANSCRIPTION
• Organism(s): Myxococcus xanthus DK 1622
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2016-05-27 Released: 2016-12-28 
• Deposition Author(s): Bock, T., Volz, C., Mueller, R., Blankenfeldt, W.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.92 Å
• R-Value Free: 
  0.245 (Depositor), 0.250 (DCC) 
• R-Value Work: 
  0.208 (Depositor), 0.210 (DCC) 
• R-Value Observed: 
  0.210 (Depositor) 

Starting Model: experimental

Literature

Crystal structure of AibR in complex with isovaleryl coenzyme A and operator DNA

Bock, T., Volz, C., Mueller, R., Blankenfeldt, W.

To be published.

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly 2  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 2 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 115.94 kDa 
• Atom Count: 7,519 
• Modeled Residue Count: 770 
• Deposited Residue Count: 956 
• Unique protein chains: 1
• Unique nucleic acid chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Transcriptional regulator, TetR family	A, B, C, D	231	Myxococcus xanthus DK 1622	Mutation(s): 0  Gene Names: MXAN_4263
UniProt
Find proteins for Q1D4I5 (Myxococcus xanthus (strain DK1622)) Explore Q1D4I5  Go to UniProtKB:  Q1D4I5

Entity ID: 2
Molecule	Chains	Length	Organism	Image
DNA (32-MER)	E, F	16	Myxococcus xanthus DK 1622

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
IVC	G [auth A], H [auth B], I [auth C], J [auth D]	Isovaleryl-coenzyme A C26 H44 N7 O17 P3 S UYVZIWWBJMYRCD-ZMHDXICWSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.92 Å
• R-Value Free:  0.245 (Depositor), 0.250 (DCC) 
• R-Value Work:  0.208 (Depositor), 0.210 (DCC) 
• R-Value Observed: 0.210 (Depositor) 

Space Group: I 4 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 164.711	α = 90
b = 164.711	β = 90
c = 203.275	γ = 90

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Released Date: 2016-12-28 
Deposition Author(s): Bock, T., Volz, C., Mueller, R., Blankenfeldt, W.

Revision History  

• Version 1.0: 2016-12-28
  Type: Initial release
  
• Version 1.1: 2024-01-10
  Changes: Data collection, Database references, Derived calculations, Refinement description