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.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.92 Å
R-Value Free:
0.245 (Depositor), 0.240 (DCC)
R-Value Work:
0.208 (Depositor), 0.210 (DCC)
R-Value Observed:
0.210 (Depositor)

Starting Model: experimental
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Ligand Structure Quality Assessment

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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.

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

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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 Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q1D4I5
Sequence Annotations Expand
Reference Sequence

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

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
IVC Query on IVC Download:Ideal Coordinates CCD File SDF format, chain J [auth D] SDF format, chain I [auth C] SDF format, chain H [auth B] SDF format, chain G [auth A] MOL2 format, chain J [auth D] MOL2 format, chain I [auth C] MOL2 format, chain H [auth B] MOL2 format, chain G [auth A] mmCIF format, chain J [auth D] mmCIF format, chain I [auth C] mmCIF format, chain H [auth B] mmCIF format, chain G [auth A]	G [auth A], H [auth B], I [auth C], J [auth D]	Isovaleryl-coenzyme A C₂₆ H₄₄ N₇ O₁₇ P₃ S UYVZIWWBJMYRCD-ZMHDXICWSA-N		Interactions Focus chain G [auth A] Focus chain H [auth B] Focus chain I [auth C] Focus chain J [auth D] Interactions & Density Focus chain G [auth A] Focus chain H [auth B] Focus chain I [auth C] Focus chain J [auth D]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.92 Å
R-Value Free: 0.245 (Depositor), 0.240 (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

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Entry History

Deposition Data

Released Date: 2016-12-28

Deposition Author(s):

Blankenfeldt, W.

Revision History (Full details and data files)

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