3K1M | pdb_00003k1m

Crystal Structure of full-length BenM, R156H mutant

• PDB DOI: https://doi.org/10.2210/pdb3K1M/pdb

• Classification: TRANSCRIPTION
• Organism(s): Acinetobacter baylyi ADP1
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2009-09-28 Released: 2010-09-29 
• Deposition Author(s): Ruangprasert, A., Momany, C., Neidle, E.L., Craven, S.H.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.29 Å
• R-Value Free: 
  0.179 (Depositor), 0.260 (DCC) 
• R-Value Work: 
  0.147 (Depositor), 0.220 (DCC) 
• R-Value Observed: 
  0.148 (Depositor) 

Starting Model: experimental

Literature

Structure of Full-length BenM

Ruangprasert, A., Craven, S.H., Neidle, E.L., Momany, C.

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors.

Biological Assembly 2  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 4-mer - A4 

Biological assembly 2 generated by PISA (software)

Biological Assembly 3  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 4-mer - A4 

Biological assembly 3 generated by PISA (software)

Biological Assembly 4  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 4 generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 71.65 kDa 
• Atom Count: 5,429 
• Modeled Residue Count: 605 
• Deposited Residue Count: 624 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
HTH-type transcriptional regulator benM	A, B	312	Acinetobacter baylyi ADP1	Mutation(s): 1  Gene Names: ACIAD1435, benM, benR
UniProt
Find proteins for O68014 (Acinetobacter baylyi (strain ATCC 33305 / BD413 / ADP1)) Explore O68014  Go to UniProtKB:  O68014

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
GOL	E [auth A], H [auth B]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N
IMD	C [auth A], F [auth B]	IMIDAZOLE C3 H5 N2 RAXXELZNTBOGNW-UHFFFAOYSA-O
CL	D [auth A], G [auth B]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.29 Å
• R-Value Free:  0.179 (Depositor), 0.260 (DCC) 
• R-Value Work:  0.147 (Depositor), 0.220 (DCC) 
• R-Value Observed: 0.148 (Depositor) 

Space Group: P 2 2 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 69.997	α = 90
b = 70.789	β = 90
c = 186.275	γ = 90

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
PHASER	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction
HKL-3000	data collection

Structure Validation

Entry History 

Deposition Data

• Released Date: 2010-09-29 
Deposition Author(s): Ruangprasert, A., Momany, C., Neidle, E.L., Craven, S.H.

Revision History  

• Version 1.0: 2010-09-29
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance
• Version 1.2: 2017-11-01
  Changes: Refinement description
• Version 1.3: 2021-10-13
  Changes: Database references, Derived calculations
• Version 1.4: 2023-09-06
  Changes: Data collection, Refinement description