4KQC | pdb_00004kqc

ABC transporter, LacI family transcriptional regulator from Brachyspira murdochii

• PDB DOI: https://doi.org/10.2210/pdb4KQC/pdb

• Classification: TRANSPORT PROTEIN
• Organism(s): Brachyspira murdochii DSM 12563
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2013-05-14 Released: 2013-05-29 
• Deposition Author(s): Osipiuk, J., Joachimiak, G., Clancy, S., Joachimiak, A., Midwest Center for Structural Genomics (MCSG)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.62 Å
• R-Value Free: 
  0.188 (Depositor), 0.201 (DCC) 
• R-Value Work: 
  0.151 (Depositor), 0.164 (DCC) 
• R-Value Observed: 
  0.153 (Depositor) 

Literature

ABC transporter, LacI family transcriptional regulator from Brachyspira murdochii

Osipiuk, J., Joachimiak, G., Clancy, S., Joachimiak, A.

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

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

Macromolecule Content 

• Total Structure Weight: 34.32 kDa 
• Atom Count: 2,913 
• Modeled Residue Count: 319 
• Deposited Residue Count: 319 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Periplasmic binding protein/LacI transcriptional regulator	A	319	Brachyspira murdochii DSM 12563	Mutation(s): 0  Gene Names: Bmur_2490
UniProt
Find proteins for D5U661 (Brachyspira murdochii (strain ATCC 51284 / DSM 12563 / 56-150)) Explore D5U661  Go to UniProtKB:  D5U661

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NO3	B [auth A], C [auth A], D [auth A], E [auth A], F [auth A]	NITRATE ION N O3 NHNBFGGVMKEFGY-UHFFFAOYSA-N

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

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.62 Å
• R-Value Free:  0.188 (Depositor), 0.201 (DCC) 
• R-Value Work:  0.151 (Depositor), 0.164 (DCC) 
• R-Value Observed: 0.153 (Depositor) 

Diffraction Data: https://doi.org/10.18430/M34KQC

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 38.356	α = 90
b = 59.241	β = 102.9
c = 65.454	γ = 90

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Released Date: 2013-05-29 
Deposition Author(s): Osipiuk, J., Joachimiak, G., Clancy, S., Joachimiak, A., Midwest Center for Structural Genomics (MCSG)

Revision History  

• Version 1.0: 2013-05-29
  Type: Initial release
  
• Version 1.1: 2017-11-15
  Changes: Refinement description
• Version 1.2: 2024-10-09
  Changes: Data collection, Database references, Derived calculations, Structure summary