4KMR | pdb_00004kmr

Structure of a putative transcriptional regulator of LacI family from Sanguibacter keddieii DSM 10542.

• PDB DOI: https://doi.org/10.2210/pdb4KMR/pdb

• Classification: Transcription regulator
• Organism(s): Sanguibacter keddieii DSM 10542
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2013-05-08 Released: 2013-06-05 
• Deposition Author(s): Filippova, E.V., Minasov, G., Shuvalova, L., Kiryukhina, O., Endres, M., Joachimiak, A., Anderson, W.F., Midwest Center for Structural Genomics (MCSG)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.45 Å
• R-Value Free: 
  0.177 (Depositor), 0.188 (DCC) 
• R-Value Work: 
  0.125 (Depositor), 0.142 (DCC) 
• R-Value Observed: 
  0.128 (Depositor) 

Literature

Structure of a putative transcriptional regulator of LacI family from Sanguibacter keddieii DSM 10542.

Filippova, E.V., Minasov, G., Shuvalova, L., Kiryukhina, O., Endres, M., Joachimiak, A., Anderson, W.F., Midwest Center for Structural Genomics (MCSG)

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)

Macromolecule Content 

• Total Structure Weight: 59.99 kDa 
• Atom Count: 4,589 
• Modeled Residue Count: 539 
• Deposited Residue Count: 560 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Transcriptional regulator, LacI family	A, B	280	Sanguibacter keddieii DSM 10542	Mutation(s): 0  Gene Names: Sked_03100
UniProt
Find proteins for D1BJM2 (Sanguibacter keddieii (strain ATCC 51767 / DSM 10542 / NCFB 3025 / ST-74)) Explore D1BJM2  Go to UniProtKB:  D1BJM2

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
MG	C [auth B]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N
NA	D [auth B]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N

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

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.45 Å
• R-Value Free:  0.177 (Depositor), 0.188 (DCC) 
• R-Value Work:  0.125 (Depositor), 0.142 (DCC) 
• R-Value Observed: 0.128 (Depositor) 

Diffraction Data: https://doi.org/10.18430/M34KMR

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 42.175	α = 90
b = 120.205	β = 92.59
c = 44.962	γ = 90

Software Package:

Software Name	Purpose
Blu-Ice	data collection
HKL-3000	phasing
REFMAC	refinement
HKL-3000	data reduction
HKL-3000	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2013-06-05 
Deposition Author(s): Filippova, E.V., Minasov, G., Shuvalova, L., Kiryukhina, O., Endres, M., Joachimiak, A., Anderson, W.F., Midwest Center for Structural Genomics (MCSG)

Revision History  

• Version 1.0: 2013-06-05
  Type: Initial release
  
• Version 1.1: 2017-11-15
  Changes: Refinement description
• Version 1.2: 2024-11-27
  Changes: Data collection, Database references, Derived calculations, Structure summary