3K69 | pdb_00003k69

CRYSTAL STRUCTURE OF A PUTATIVE TRANSCRIPTIONAL REGULATOR (LP_0360) FROM LACTOBACILLUS PLANTARUM AT 1.95 A RESOLUTION

• PDB DOI: https://doi.org/10.2210/pdb3K69/pdb

• Classification: TRANSCRIPTION
• Organism(s): Lactiplantibacillus plantarum
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2009-10-08 Released: 2009-11-03 
• Deposition Author(s): Joint Center for Structural Genomics (JCSG)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.95 Å
• R-Value Free: 
  0.218 (Depositor), 0.220 (DCC) 
• R-Value Work: 
  0.172 (Depositor), 0.180 (DCC) 
• R-Value Observed: 
  0.174 (Depositor) 

Literature

Crystal structure of Putative transcriptional regulator (NP_784167.1) from LACTOBACILLUS PLANTARUM at 1.95 A resolution

Joint Center for Structural Genomics (JCSG)

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: 18.36 kDa 
• Atom Count: 1,354 
• Modeled Residue Count: 151 
• Deposited Residue Count: 162 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Putative transcription regulator	A	162	Lactiplantibacillus plantarum	Mutation(s): 0  Gene Names: lp_0360

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
DMS	B [auth A], C [auth A]	DIMETHYL SULFOXIDE C2 H6 O S IAZDPXIOMUYVGZ-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: 1.95 Å
• R-Value Free:  0.218 (Depositor), 0.220 (DCC) 
• R-Value Work:  0.172 (Depositor), 0.180 (DCC) 
• R-Value Observed: 0.174 (Depositor) 

Diffraction Data: https://doi.org/10.18430/M33K69

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 114.173	α = 90
b = 38.054	β = 110.73
c = 42.275	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
PHENIX	refinement
SOLVE	phasing
MolProbity	model building
SCALA	data scaling
PDB_EXTRACT	data extraction
MOSFLM	data reduction

Structure Validation

Entry History 

Deposition Data

• Released Date: 2009-11-03 
Deposition Author(s): Joint Center for Structural Genomics (JCSG)

Revision History  

• Version 1.0: 2009-11-03
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Advisory, Version format compliance
• Version 1.2: 2017-11-01
  Changes: Refinement description
• Version 1.3: 2019-07-17
  Changes: Data collection, Derived calculations, Refinement description
• Version 1.4: 2023-02-01
  Changes: Database references, Derived calculations
• Version 1.5: 2024-11-27
  Changes: Data collection, Structure summary