3NUF | pdb_00003nuf

Crystal structure of a PRD-containing transcription regulator (LSEI_2718) from Lactobacillus casei ATCC 334 at 1.38 A resolution

• PDB DOI: https://doi.org/10.2210/pdb3NUF/pdb

• Classification: Transcription regulator
• Organism(s): Lacticaseibacillus paracasei ATCC 334
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2010-07-06 Released: 2010-09-08 
• Deposition Author(s): Joint Center for Structural Genomics (JCSG)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.38 Å
• R-Value Free: 
  0.192 (Depositor), 0.196 (DCC) 
• R-Value Work: 
  0.171 (Depositor), 0.176 (DCC) 
• R-Value Observed: 
  0.172 (Depositor) 

Literature

Crystal structure of a PRD-containing transcription regulator (LSEI_2718) from Lactobacillus casei ATCC 334 at 1.38 A resolution

Joint Center for Structural Genomics (JCSG)

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)

Biological Assembly Evidence: gel filtration, light scattering

Biological Assembly 2  

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

Biological assembly 2 assigned by authors and generated by PISA (software)

Biological Assembly Evidence: gel filtration, light scattering

Biological Assembly 3  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 3 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 27.13 kDa 
• Atom Count: 2,330 
• Modeled Residue Count: 230 
• Deposited Residue Count: 238 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
PRD-containing transcription regulator	A, B	119	Lacticaseibacillus paracasei ATCC 334	Mutation(s): 0  Gene Names: LSEI_2718
UniProt
Find proteins for Q034D9 (Lacticaseibacillus paracasei (strain ATCC 334 / BCRC 17002 / CCUG 31169 / CIP 107868 / KCTC 3260 / NRRL B-441)) Explore Q034D9  Go to UniProtKB:  Q034D9

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
PG4	L [auth B]	TETRAETHYLENE GLYCOL C8 H18 O5 UWHCKJMYHZGTIT-UHFFFAOYSA-N
PEG	H [auth A]	DI(HYDROXYETHYL)ETHER C4 H10 O3 MTHSVFCYNBDYFN-UHFFFAOYSA-N
SO4	I [auth B]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L
EDO	C [auth A], D [auth A], E [auth A], F [auth A], G [auth A], J [auth B], K [auth B]	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-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: 1.38 Å
• R-Value Free:  0.192 (Depositor), 0.196 (DCC) 
• R-Value Work:  0.171 (Depositor), 0.176 (DCC) 
• R-Value Observed: 0.172 (Depositor) 

Diffraction Data: https://doi.org/10.18430/M33NUF

Space Group: P 4₃ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 67.16	α = 90
b = 67.16	β = 90
c = 99.733	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
PHENIX	refinement
SHELX	phasing
MolProbity	model building
XSCALE	data scaling
PDB_EXTRACT	data extraction
XDS	data reduction
SHELXD	phasing
autoSHARP	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2010-09-08 
Deposition Author(s): Joint Center for Structural Genomics (JCSG)

Revision History  

• Version 1.0: 2010-09-08
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance
• Version 1.2: 2011-07-20
  Changes: Structure summary
• Version 1.3: 2017-10-25
  Changes: Author supporting evidence, Refinement description
• Version 1.4: 2019-07-17
  Changes: Data collection, Derived calculations, Refinement description
• Version 1.5: 2024-11-06
  Changes: Data collection, Database references, Derived calculations, Structure summary