3B49 | pdb_00003b49

Crystal structure of an uncharacterized conserved protein from Listeria innocua

• PDB DOI: https://doi.org/10.2210/pdb3B49/pdb

• Classification: STRUCTURAL GENOMICS, UNKNOWN FUNCTION
• Organism(s): Listeria innocua Clip11262
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2007-10-23 Released: 2007-11-13 
• Deposition Author(s): Nocek, B., Duggan, E., Freeman, L., Joachimiak, A., Midwest Center for Structural Genomics (MCSG)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.60 Å
• R-Value Free: 
  0.198 (Depositor), 0.205 (DCC) 
• R-Value Work: 
  0.170 (Depositor), 0.177 (DCC) 
• R-Value Observed: 
  0.171 (Depositor) 

Literature

Crystal structure of an uncharacterized conserved protein from Listeria innocua.

Nocek, B., Duggan, E., Freeman, L., 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: 25.39 kDa 
• Atom Count: 2,027 
• Modeled Residue Count: 204 
• Deposited Residue Count: 211 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Lin2189 protein	A	211	Listeria innocua Clip11262	Mutation(s): 0  Gene Names: lin2189
UniProt
Find proteins for Q929T5 (Listeria innocua serovar 6a (strain ATCC BAA-680 / CLIP 11262)) Explore Q929T5  Go to UniProtKB:  Q929T5

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
GOL	B [auth A], C [auth A]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-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: 1.60 Å
• R-Value Free:  0.198 (Depositor), 0.205 (DCC) 
• R-Value Work:  0.170 (Depositor), 0.177 (DCC) 
• R-Value Observed: 0.171 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 50.506	α = 90
b = 68.108	β = 90
c = 69.853	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
PDB_EXTRACT	data extraction
SBC-Collect	data collection
HKL-3000	data reduction
HKL-3000	data scaling
HKL2Map	phasing
SHELXCD	phasing
SHELXE	model building
SHELXD	phasing
ARP/wARP	model building

Structure Validation

Entry History 

Deposition Data

• Released Date: 2007-11-13 
Deposition Author(s): Nocek, B., Duggan, E., Freeman, L., Joachimiak, A., Midwest Center for Structural Genomics (MCSG)

Revision History  

• Version 1.0: 2007-11-13
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Advisory, Version format compliance
• Version 1.2: 2017-10-25
  Changes: Refinement description
• Version 1.3: 2024-11-13
  Changes: Data collection, Database references, Derived calculations, Structure summary