3DC7

Crystal structure of the protein Q88SR8 from Lactobacillus plantarum. Northeast Structural Genomics consortium target LpR109.

• PDB DOI: https://doi.org/10.2210/pdb3DC7/pdb

• Classification: structural genomics, unknown function
• Organism(s): Lactiplantibacillus plantarum
• Mutation(s): No 


• Deposited: 2008-06-03 Released: 2008-08-05 
• Deposition Author(s): Kuzin, A.P., Abashidze, M., Vorobiev, S.M., Seetharaman, J., Zhao, L., Mao, L., Ciccosanti, C., Xiao, R., Nair, R., Baran, M.C., Acton, T.B., Rost, B., Montelione, G.T., Hunt, J.F., Tong, L., Northeast Structural Genomics Consortium (NESG)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.12 Å
• R-Value Free: 
  0.224 (Depositor), 0.227 (DCC) 
• R-Value Work: 
  0.184 (Depositor), 0.186 (DCC) 
• R-Value Observed: 
  0.186 (Depositor) 

Literature

Crystal structure of the protein Q88SR8 from Lactobacillus plantarum. Northeast Structural Genomics consortium target LpR109. (CASP Target)

Kuzin, A.P., Abashidze, M., Vorobiev, S.M., Seetharaman, J., Zhao, L., Mao, L., Ciccosanti, C., Xiao, R., Nair, R., Baran, M.C., Acton, T.B., Rost, B., Montelione, G.T., Hunt, J.F., Tong, L.

To be published.

Biological Assembly 1  

Global Symmetry: Cyclic - C3  (Explore in 3D)
Global Stoichiometry: Homo 3-mer - A3 

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

Macromolecule Content

• Total Structure Weight: 77.48 kDa 
• Atom Count: 5,071 
• Modelled Residue Count: 630 
• Deposited Residue Count: 696 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Putative uncharacterized protein lp_3323	A, B, C	232	Lactiplantibacillus plantarum	Mutation(s): 0

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
SO4	D [auth A], E [auth A], I [auth C]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L
MG	G [auth B]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N
NA	F [auth B], H [auth C]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N

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

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.12 Å
• R-Value Free:  0.224 (Depositor), 0.227 (DCC) 
• R-Value Work:  0.184 (Depositor), 0.186 (DCC) 
• R-Value Observed: 0.186 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 48.61	α = 90
b = 101.44	β = 90
c = 125.55	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
HKL-2000	data collection
HKL-2000	data reduction
SCALEPACK	data scaling
SnB	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2008-08-05 
Deposition Author(s): Kuzin, A.P., Abashidze, M., Vorobiev, S.M., Seetharaman, J., Zhao, L., Mao, L., Ciccosanti, C., Xiao, R., Nair, R., Baran, M.C., Acton, T.B., Rost, B., Montelione, G.T., Hunt, J.F., Tong, L., Northeast Structural Genomics Consortium (NESG)

Revision History  

• Version 1.0: 2008-08-05
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Refinement description, 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