2P0Y | pdb_00002p0y

Crystal structure of Q88YI3_LACPL from Lactobacillus plantarum. Northeast Structural Genomics Consortium target LpR6

PDB DOI: https://doi.org/10.2210/pdb2P0Y/pdb

Classification: STRUCTURAL GENOMICS, UNKNOWN FUNCTION
Organism(s): Lactiplantibacillus plantarum
Expression System: Escherichia coli
Mutation(s): Yes

Deposited: 2007-03-01 Released: 2007-03-27
Deposition Author(s): Benach, J., Chen, Y., Seetharaman, J., Chi, K.H., Janjua, H., Cunningham, K., Ma, L.C., Xiao, R., Liu, J., Baran, M.C., Acton, T.B., Rost, B., Montelione, G.T., Tong, L., Hunt, J.F., Northeast Structural Genomics Consortium (NESG)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 3.00 Å
R-Value Free:
0.339 (Depositor), 0.333 (DCC)
R-Value Work:
0.274 (Depositor), 0.284 (DCC)

wwPDB Validation 3D Report Full Report

This is version 1.4 of the entry. See complete history.

Literature

Crystal structure of Q88YI3_LACPL from Lactobacillus plantarum.

Benach, J., Chen, Y., Seetharaman, J., Chi, K.H., Janjua, H., Cunningham, K., Ma, L.C., Xiao, R., Liu, J., Baran, M.C., Acton, T.B., Rost, B., Montelione, G.T., Tong, L., Hunt, J.F.

To be published.

Macromolecule Content

Total Structure Weight: 38.14 kDa
Atom Count: 1,855
Modeled Residue Count: 240
Deposited Residue Count: 341
Unique protein chains: 1

Macromolecules

Find similar proteins by:

| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Hypothetical protein lp_0780	A	341	Lactiplantibacillus plantarum	Mutation(s): 9 Gene Names: lp_0780
UniProt
Find proteins for F9UM03 (Lactiplantibacillus plantarum (strain ATCC BAA-793 / NCIMB 8826 / WCFS1)) Explore F9UM03 Go to UniProtKB: F9UM03
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	F9UM03
Sequence Annotations Expand
Reference Sequence

Small Molecules

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

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 3.00 Å
R-Value Free: 0.339 (Depositor), 0.333 (DCC)
R-Value Work: 0.274 (Depositor), 0.284 (DCC)

Space Group: C 2 2 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 70.658	α = 90
b = 78.13	β = 90
c = 149.559	γ = 90

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
RESOLVE	phasing
CNS	refinement
PDB_EXTRACT	data extraction
ADSC	data collection
HKL-2000	data reduction
SnB	phasing

Structure Validation

View Full Validation Report

View more in-depth experimental data

Entry History

Deposition Data

Released Date: 2007-03-27

Deposition Author(s):

Northeast Structural Genomics Consortium (NESG)

Revision History (Full details and data files)

Version 1.0: 2007-03-27
Type: Initial release
Version 1.1: 2008-05-01
Changes: Version format compliance
Version 1.2: 2011-07-13
Changes: Version format compliance
Version 1.3: 2017-10-18
Changes: Refinement description
Version 1.4: 2024-11-20
Changes: Data collection, Database references, Derived calculations, Structure summary