3DC7 | pdb_00003dc7

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)

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)

wwPDB Validation 3D Report Full Report

This is version 1.3 of the entry. See complete history.

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.

Macromolecule Content

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

Macromolecules

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| 3D Structure

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	3D Interactions
SO4 Query on SO4 Download:Ideal Coordinates CCD File SDF format, chain D [auth A] SDF format, chain E [auth A] SDF format, chain I [auth C] MOL2 format, chain D [auth A] MOL2 format, chain E [auth A] MOL2 format, chain I [auth C] mmCIF format, chain D [auth A] mmCIF format, chain E [auth A] mmCIF format, chain I [auth C]	D [auth A], E [auth A], I [auth C]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain D [auth A] Focus chain E [auth A] Focus chain I [auth C] Interactions & Density Focus chain D [auth A] Focus chain E [auth A] Focus chain I [auth C]
MG Query on MG Download:Ideal Coordinates CCD File SDF format, chain G [auth B] MOL2 format, chain G [auth B] mmCIF format, chain G [auth B]	G [auth B]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain G [auth B] Interactions & Density Focus chain G [auth B]
NA Query on NA Download:Ideal Coordinates CCD File SDF format, chain F [auth B] SDF format, chain H [auth C] MOL2 format, chain F [auth B] MOL2 format, chain H [auth C] mmCIF format, chain F [auth B] mmCIF format, chain H [auth C]	F [auth B], H [auth C]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N		Interactions Focus chain F [auth B] Focus chain H [auth C] Interactions & Density Focus chain F [auth B] Focus chain H [auth C]

Modified Residues 1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
MSE Query on 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

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View more in-depth experimental data

Entry History

Deposition Data

Released Date: 2008-08-05

Deposition Author(s):

Northeast Structural Genomics Consortium (NESG)

Revision History (Full details and data files)

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