3HFQ | pdb_00003hfq

Crystal structure of the lp_2219 protein from Lactobacillus plantarum. Northeast Structural Genomics Consortium Target LpR118.

PDB DOI: https://doi.org/10.2210/pdb3HFQ/pdb

Classification: structural genomics, unknown function
Organism(s): Lactiplantibacillus plantarum
Expression System: Escherichia coli BL21(DE3)
Mutation(s): Yes

Deposited: 2009-05-12 Released: 2009-05-26
Deposition Author(s): Vorobiev, S.M., Scott, L., Schauder, C., Xiao, R., Ciccosanti, C., Foote, E.L., Maglaqui, M., Everett, J.K., Nair, R., 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: 1.96 Å
R-Value Free:
0.178 (Depositor), 0.174 (DCC)
R-Value Work:
0.169 (Depositor), 0.165 (DCC)
R-Value Observed:
0.170 (Depositor)

wwPDB Validation 3D Report Full Report

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

Literature

Crystal structure of the lp_2219 protein from Lactobacillus plantarum.

Vorobiev, S.M., Scott, L., Schauder, C., Xiao, R., Ciccosanti, C., Foote, E.L., Maglaqui, M., Everett, J.K., Nair, R., Acton, T.B., Rost, B., Montelione, G.T., Tong, L., Hunt, J.F.

To be published.

Macromolecule Content

Total Structure Weight: 75.82 kDa
Atom Count: 5,584
Modeled Residue Count: 682
Deposited Residue Count: 694
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
uncharacterized protein lp_2219	A, B	347	Lactiplantibacillus plantarum	Mutation(s): 1 Gene Names: lp_2219 EC: 3.1.1.31
UniProt
Find proteins for F9UQE3 (Lactiplantibacillus plantarum (strain ATCC BAA-793 / NCIMB 8826 / WCFS1)) Explore F9UQE3 Go to UniProtKB: F9UQE3
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	F9UQE3
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
PO4 Query on PO4 Download:Ideal Coordinates CCD File SDF format, chain D [auth B] SDF format, chain C [auth A] MOL2 format, chain D [auth B] MOL2 format, chain C [auth A] mmCIF format, chain D [auth B] mmCIF format, chain C [auth A]	C [auth A], D [auth B]	PHOSPHATE ION O₄ P NBIIXXVUZAFLBC-UHFFFAOYSA-K		Interactions Focus chain C [auth A] Focus chain D [auth B] Interactions & Density Focus chain C [auth A] Focus chain D [auth B]

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

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.96 Å
R-Value Free: 0.178 (Depositor), 0.174 (DCC)
R-Value Work: 0.169 (Depositor), 0.165 (DCC)
R-Value Observed: 0.170 (Depositor)

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 78.543	α = 90
b = 54.029	β = 104.18
c = 79.584	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
PDB_EXTRACT	data extraction
HKL-2000	data collection
HKL-2000	data reduction
HKL-2000	data scaling
SHELXDE	phasing
RESOLVE	phasing
REFMAC	refinement

Structure Validation

View Full Validation Report

View more in-depth experimental data

Entry History

Deposition Data

Released Date: 2009-05-26

Deposition Author(s):

Northeast Structural Genomics Consortium (NESG)

Revision History (Full details and data files)

Version 1.0: 2009-05-26
Type: Initial release
Version 1.1: 2011-07-13
Changes: Version format compliance
Version 1.2: 2019-07-24
Changes: Data collection, Derived calculations, Refinement description
Version 1.3: 2021-10-13
Changes: Database references, Derived calculations
Version 1.4: 2024-11-06
Changes: Data collection, Structure summary