3K7X | pdb_00003k7x

Crystal structure of the Lin0763 protein from Listeria innocua. Northeast Structural Genomics Consortium Target LkR23.

PDB DOI: https://doi.org/10.2210/pdb3K7X/pdb

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

Deposited: 2009-10-13 Released: 2009-10-27
Deposition Author(s): Vorobiev, S., Su, M., Seetharaman, J., Maglaqui, M., Ciccosanti, C., Buchwald, W.A., Sahdev, S., Xiao, R., Acton, T.B., Montelione, G.T., Tong, L., Hunt, J.F., Northeast Structural Genomics Consortium (NESG)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.89 Å
R-Value Free:
0.184 (Depositor), 0.176 (DCC)
R-Value Work:
0.167 (Depositor), 0.159 (DCC)
R-Value Observed:
0.168 (Depositor)

wwPDB Validation 3D Report Full Report

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

Literature

Crystal structure of the Lin0763 protein from Listeria innocua.

Vorobiev, S., Su, M., Seetharaman, J., Maglaqui, M., Ciccosanti, C., Buchwald, W.A., Sahdev, S., Xiao, R., Acton, T.B., Montelione, G.T., Tong, L., Hunt, J.F.

To be published.

Macromolecule Content

Total Structure Weight: 41.53 kDa
Atom Count: 3,332
Modeled Residue Count: 348
Deposited Residue Count: 349
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Lin0763 protein	A	349	Listeria innocua	Mutation(s): 1 Gene Names: lin0763
UniProt
Find proteins for Q92DQ0 (Listeria innocua serovar 6a (strain ATCC BAA-680 / CLIP 11262)) Explore Q92DQ0 Go to UniProtKB: Q92DQ0
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q92DQ0
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 B [auth A] MOL2 format, chain B [auth A] mmCIF format, chain B [auth A]	B [auth A]	PHOSPHATE ION O₄ P NBIIXXVUZAFLBC-UHFFFAOYSA-K		Interactions Focus chain B [auth A] Interactions & Density Focus chain B [auth A]

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: 1.89 Å
R-Value Free: 0.184 (Depositor), 0.176 (DCC)
R-Value Work: 0.167 (Depositor), 0.159 (DCC)
R-Value Observed: 0.168 (Depositor)

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 46.194	α = 90
b = 75.333	β = 95.28
c = 53.756	γ = 90

Software Package:

Software Name	Purpose
HKL-2000	data collection
SnB	phasing
RESOLVE	model building
PHENIX	refinement
HKL-2000	data reduction
HKL-2000	data scaling
RESOLVE	phasing

Structure Validation

View Full Validation Report

View more in-depth experimental data

Entry History

Deposition Data

Released Date: 2009-10-27

Deposition Author(s):

Northeast Structural Genomics Consortium (NESG)

Revision History (Full details and data files)

Version 1.0: 2009-10-27
Type: Initial release
Version 1.1: 2011-07-13
Changes: Version format compliance
Version 1.2: 2017-10-25
Changes: Author supporting evidence, Refinement description
Version 1.3: 2021-10-13
Changes: Database references, Derived calculations
Version 1.4: 2024-11-06
Changes: Data collection, Structure summary