3OWQ | pdb_00003owq

X-Ray Structure of Lin1025 protein from Listeria innocua, Northeast Structural Genomics Consortium Target LkR164

PDB DOI: https://doi.org/10.2210/pdb3OWQ/pdb

Classification: STRUCTURAL GENOMICS, UNKNOWN FUNCTION
Organism(s): Listeria innocua
Mutation(s): No

Deposited: 2010-09-20 Released: 2010-10-20
Deposition Author(s): Kuzin, A., Su, M., Lew, S., Seetharaman, J., Patel, P., Xiao, R., Ciccosanti, C., Lee, D., Everett, J.K., Nair, R., 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: 2.61 Å
R-Value Free:
0.260 (Depositor), 0.256 (DCC)
R-Value Work:
0.225 (Depositor), 0.222 (DCC)
R-Value Observed:
0.227 (Depositor)

wwPDB Validation 3D Report Full Report

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

Literature

Northeast Structural Genomics Consortium Target LkR164

Kuzin, A., Su, M., Lew, S., Seetharaman, J., Patel, P., Xiao, R., Ciccosanti, C., Lee, D., Everett, J.K., Nair, R., Acton, T.B., Rost, B., Montelione, G.T., Hunt, J.F., Tong, L.

To be published.

Macromolecule Content

Total Structure Weight: 143.86 kDa
Atom Count: 7,361
Modeled Residue Count: 944
Deposited Residue Count: 1,284
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Lin1025 protein	A, B, C, D	321	Listeria innocua	Mutation(s): 0 Gene Names: lin1025
UniProt
Find proteins for Q92CZ6 (Listeria innocua serovar 6a (strain ATCC BAA-680 / CLIP 11262)) Explore Q92CZ6 Go to UniProtKB: Q92CZ6
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q92CZ6
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
PEG Query on PEG Download:Ideal Coordinates CCD File SDF format, chain G [auth D] SDF format, chain F [auth C] SDF format, chain E [auth B] MOL2 format, chain G [auth D] MOL2 format, chain F [auth C] MOL2 format, chain E [auth B] mmCIF format, chain G [auth D] mmCIF format, chain F [auth C] mmCIF format, chain E [auth B]	E [auth B], F [auth C], G [auth D]	DI(HYDROXYETHYL)ETHER C₄ H₁₀ O₃ MTHSVFCYNBDYFN-UHFFFAOYSA-N		Interactions Focus chain E [auth B] Focus chain F [auth C] Focus chain G [auth D] Interactions & Density Focus chain E [auth B] Focus chain F [auth C] Focus chain G [auth D]

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

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.61 Å
R-Value Free: 0.260 (Depositor), 0.256 (DCC)
R-Value Work: 0.225 (Depositor), 0.222 (DCC)
R-Value Observed: 0.227 (Depositor)

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 56.51	α = 90
b = 157.041	β = 98.38
c = 57.277	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
PDB_EXTRACT	data extraction
ADSC	data collection
HKL-2000	data reduction
SCALA	data scaling
PHENIX	phasing

Structure Validation

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Entry History

Deposition Data

Released Date: 2010-10-20

Deposition Author(s):

Northeast Structural Genomics Consortium (NESG)

Revision History (Full details and data files)

Version 1.0: 2010-10-20
Type: Initial release
Version 1.1: 2011-07-13
Changes: Version format compliance
Version 1.2: 2012-02-22
Changes: Structure summary
Version 1.3: 2024-11-06
Changes: Data collection, Database references, Derived calculations, Structure summary