3K17 | pdb_00003k17

Crystal structure of a Lin0012 protein from Listeria innocua

PDB DOI: https://doi.org/10.2210/pdb3K17/pdb

Classification: TRANSFERASE
Organism(s): Listeria innocua
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2009-09-25 Released: 2009-10-06
Deposition Author(s): Palani, K., Burley, S.K., Swaminathan, S., New York SGX Research Center for Structural Genomics (NYSGXRC)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.10 Å
R-Value Free:
0.252 (Depositor), 0.251 (DCC)
R-Value Work:
0.223 (Depositor), 0.222 (DCC)
R-Value Observed:
0.223 (Depositor)

wwPDB Validation 3D Report Full Report

Validation slider image for 3K17

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

Literature

Crystal structure of a Lin0012 protein from Listeria innocua

Palani, K., Burley, S.K., Swaminathan, S.

To be published.

Macromolecule Content

Total Structure Weight: 164.66 kDa
Atom Count: 11,491
Modeled Residue Count: 1,420
Deposited Residue Count: 1,460
Unique protein chains: 1

Macromolecules

Find similar proteins by:

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Lin0012 protein	A, B, C, D	365	Listeria innocua	Mutation(s): 0 Gene Names: lin0012 EC: 2.7.4.2
UniProt
Find proteins for Q92FU1 (Listeria innocua serovar 6a (strain ATCC BAA-680 / CLIP 11262)) Explore Q92FU1 Go to UniProtKB: Q92FU1
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q92FU1
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
PGE Query on PGE Download:Ideal Coordinates CCD File SDF format, chain E [auth A] MOL2 format, chain E [auth A] mmCIF format, chain E [auth A]	E [auth A]	TRIETHYLENE GLYCOL C₆ H₁₄ O₄ ZIBGPFATKBEMQZ-UHFFFAOYSA-N		Interactions Focus chain E [auth A] Interactions & Density Focus chain E [auth A]

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: 2.10 Å
R-Value Free: 0.252 (Depositor), 0.251 (DCC)
R-Value Work: 0.223 (Depositor), 0.222 (DCC)
R-Value Observed: 0.223 (Depositor)

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 105.966	α = 90
b = 122.362	β = 90
c = 138	γ = 90

Software Package:

Software Name	Purpose
CNS	refinement
CBASS	data collection
HKL-2000	data reduction
HKL-2000	data scaling
SHELXD	phasing
SHARP	phasing
ARP/wARP	model building

Structure Validation

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View more in-depth experimental data

Entry History

Deposition Data

Released Date: 2009-10-06

Deposition Author(s):

Swaminathan, S.

New York SGX Research Center for Structural Genomics (NYSGXRC)

Revision History (Full details and data files)

Version 1.0: 2009-10-06
Type: Initial release
Version 1.1: 2011-07-13
Changes: Version format compliance
Version 1.2: 2021-02-10
Changes: Database references, Derived calculations, Structure summary
Version 1.3: 2024-11-27
Changes: Data collection, Database references, Structure summary

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RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.