4MK6 | pdb_00004mk6

Crystal Structure of Probable Dihydroxyacetone Kinase Regulator DHSK_reg from Listeria monocytogenes EGD-e

PDB DOI: https://doi.org/10.2210/pdb4MK6/pdb

Classification: TRANSCRIPTION REGULATOR
Organism(s): Listeria monocytogenes EGD-e
Expression System: Escherichia coli BL21
Mutation(s): No

Deposited: 2013-09-04 Released: 2013-09-18
Deposition Author(s): Kim, Y., Wu, R., Clancy, S., Joachimiak, A., Midwest Center for Structural Genomics (MCSG)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.35 Å
R-Value Free:
0.232 (Depositor), 0.235 (DCC)
R-Value Work:
0.197 (Depositor), 0.200 (DCC)
R-Value Observed:
0.198 (Depositor)

wwPDB Validation 3D Report Full Report

Validation slider image for 4MK6

This is version 1.1 of the entry. See complete history.

Literature

Crystal Structure of Probable Dihydroxyacetone Kinase Regulator DHSK_reg from Listeria monocytogenes EGD-e

Kim, Y., Wu, R., Clancy, S., Joachimiak, A., Midwest Center for Structural Genomics (MCSG)

To be published.

Macromolecule Content

Total Structure Weight: 22.15 kDa
Atom Count: 1,573
Modeled Residue Count: 188
Deposited Residue Count: 189
Unique protein chains: 1

Macromolecules

Find similar proteins by:

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Probable Dihydroxyacetone Kinase Regulator DHSK_reg	A	189	Listeria monocytogenes EGD-e	Mutation(s): 0 Gene Names: lmo0480
UniProt
Find proteins for Q8Y9P4 (Listeria monocytogenes serovar 1/2a (strain ATCC BAA-679 / EGD-e)) Explore Q8Y9P4 Go to UniProtKB: Q8Y9P4
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q8Y9P4
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
EDO Query on EDO Download:Ideal Coordinates CCD File SDF format, chain C [auth A] SDF format, chain B [auth A] MOL2 format, chain C [auth A] MOL2 format, chain B [auth A] mmCIF format, chain C [auth A] mmCIF format, chain B [auth A]	B [auth A], C [auth A]	1,2-ETHANEDIOL C₂ H₆ O₂ LYCAIKOWRPUZTN-UHFFFAOYSA-N		Interactions Focus chain B [auth A] Focus chain C [auth A] Interactions & Density Focus chain B [auth A] Focus chain C [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: 2.35 Å
R-Value Free: 0.232 (Depositor), 0.235 (DCC)
R-Value Work: 0.197 (Depositor), 0.200 (DCC)
R-Value Observed: 0.198 (Depositor)

Space Group: P 6₁ 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 77.039	α = 90
b = 77.039	β = 90
c = 142.027	γ = 120

Software Package:

Software Name	Purpose
SBC-Collect	data collection
HKL-3000	data collection
HKL-3000	phasing
SHELXS	phasing
MLPHARE	phasing
DM	model building
PHENIX	refinement
HKL-3000	data reduction
HKL-3000	data scaling
DM	phasing

Structure Validation

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View more in-depth experimental data

Entry History

Deposition Data

Released Date: 2013-09-18

Deposition Author(s):

Midwest Center for Structural Genomics (MCSG)

Revision History (Full details and data files)

Version 1.0: 2013-09-18
Type: Initial release
Version 1.1: 2024-10-09
Changes: Data collection, Database references, Derived calculations, 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.