6N39 | pdb_00006n39

Crystal structure of an dephospho-CoA kinase CoaE from Mycobacterium paratuberculosis

PDB DOI: https://doi.org/10.2210/pdb6N39/pdb

Classification: TRANSFERASE
Organism(s): Mycobacterium avium subsp. paratuberculosis K-10
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2018-11-14 Released: 2018-11-21
Deposition Author(s): Seattle Structural Genomics Center for Infectious Disease (SSGCID)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.15 Å
R-Value Free:
0.193 (Depositor), 0.197 (DCC)
R-Value Work:
0.170 (Depositor), 0.174 (DCC)
R-Value Observed:
0.171 (Depositor)

wwPDB Validation 3D Report Full Report

Validation slider image for 6N39

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

Literature

Crystal structure of an dephospho-CoA kinase CoaE from Mycobacterium paratuberculosis

Mayclin, S.J., Irwin, R.M., Abendroth, J., Horanyi, P.S., Lorimer, D.D., Edwards, T.E.

To be published.

Macromolecule Content

Total Structure Weight: 45.59 kDa
Atom Count: 3,381
Modeled Residue Count: 404
Deposited Residue Count: 415
Unique protein chains: 1

Macromolecules

Find similar proteins by:

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Dephospho-CoA kinase	A	415	Mycobacterium avium subsp. paratuberculosis K-10	Mutation(s): 0 Gene Names: coaE, MAP_1326 EC: 2.7.1.24
UniProt
Find proteins for Q740M4 (Mycolicibacterium paratuberculosis (strain ATCC BAA-968 / K-10)) Explore Q740M4 Go to UniProtKB: Q740M4
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q740M4
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
ACT Query on ACT Download:Ideal Coordinates CCD File SDF format, chain B [auth A] SDF format, chain C [auth A] SDF format, chain D [auth A] SDF format, chain E [auth A] SDF format, chain F [auth A] SDF format, chain G [auth A] MOL2 format, chain B [auth A] MOL2 format, chain C [auth A] MOL2 format, chain D [auth A] MOL2 format, chain E [auth A] MOL2 format, chain F [auth A] MOL2 format, chain G [auth A] mmCIF format, chain B [auth A] mmCIF format, chain C [auth A] mmCIF format, chain D [auth A] mmCIF format, chain E [auth A] mmCIF format, chain F [auth A] mmCIF format, chain G [auth A]	B [auth A] C [auth A] D [auth A] E [auth A] F [auth A] B [auth A], C [auth A], D [auth A], E [auth A], F [auth A], G [auth A]	ACETATE ION C₂ H₃ O₂ QTBSBXVTEAMEQO-UHFFFAOYSA-M		Interactions Focus chain B [auth A] Focus chain C [auth A] Focus chain D [auth A] Focus chain E [auth A] Focus chain F [auth A] Focus chain G [auth A] Interactions & Density Focus chain B [auth A] Focus chain C [auth A] Focus chain D [auth A] Focus chain E [auth A] Focus chain F [auth A] Focus chain G [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.15 Å
R-Value Free: 0.193 (Depositor), 0.197 (DCC)
R-Value Work: 0.170 (Depositor), 0.174 (DCC)
R-Value Observed: 0.171 (Depositor)

Diffraction Data:

Space Group: P 4₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 85.17	α = 90
b = 85.17	β = 90
c = 198.78	γ = 90

Software Package:

Software Name	Purpose
XDS	data reduction
XSCALE	data scaling
PHENIX	refinement
PDB_EXTRACT	data extraction
PHASER	phasing
BUCCANEER	phasing
ARP/wARP	model building

Structure Validation

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View more in-depth experimental data

Entry History

Deposition Data

Released Date: 2018-11-21

Deposition Author(s):

Seattle Structural Genomics Center for Infectious Disease (SSGCID)

Revision History (Full details and data files)

Version 1.0: 2018-11-21
Type: Initial release
Version 1.1: 2024-03-13
Changes: Data collection, Database references

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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.