5YWM | pdb_00005ywm

Crystal structure of CK2a2 form-1

PDB DOI: https://doi.org/10.2210/pdb5YWM/pdb

Classification: TRANSFERASE
Organism(s): Homo sapiens
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2017-11-29 Released: 2018-12-05
Deposition Author(s): Tsuyuguchi, M., Kinoshita, T.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.94 Å
R-Value Free:
0.243 (Depositor), 0.248 (DCC)
R-Value Work:
0.191 (Depositor), 0.198 (DCC)
R-Value Observed:
0.195 (Depositor)

Starting Model: experimental
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This is version 1.1 of the entry. See complete history.

Literature

Crystal structure of human CK2a2 in a new crystal form at 1.89 angstrom resolution

Tsuyuguchi, M., Nakaniwa, T., Kinoshita, T.

To be published.

Macromolecule Content

Total Structure Weight: 40.48 kDa
Atom Count: 2,799
Modeled Residue Count: 313
Deposited Residue Count: 339
Unique protein chains: 1

Macromolecules

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Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Casein kinase II subunit alpha'	A [auth X]	339	Homo sapiens	Mutation(s): 0 Gene Names: CSNK2A2, CK2A2 EC: 2.7.11.1
UniProt & NIH Common Fund Data Resources
Find proteins for P19784 (Homo sapiens) Explore P19784 Go to UniProtKB: P19784
PHAROS: P19784 GTEx: ENSG00000070770
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P19784
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
NIO Query on NIO Download:Ideal Coordinates CCD File SDF format, chain D [auth X] MOL2 format, chain D [auth X] mmCIF format, chain D [auth X]	D [auth X]	NICOTINIC ACID C₆ H₅ N O₂ PVNIIMVLHYAWGP-UHFFFAOYSA-N		Interactions Focus chain D [auth X] Interactions & Density Focus chain D [auth X]
SO4 Query on SO4 Download:Ideal Coordinates CCD File SDF format, chain B [auth X] SDF format, chain C [auth X] MOL2 format, chain B [auth X] MOL2 format, chain C [auth X] mmCIF format, chain B [auth X] mmCIF format, chain C [auth X]	B [auth X], C [auth X]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain B [auth X] Focus chain C [auth X] Interactions & Density Focus chain B [auth X] Focus chain C [auth X]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.94 Å
R-Value Free: 0.243 (Depositor), 0.248 (DCC)
R-Value Work: 0.191 (Depositor), 0.198 (DCC)
R-Value Observed: 0.195 (Depositor)

Space Group: P 2₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 67.292	α = 90
b = 101.023	β = 90
c = 45.764	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data reduction
XDS	data scaling
PHASER	phasing

Structure Validation

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Entry History

Deposition Data

Released Date: 2018-12-05

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2018-12-05
Type: Initial release
Version 1.1: 2023-11-22
Changes: Data collection, Database references, Refinement description

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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.