9WDJ | pdb_00009wdj

Crystal structure of PI5P4K beta apo form using low energy X-ray

PDB DOI: https://doi.org/10.2210/pdb9WDJ/pdb

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

Deposited: 2025-08-19 Released: 2026-09-02
Deposition Author(s): Senda, M., Takeuchi, K., Senda, T.
Funding Organization(s): Japan Agency for Medical Research and Development (AMED)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 3.15 Å
R-Value Free:
0.271 (Depositor), 0.271 (DCC)
R-Value Work:
0.210 (Depositor), 0.210 (DCC)
R-Value Observed:
0.213 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

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This is version 1.0 of the entry. See complete history.

Literature

Use of low-energy X-rays for MR-SAD phasing

Senda, M., Senda, T.

To be published.

Macromolecule Content

Total Structure Weight: 89.86 kDa
Atom Count: 4,720
Modeled Residue Count: 633
Deposited Residue Count: 786
Unique protein chains: 1

Macromolecules

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Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Phosphatidylinositol 5-phosphate 4-kinase type-2 beta	A, B	393	Homo sapiens	Mutation(s): 0 Gene Names: PIP4K2B, PIP5K2B EC: 2.7.1.149
UniProt & NIH Common Fund Data Resources
Find proteins for P78356 (Homo sapiens) Explore P78356 Go to UniProtKB: P78356
PHAROS: P78356 GTEx: ENSG00000276293
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P78356
Sequence Annotations Expand
Reference Sequence

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 3.15 Å
R-Value Free: 0.271 (Depositor), 0.271 (DCC)
R-Value Work: 0.210 (Depositor), 0.210 (DCC)
R-Value Observed: 0.213 (Depositor)

Space Group: C 2 2 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 106.924	α = 90
b = 184.032	β = 90
c = 105.494	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data reduction
Aimless	data scaling
MOLREP	phasing

Structure Validation

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Entry History

& Funding Information

Deposition Data

Released Date: 2026-09-02

Deposition Author(s):

Funding Organization	Location	Grant Number
Japan Agency for Medical Research and Development (AMED)	Japan	JP23am0100001

Revision History (Full details and data files)

Version 1.0: 2026-09-02
Type: Initial release

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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.