9T2D | pdb_00009t2d

Jumonji domain-containing protein 2B with crystallization epitope mutations L916G:R917A:A918D

PDB DOI: https://doi.org/10.2210/pdb9T2D/pdb

Classification: OXIDOREDUCTASE
Organism(s): Homo sapiens
Expression System: Escherichia coli
Mutation(s): Yes

Deposited: 2025-10-22 Released: 2025-12-03
Deposition Author(s): Fairhead, M., Strain-Damerell, C., Ye, M., Mackinnon, S.R., Pinkas, D., MacLean, E.M., Koekemoer, L., Damerell, D., Krojer, T., Arrowsmith, C.H., Edwards, A., Bountra, C., Yue, W., Burgess-Brown, N., Marsden, B., von Delft, F.
Funding Organization(s): The Structural Genomics Consortium (SGC)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.80 Å
R-Value Free:
0.255 (Depositor), 0.252 (DCC)
R-Value Work:
0.237 (Depositor), 0.229 (DCC)
R-Value Observed:
0.238 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Validation slider image for 9T2D

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

Literature

A fast, parallel method for efficiently exploring crystallization behaviour of large numbers of protein variants

Fairhead, M., Strain-Damerell, C., Ye, M., Mackinnon, S.R., Pinkas, D., MacLean, E.M., Koekemoer, L., Damerell, D., Krojer, T., Arrowsmith, C.H., Edwards, A., Bountra, C., Yue, W., Burgess-Brown, N., Marsden, B., von Delft, F.

To be published.

Macromolecule Content

Total Structure Weight: 15.33 kDa
Atom Count: 1,137
Modeled Residue Count: 128
Deposited Residue Count: 132
Unique protein chains: 1

Macromolecules

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Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Lysine-specific demethylase 4B	A	132	Homo sapiens	Mutation(s): 3 Gene Names: KDM4B, JHDM3B, JMJD2B, KIAA0876 EC: 1.14.11.66
UniProt & NIH Common Fund Data Resources
Find proteins for O94953 (Homo sapiens) Explore O94953 Go to UniProtKB: O94953
PHAROS: O94953 GTEx: ENSG00000127663
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	O94953
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
PEG Query on PEG Download:Ideal Coordinates CCD File SDF format, chain I [auth A] SDF format, chain H [auth A] MOL2 format, chain I [auth A] MOL2 format, chain H [auth A] mmCIF format, chain I [auth A] mmCIF format, chain H [auth A]	H [auth A], I [auth A]	DI(HYDROXYETHYL)ETHER C₄ H₁₀ O₃ MTHSVFCYNBDYFN-UHFFFAOYSA-N		Interactions Focus chain H [auth A] Focus chain I [auth A] Interactions & Density Focus chain H [auth A] Focus chain I [auth A]
EDO Query on EDO Download:Ideal Coordinates CCD File SDF format, chain G [auth A] SDF format, chain F [auth A] SDF format, chain E [auth A] SDF format, chain D [auth A] SDF format, chain C [auth A] SDF format, chain B [auth A] MOL2 format, chain G [auth A] MOL2 format, chain F [auth A] MOL2 format, chain E [auth A] MOL2 format, chain D [auth A] MOL2 format, chain C [auth A] MOL2 format, chain B [auth A] mmCIF format, chain G [auth A] mmCIF format, chain F [auth A] mmCIF format, chain E [auth A] mmCIF format, chain D [auth A] mmCIF format, chain C [auth A] mmCIF format, chain B [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]	1,2-ETHANEDIOL C₂ H₆ O₂ LYCAIKOWRPUZTN-UHFFFAOYSA-N		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]
NH4 Query on NH4 Download:Ideal Coordinates CCD File SDF format, chain J [auth A] MOL2 format, chain J [auth A] mmCIF format, chain J [auth A]	J [auth A]	AMMONIUM ION H₄ N QGZKDVFQNNGYKY-UHFFFAOYSA-O		Interactions Focus chain J [auth A] Interactions & Density Focus chain J [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.80 Å
R-Value Free: 0.255 (Depositor), 0.252 (DCC)
R-Value Work: 0.237 (Depositor), 0.229 (DCC)
R-Value Observed: 0.238 (Depositor)

Space Group: H 3 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 88.85	α = 90
b = 88.85	β = 90
c = 143.86	γ = 120

Software Package:

Software Name	Purpose
BUSTER	refinement
xia2	data reduction
xia2	data scaling
PHASER	phasing

Structure Validation

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Entry History

& Funding Information

Deposition Data

Released Date: 2025-12-03

Deposition Author(s):

Strain-Damerell, C.

Mackinnon, S.R.

Arrowsmith, C.H.

Burgess-Brown, N.

Funding Organization	Location	Grant Number
The Structural Genomics Consortium (SGC)	Canada	--

Revision History (Full details and data files)

Version 1.0: 2025-12-03
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.