9GDK | pdb_00009gdk

Jumonji domain-containing protein 1C with crystallization epitope mutations L2440Y:G2444H

PDB DOI: https://doi.org/10.2210/pdb9GDK/pdb

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

Deposited: 2024-08-05 Released: 2024-08-21
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., Structural Genomics Consortium (SGC)
Funding Organization(s): Not funded

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.78 Å
R-Value Free:
0.242 (Depositor), 0.241 (DCC)
R-Value Work:
0.209 (Depositor), 0.210 (DCC)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

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This is version 1.1 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., Damerell, D., Krojer, T., Yue, W., Burgess-Brown, N., Marsden, B., von Delft, F.

To be published.

Macromolecule Content

Total Structure Weight: 79.9 kDa
Atom Count: 5,918
Modeled Residue Count: 679
Deposited Residue Count: 696
Unique protein chains: 1

Macromolecules

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Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Probable JmjC domain-containing histone demethylation protein 2C	A, B	348	Homo sapiens	Mutation(s): 2 Gene Names: JMJD1C, JHDM2C, KIAA1380, TRIP8 EC: 1.14.11
UniProt & NIH Common Fund Data Resources
Find proteins for Q15652 (Homo sapiens) Explore Q15652 Go to UniProtKB: Q15652
PHAROS: Q15652 GTEx: ENSG00000171988
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q15652
Sequence Annotations Expand
Reference Sequence

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.78 Å
R-Value Free: 0.242 (Depositor), 0.241 (DCC)
R-Value Work: 0.209 (Depositor), 0.210 (DCC)

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 45.2	α = 90
b = 98.25	β = 92.04
c = 87.4	γ = 90

Software Package:

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

Structure Validation

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Entry History

& Funding Information

Deposition Data

Released Date: 2024-08-21

Deposition Author(s):

Strain-Damerell, C.

Mackinnon, S.R.

Arrowsmith, C.H.

Burgess-Brown, N.

Structural Genomics Consortium (SGC)

Funding Organization	Location	Grant Number
Not funded		--

Revision History (Full details and data files)

Version 1.0: 2024-08-21
Type: Initial release
Version 1.1: 2024-11-06
Changes: 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.