2XDP | pdb_00002xdp

Crystal structure of the tudor domain of human JMJD2C

PDB DOI: https://doi.org/10.2210/pdb2XDP/pdb

Classification: OXIDOREDUCTASE
Organism(s): Homo sapiens
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2010-05-06 Released: 2010-06-09
Deposition Author(s): Yue, W.W., Gileadi, C., Krojer, T., Weisbach, H., Ugochukwu, E., Daniel, M., Phillips, C., Chaikuad, A., von Delft, F., Allerston, C., Arrowsmith, C., Weigelt, J., Edwards, A., Bountra, C., Oppermann, U.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.56 Å
R-Value Free:
0.206 (Depositor), 0.210 (DCC)
R-Value Work:
0.186 (Depositor)
R-Value Observed:
0.187 (Depositor)

Starting Model: experimental
View more details

wwPDB Validation 3D Report Full Report

This is version 1.3 of the entry. See complete history.

Literature

Crystal Structure of the Tudor Domain of Human Jmjd2C

Yue, W.W., Gileadi, C., Krojer, T., Weisbach, H., Ugochukwu, E., Daniel, M., Phillips, C., Chaikuad, A., von Delft, F., Allerston, C., Arrowsmith, C., Weigelt, J., Edwards, A., Bountra, C., Oppermann, U.

To be published.

Macromolecule Content

Total Structure Weight: 14.25 kDa
Atom Count: 1,155
Modeled Residue Count: 119
Deposited Residue Count: 123
Unique protein chains: 1

Macromolecules

Find similar proteins by:

| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
LYSINE-SPECIFIC DEMETHYLASE 4C	A	123	Homo sapiens	Mutation(s): 0 EC: 1.14.11 (PDB Primary Data), 1.14.11.66 (UniProt)
UniProt & NIH Common Fund Data Resources
Find proteins for Q9H3R0 (Homo sapiens) Explore Q9H3R0 Go to UniProtKB: Q9H3R0
PHAROS: Q9H3R0 GTEx: ENSG00000107077
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q9H3R0
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
SO4 Query on SO4 Download:Ideal Coordinates CCD File SDF format, chain B [auth A] MOL2 format, chain B [auth A] mmCIF format, chain B [auth A]	B [auth A]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain B [auth A] Interactions & Density Focus chain B [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.56 Å
R-Value Free: 0.206 (Depositor), 0.210 (DCC)
R-Value Work: 0.186 (Depositor)
R-Value Observed: 0.187 (Depositor)

Space Group: I 2 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 52.815	α = 90
b = 79.646	β = 90
c = 81.614	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
MOSFLM	data reduction
SCALA	data scaling
PHASER	phasing

Structure Validation

View Full Validation Report

View more in-depth experimental data

Entry History

Deposition Data

Released Date: 2010-06-09

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2010-06-09
Type: Initial release
Version 1.1: 2012-12-05
Changes: Database references, Other, Source and taxonomy, Structure summary, Version format compliance
Version 1.2: 2018-01-24
Changes: Database references
Version 1.3: 2023-12-20
Changes: Data collection, Database references, Derived calculations, Other, Refinement description