6GDJ | pdb_00006gdj

Crystal structure of Mto2 twin-cysteine dimerisation domain

PDB DOI: https://doi.org/10.2210/pdb6GDJ/pdb

Classification: STRUCTURAL PROTEIN
Organism(s): Schizosaccharomyces pombe
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2018-04-23 Released: 2019-05-01
Deposition Author(s): Thakur, H.C., Sawin, K.E., Cook, A.G.
Funding Organization(s): Wellcome Trust

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.50 Å
R-Value Free:
0.183 (Depositor), 0.183 (DCC)
R-Value Work:
0.152 (Depositor), 0.153 (DCC)
R-Value Observed:
0.154 (Depositor)

wwPDB Validation 3D Report Full Report

Validation slider image for 6GDJ

This is version 1.1 of the entry. See complete history.

Literature

Crystal structure of Mto2 twin-cysteine dimerisation domain

Thakur, H.C., Sawin, K.E., Cook, A.G.

To be published.

Macromolecule Content

Total Structure Weight: 18.95 kDa
Atom Count: 1,101
Modeled Residue Count: 140
Deposited Residue Count: 176
Unique protein chains: 1

Macromolecules

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Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Mto2	A, B	88	Schizosaccharomyces pombe	Mutation(s): 0 Gene Names: SPBC902.06
UniProt
Find proteins for Q9USP7 (Schizosaccharomyces pombe (strain 972 / ATCC 24843)) Explore Q9USP7 Go to UniProtKB: Q9USP7
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q9USP7
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
GOL Query on GOL Download:Ideal Coordinates CCD File SDF format, chain D [auth B] SDF format, chain C [auth A] MOL2 format, chain D [auth B] MOL2 format, chain C [auth A] mmCIF format, chain D [auth B] mmCIF format, chain C [auth A]	C [auth A], D [auth B]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain C [auth A] Focus chain D [auth B] Interactions & Density Focus chain C [auth A] Focus chain D [auth B]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.50 Å
R-Value Free: 0.183 (Depositor), 0.183 (DCC)
R-Value Work: 0.152 (Depositor), 0.153 (DCC)
R-Value Observed: 0.154 (Depositor)

Space Group: P 6₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 73.704	α = 90
b = 73.704	β = 90
c = 54.363	γ = 120

Software Package:

Software Name	Purpose
REFMAC	refinement
XDS	data reduction
SCALA	data scaling
PHASER	phasing

Structure Validation

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View more in-depth experimental data

Entry History

& Funding Information

Deposition Data

Released Date: 2019-05-01

Deposition Author(s):

Funding Organization	Location	Grant Number
Wellcome Trust	United Kingdom	094517/z/10/z

Revision History (Full details and data files)

Version 1.0: 2019-05-01
Type: Initial release
Version 1.1: 2024-05-15
Changes: Data collection, Database references

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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.