7HI9 | pdb_00007hi9

PanDDA analysis group deposition of ground-state model of human Brachyury G177D variant

PDB DOI: https://doi.org/10.2210/pdb7HI9/pdb
Deposition Group: G_1002308 (ground state) | Explore G_1002308

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

Deposited: 2024-09-20 Released: 2024-10-16
Deposition Author(s): Newman, J.A., Gavard, A.E., Sherestha, L., Burgess-Brown, N.A., von Delft, F., Arrowsmith, C.H., Edwards, A., Bountra, C., Gileadi, O.
Funding Organization(s): Wellcome Trust

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.42 Å
R-Value Free:
0.223 (Depositor), 0.220 (DCC)
R-Value Work:
0.198 (Depositor), 0.206 (DCC)
R-Value Observed:
0.199 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Validation slider image for 7HI9

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

Literature

PanDDA analysis group deposition of ground-state model

Newman, J.A., Gavard, A.E., Sherestha, L., Burgess-Brown, N.A., von Delft, F., Arrowsmith, C.H., Edwards, A., Bountra, C., Gileadi, O.

To be published.

Macromolecule Content

Total Structure Weight: 19.78 kDa
Atom Count: 1,611
Modeled Residue Count: 171
Deposited Residue Count: 173
Unique protein chains: 1

Macromolecules

Find similar proteins by:

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
T-box transcription factor T	A	173	Homo sapiens	Mutation(s): 1 Gene Names: TBXT, T
UniProt & NIH Common Fund Data Resources
Find proteins for O15178 (Homo sapiens) Explore O15178 Go to UniProtKB: O15178
PHAROS: O15178 GTEx: ENSG00000164458
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	O15178
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
NA Query on NA 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]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N		Interactions Focus chain B [auth A] Interactions & Density Focus chain B [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.42 Å
R-Value Free: 0.223 (Depositor), 0.220 (DCC)
R-Value Work: 0.198 (Depositor), 0.206 (DCC)
R-Value Observed: 0.199 (Depositor)

Space Group: H 3 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 99.734	α = 90
b = 99.734	β = 90
c = 99.325	γ = 120

Software Package:

Software Name	Purpose
REFMAC	refinement
Aimless	data scaling
PDB_EXTRACT	data extraction
XDS	data reduction
REFMAC	phasing

Structure Validation

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Entry History

& Funding Information

Deposition Data

Released Date: 2024-10-16

Deposition Author(s):

Burgess-Brown, N.A.

Arrowsmith, C.H.

Funding Organization	Location	Grant Number
Wellcome Trust	United Kingdom	--

Revision History (Full details and data files)

Version 1.0: 2024-10-16
Type: Initial release
Version 1.1: 2026-02-18
Changes: Refinement description

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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.