7DCI | pdb_00007dci

Crystal structure of HSF2 DNA-binding domain in complex with 2-site HSE DNA in the head-to-head orientation

PDB DOI: https://doi.org/10.2210/pdb7DCI/pdb
NAKB: 7DCI

Classification: DNA BINDING PROTEIN/DNA
Organism(s): Homo sapiens
Expression System: DNA satellites
Mutation(s): Yes

Deposited: 2020-10-26 Released: 2021-07-14
Deposition Author(s): Wei, L., Wei, L.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.70 Å
R-Value Free:
0.209 (Depositor), 0.209 (DCC)
R-Value Work:
0.179 (Depositor), 0.180 (DCC)
R-Value Observed:
0.181 (Depositor)

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

Crystal structure of HSF2 DNA-binding domain in complex with 2-site HSE DNA in the head-to-head orientation

Wei, L., Wei, L.

To be published.

Macromolecule Content

Total Structure Weight: 16.07 kDa
Atom Count: 1,202
Modeled Residue Count: 105
Deposited Residue Count: 116
Unique protein chains: 1
Unique nucleic acid chains: 1

Macromolecules

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Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Heat shock factor protein 2	A	104	Homo sapiens	Mutation(s): 1 Gene Names: HSF2, HSTF2
UniProt & NIH Common Fund Data Resources
Find proteins for Q03933 (Homo sapiens) Explore Q03933 Go to UniProtKB: Q03933
PHAROS: Q03933 GTEx: ENSG00000025156
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q03933
Sequence Annotations Expand
Reference Sequence

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Molecule	Chains	Length	Organism	Image
Entity ID: 2
DNA (5'-D(GPGPGPAPAPTPAPTPTPCPCPC)-3')	B	12	Homo sapiens
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
NA (Subject of Investigation/LOI) Query on NA Download:Ideal Coordinates CCD File SDF format, chain C [auth A] MOL2 format, chain C [auth A] mmCIF format, chain C [auth A]	C [auth A]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N		Interactions Focus chain C [auth A] Interactions & Density Focus chain C [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.70 Å
R-Value Free: 0.209 (Depositor), 0.209 (DCC)
R-Value Work: 0.179 (Depositor), 0.180 (DCC)
R-Value Observed: 0.181 (Depositor)

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 92.268	α = 90
b = 38.472	β = 100.74
c = 38.654	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
PDB_EXTRACT	data extraction
HKL-2000	data reduction
HKL-2000	data scaling
PHENIX	phasing

Structure Validation

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Entry History

Deposition Data

Released Date: 2021-07-14

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2021-07-14
Type: Initial release
Version 1.1: 2023-11-29
Changes: Data collection, Database references, 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.