7OON | pdb_00007oon

The X-ray structure of heme-bound murine HEBP1

PDB DOI: https://doi.org/10.2210/pdb7OON/pdb

Classification: APOPTOSIS
Organism(s): Mus musculus
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2021-05-28 Released: 2022-01-26
Deposition Author(s): McEwen, A.G., Poussin-Courmontagne, P., Birck, C., Goodfellow, B.J.
Funding Organization(s): French National Research Agency

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.80 Å
R-Value Free:
0.232 (Depositor), 0.231 (DCC)
R-Value Work:
0.210 (Depositor)
R-Value Observed:
0.211 (Depositor)

Starting Model: experimental
View more details

wwPDB Validation 3D Report Full Report

Validation slider image for 7OON

Ligand Structure Quality Assessment

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

Literature

The SOUL family of heme-binding proteins: Structure and function 15 years later

Goodfellow, B.J., Freire, F., Carvalho, A.L., Aveiro, S.S., Charbonnier, P., Moulis, J.M., Delgado, L., Ferreira, G.C., Rodrigues, J.E., Poussin-Courmontagne, P., Birck, C., McEwen, A., Macedo, A.L.

(2021) Coord Chem Rev 448: 214189

DOI: https://doi.org/10.1016/j.ccr.2021.214189

Macromolecule Content

Total Structure Weight: 42.46 kDa
Atom Count: 2,969
Modeled Residue Count: 369
Deposited Residue Count: 372
Unique protein chains: 1

Macromolecules

Find similar proteins by:

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Heme-binding protein 1	A, B	186	Mus musculus	Mutation(s): 0 Gene Names: Hebp1, Hbp
UniProt
Find proteins for Q9R257 (Mus musculus) Explore Q9R257 Go to UniProtKB: Q9R257
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q9R257
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
HEM (Subject of Investigation/LOI) Query on HEM Download:Ideal Coordinates CCD File SDF format, chain C [auth A] SDF format, chain F [auth B] MOL2 format, chain C [auth A] MOL2 format, chain F [auth B] mmCIF format, chain C [auth A] mmCIF format, chain F [auth B]	C [auth A], F [auth B]	PROTOPORPHYRIN IX CONTAINING FE C₃₄ H₃₂ Fe N₄ O₄ KABFMIBPWCXCRK-RGGAHWMASA-L		Interactions Focus chain C [auth A] Focus chain F [auth B] Interactions & Density Focus chain C [auth A] Focus chain F [auth B]
SO4 Query on SO4 Download:Ideal Coordinates CCD File SDF format, chain D [auth A] SDF format, chain E [auth A] MOL2 format, chain D [auth A] MOL2 format, chain E [auth A] mmCIF format, chain D [auth A] mmCIF format, chain E [auth A]	D [auth A], E [auth A]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain D [auth A] Focus chain E [auth A] Interactions & Density Focus chain D [auth A] Focus chain E [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.80 Å
R-Value Free: 0.232 (Depositor), 0.231 (DCC)
R-Value Work: 0.210 (Depositor)
R-Value Observed: 0.211 (Depositor)

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 63.493	α = 90
b = 79.492	β = 102.01
c = 85.074	γ = 90

Software Package:

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

Structure Validation

View Full Validation Report

Ligand Structure Quality Assessment

View more in-depth experimental data

Entry History

& Funding Information

Deposition Data

Released Date: 2022-01-26

Deposition Author(s):

Poussin-Courmontagne, P.

Goodfellow, B.J.

Funding Organization	Location	Grant Number
French National Research Agency	France	ANR-10-INSB-05-01

Revision History (Full details and data files)

Version 1.0: 2022-01-26
Type: Initial release
Version 1.1: 2024-01-31
Changes: Data collection, Database references, Refinement description

RCSB PDB is hosted by

RCSB PDB is a member of

RCSB Partners
Nucleic Acid Knowledgebase

CoreTrustSeal

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.