9X07 | pdb_00009x07

Serial Femtosecond Crystallography Structure of Myoglobin from equine skeletal muscle

PDB DOI: https://doi.org/10.2210/pdb9X07/pdb

Classification: OXYGEN STORAGE
Organism(s): Equus caballus
Mutation(s): No

Deposited: 2025-09-30 Released: 2025-11-12
Deposition Author(s): Nam, K.H.
Funding Organization(s): National Research Foundation (NRF, Korea)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.30 Å
R-Value Free:
0.317 (Depositor), 0.318 (DCC)
R-Value Work:
0.247 (Depositor), 0.247 (DCC)
R-Value Observed:
0.254 (Depositor)

Starting Model: experimental
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Ligand Structure Quality Assessment

This is version 1.0 of the entry. See complete history.

Literature

Preliminary Serial Femtosecond Crystallography Studies of Myoglobin from Equine Skeletal Muscle

Park, J., Park, S., Nam, K.H.

(2025) Crystals (Basel) 15

DOI: https://doi.org/10.3390/cryst15100905

Macromolecule Content

Total Structure Weight: 17.51 kDa
Atom Count: 1,287
Modeled Residue Count: 151
Deposited Residue Count: 151
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Myoglobin	A	151	Equus caballus	Mutation(s): 0 EC: 1.7 (PDB Primary Data), 1.11.1 (PDB Primary Data)
UniProt
Find proteins for P68082 (Equus caballus) Explore P68082 Go to UniProtKB: P68082
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P68082
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] MOL2 format, chain C [auth A] mmCIF format, chain C [auth A]	C [auth A]	PROTOPORPHYRIN IX CONTAINING FE C₃₄ H₃₂ Fe N₄ O₄ KABFMIBPWCXCRK-RGGAHWMASA-L		Interactions Focus chain C [auth A] Interactions & Density Focus chain C [auth A]
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: 2.30 Å
R-Value Free: 0.317 (Depositor), 0.318 (DCC)
R-Value Work: 0.247 (Depositor), 0.247 (DCC)
R-Value Observed: 0.254 (Depositor)

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 63.69	α = 90
b = 28.62	β = 107.19
c = 35.59	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
CrystFEL	data scaling
CrystFEL	data reduction
PHASER	phasing
PDB_EXTRACT	data extraction

Structure Validation

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Ligand Structure Quality Assessment

Entry History & Funding Information

Deposition Data

Released Date: 2025-11-12

Deposition Author(s):

Funding Organization	Location	Grant Number
National Research Foundation (NRF, Korea)	Korea, Republic Of	NRF-2021R1I1A1A01050838

Revision History (Full details and data files)

Version 1.0: 2025-11-12
Type: Initial release

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.