9MT0 | pdb_00009mt0

1.2 A Crystal Structure of Housefly cytochrome c at pH 11

PDB DOI: https://doi.org/10.2210/pdb9MT0/pdb

Classification: ELECTRON TRANSPORT
Organism(s): Musca domestica
Mutation(s): No

Deposited: 2025-01-10 Released: 2025-02-12
Deposition Author(s): Zafreen, L., Huang, L.-S., Luemmen, P., Berry, E.A.
Funding Organization(s): Not funded

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.20 Å
R-Value Free:
0.165 (Depositor), 0.168 (DCC)
R-Value Work:
0.126 (Depositor), 0.131 (DCC)
R-Value Observed:
0.127 (Depositor)

Starting Model: experimental
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Ligand Structure Quality Assessment

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Literature

Crystal Structure of Insect Cytochrome c at different pH values.

Zafreen, L., Huang, L.-S., Luemmen, P., Berry, E.A.

To be published.

Macromolecule Content

Total Structure Weight: 24.6 kDa
Atom Count: 2,153
Modeled Residue Count: 214
Deposited Residue Count: 214
Unique protein chains: 1

Macromolecules

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Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Cytochrome c	A, B	107	Musca domestica	Mutation(s): 0
UniProt
Find proteins for A0A1I8N8V4 (Musca domestica) Explore A0A1I8N8V4 Go to UniProtKB: A0A1I8N8V4
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	A0A1I8N8V4
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
HEC (Subject of Investigation/LOI) Query on HEC Download:Ideal Coordinates CCD File SDF format, chain E [auth B] SDF format, chain C [auth A] MOL2 format, chain E [auth B] MOL2 format, chain C [auth A] mmCIF format, chain E [auth B] mmCIF format, chain C [auth A]	C [auth A], E [auth B]	HEME C C₃₄ H₃₄ Fe N₄ O₄ HXQIYSLZKNYNMH-LJNAALQVSA-N		Interactions Focus chain C [auth A] Focus chain E [auth B] Interactions & Density Focus chain C [auth A] Focus chain E [auth B]
EOH Query on EOH Download:Ideal Coordinates CCD File SDF format, chain D [auth A] MOL2 format, chain D [auth A] mmCIF format, chain D [auth A]	D [auth A]	ETHANOL C₂ H₆ O LFQSCWFLJHTTHZ-UHFFFAOYSA-N		Interactions Focus chain D [auth A] Interactions & Density Focus chain D [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.20 Å
R-Value Free: 0.165 (Depositor), 0.168 (DCC)
R-Value Work: 0.126 (Depositor), 0.131 (DCC)
R-Value Observed: 0.127 (Depositor)

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 33.876	α = 90
b = 58.634	β = 106.772
c = 51.674	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
PHENIX	refinement
DENZO	data reduction
SCALEPACK	data scaling
PHASER	phasing

Structure Validation

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Entry History

& Funding Information

Deposition Data

Released Date: 2025-02-12

Deposition Author(s):

Funding Organization	Location	Grant Number
Not funded		--

Revision History (Full details and data files)

Version 1.0: 2025-02-12
Type: Initial release

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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.