9CUF

Room temperature SSX structure of ccNiR

PDB DOI: https://doi.org/10.2210/pdb9CUF/pdb

Classification: ELECTRON TRANSPORT
Organism(s): Shewanella oneidensis
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2024-07-26 Released: 2025-01-15
Deposition Author(s): Malla, T.N., Schmidt, M.
Funding Organization(s): National Science Foundation (NSF, United States)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 3.30 Å
R-Value Free: 0.298
R-Value Work: 0.212
R-Value Observed: 0.221

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

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

Literature

Exploiting fourth-generation synchrotron radiation for enzyme and photoreceptor characterization.

Malla, T.N., Muniyappan, S., Menendez, D., Ogukwe, F., Dale, A.N., Clayton, J.D., Weatherall, D.D., Karki, P., Dangi, S., Mandella, V., Pacheco, A.A., Stojkovic, E.A., Rose, S.L., Orlans, J., Basu, S., de Sanctis, D., Schmidt, M.

(2025) IUCrJ 12: 36-48

PubMed: 39575537 Search on PubMedSearch on PubMed Central
DOI: https://doi.org/10.1107/S2052252524010868
Primary Citation of Related Structures:
9CUF, 9D10, 9D2H

PubMed Abstract:
The upgrade of the European Synchrotron Radiation Facility (ESRF) in Grenoble, France to an Extremely Brilliant Source (EBS) is expected to enable time-resolved synchrotron serial crystallography (SSX) experiments with sub-millisecond time resolution. ID29 is a new beamline dedicated to SSX experiments at ESRF-EBS. Here, we report experiments emerging from the initial phase of user operation at ID29. We first used microcrystals of photoactive yellow protein as a model system to exploit the potential of microsecond pulses for SSX. Subsequently, we investigated microcrystals of cytochrome c nitrite reductase (ccNiR) with microsecond X-ray pulses. CcNiR is a decaheme protein that is ideal for the investigation of radiation damage at the various heme-iron sites. Finally, we performed a proof-of-concept subsecond time-resolved SSX experiment by photoactivating microcrystals of a myxobacterial phytochrome.

Organizational Affiliation

Department of Physics, University of Wisconsin-Milwaukee, Milwaukee, USA.

Macromolecule Content

Total Structure Weight: 106.03 kDa
Atom Count: 7,421
Modelled Residue Count: 878
Deposited Residue Count: 878
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Cytochrome c-552	A, B	439	Shewanella oneidensis	Mutation(s): 0 Gene Names: nrfA, SO_3980 EC: 1.7.2.2
UniProt
Find proteins for Q8EAC7 (Shewanella oneidensis (strain ATCC 700550 / JCM 31522 / CIP 106686 / LMG 19005 / NCIMB 14063 / MR-1)) Explore Q8EAC7 Go to UniProtKB: Q8EAC7
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q8EAC7
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
PE3 Query on PE3 Download Ideal Coordinates CCD File SDF format, chain O [auth B] MOL2 format, chain O [auth B] mmCIF format, chain O [auth B]	O [auth B]	3,6,9,12,15,18,21,24,27,30,33,36,39-TRIDECAOXAHENTETRACONTANE-1,41-DIOL C₂₈ H₅₈ O₁₅ ILLKMACMBHTSHP-UHFFFAOYSA-N		Interactions Focus chain O [auth B] Interactions & Density Focus chain O [auth B]
HEC (Subject of Investigation/LOI) Query on HEC Download Ideal Coordinates CCD File SDF format, chain C [auth A] SDF format, chain D [auth A] SDF format, chain E [auth A] SDF format, chain F [auth A] SDF format, chain G [auth A] SDF format, chain I [auth B] SDF format, chain J [auth B] SDF format, chain K [auth B] SDF format, chain L [auth B] SDF format, chain M [auth B] MOL2 format, chain C [auth A] MOL2 format, chain D [auth A] MOL2 format, chain E [auth A] MOL2 format, chain F [auth A] MOL2 format, chain G [auth A] MOL2 format, chain I [auth B] MOL2 format, chain J [auth B] MOL2 format, chain K [auth B] MOL2 format, chain L [auth B] MOL2 format, chain M [auth B] mmCIF format, chain C [auth A] mmCIF format, chain D [auth A] mmCIF format, chain E [auth A] mmCIF format, chain F [auth A] mmCIF format, chain G [auth A] mmCIF format, chain I [auth B] mmCIF format, chain J [auth B] mmCIF format, chain K [auth B] mmCIF format, chain L [auth B] mmCIF format, chain M [auth B]	C [auth A] D [auth A] E [auth A] F [auth A] G [auth A] C [auth A], D [auth A], E [auth A], F [auth A], G [auth A], I [auth B], J [auth B], K [auth B], L [auth B], M [auth B]	HEME C C₃₄ H₃₄ Fe N₄ O₄ HXQIYSLZKNYNMH-LJNAALQVSA-N		Interactions Focus chain C [auth A] Focus chain D [auth A] Focus chain E [auth A] Focus chain F [auth A] Focus chain G [auth A] Focus chain I [auth B] Focus chain J [auth B] Focus chain K [auth B] Focus chain L [auth B] Focus chain M [auth B] Interactions & Density Focus chain C [auth A] Focus chain D [auth A] Focus chain E [auth A] Focus chain F [auth A] Focus chain G [auth A] Focus chain I [auth B] Focus chain J [auth B] Focus chain K [auth B] Focus chain L [auth B] Focus chain M [auth B]
CA Query on CA Download Ideal Coordinates CCD File SDF format, chain H [auth A] SDF format, chain N [auth B] MOL2 format, chain H [auth A] MOL2 format, chain N [auth B] mmCIF format, chain H [auth A] mmCIF format, chain N [auth B]	H [auth A], N [auth B]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N		Interactions Focus chain H [auth A] Focus chain N [auth B] Interactions & Density Focus chain H [auth A] Focus chain N [auth B]