8R96 | pdb_00008r96

Crystal structure of the cryorhodopsin CryoR2 at pH 4.6, type A crystals

PDB DOI: https://doi.org/10.2210/pdb8R96/pdb

Classification: MEMBRANE PROTEIN
Organism(s): Subtercola endophyticus
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2023-11-30 Released: 2024-12-11
Deposition Author(s): Kovalev, K., Lamm, G.H.U., Marin, E.
Funding Organization(s): EIPOD fellowship under Marie Sklodowska-Curie Actions COFUND

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.46 Å
R-Value Free:
0.254 (Depositor), 0.263 (DCC)
R-Value Work:
0.239 (Depositor), 0.246 (DCC)
R-Value Observed:
0.240 (Depositor)

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

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

Literature

CryoRhodopsins: a new clade of microbial rhodopsins from cold environments

Lamm, G.H.U., Marin, E., Guskov, A., Kovalev, K.

To be published.

Macromolecule Content

Total Structure Weight: 181 kDa
Atom Count: 11,044
Modeled Residue Count: 1,440
Deposited Residue Count: 1,635
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
cryorhodopsin	A, B, C, D, E	327	Subtercola endophyticus	Mutation(s): 0
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
RET (Subject of Investigation/LOI) Query on RET Download Ideal Coordinates CCD File SDF format, chain DA [auth E] SDF format, chain L [auth A] SDF format, chain P [auth B] SDF format, chain T [auth C] SDF format, chain Z [auth D] MOL2 format, chain DA [auth E] MOL2 format, chain L [auth A] MOL2 format, chain P [auth B] MOL2 format, chain T [auth C] MOL2 format, chain Z [auth D] mmCIF format, chain DA [auth E] mmCIF format, chain L [auth A] mmCIF format, chain P [auth B] mmCIF format, chain T [auth C] mmCIF format, chain Z [auth D]	DA [auth E], L [auth A], P [auth B], T [auth C], Z [auth D]	RETINAL C₂₀ H₂₈ O NCYCYZXNIZJOKI-OVSJKPMPSA-N		Interactions Focus chain DA [auth E] Focus chain L [auth A] Focus chain P [auth B] Focus chain T [auth C] Focus chain Z [auth D] Interactions & Density Focus chain DA [auth E] Focus chain L [auth A] Focus chain P [auth B] Focus chain T [auth C] Focus chain Z [auth D]
LFA Query on LFA Download Ideal Coordinates CCD File SDF format, chain AA [auth E] SDF format, chain CA [auth E] SDF format, chain F [auth A] SDF format, chain G [auth A] SDF format, chain I [auth A] SDF format, chain J [auth A] SDF format, chain K [auth A] SDF format, chain M [auth B] SDF format, chain N [auth B] SDF format, chain Q [auth C] SDF format, chain S [auth C] SDF format, chain W [auth D] SDF format, chain X [auth D] SDF format, chain Y [auth D] MOL2 format, chain AA [auth E] MOL2 format, chain CA [auth E] MOL2 format, chain F [auth A] MOL2 format, chain G [auth A] MOL2 format, chain I [auth A] MOL2 format, chain J [auth A] MOL2 format, chain K [auth A] MOL2 format, chain M [auth B] MOL2 format, chain N [auth B] MOL2 format, chain Q [auth C] MOL2 format, chain S [auth C] MOL2 format, chain W [auth D] MOL2 format, chain X [auth D] MOL2 format, chain Y [auth D] mmCIF format, chain AA [auth E] mmCIF format, chain CA [auth E] mmCIF format, chain F [auth A] mmCIF format, chain G [auth A] mmCIF format, chain I [auth A] mmCIF format, chain J [auth A] mmCIF format, chain K [auth A] mmCIF format, chain M [auth B] mmCIF format, chain N [auth B] mmCIF format, chain Q [auth C] mmCIF format, chain S [auth C] mmCIF format, chain W [auth D] mmCIF format, chain X [auth D] mmCIF format, chain Y [auth D]	AA [auth E] CA [auth E] F [auth A] G [auth A] I [auth A] AA [auth E], CA [auth E], F [auth A], G [auth A], I [auth A], J [auth A], K [auth A], M [auth B], N [auth B], Q [auth C], S [auth C], W [auth D], X [auth D], Y [auth D]	EICOSANE C₂₀ H₄₂ CBFCDTFDPHXCNY-UHFFFAOYSA-N		Interactions Focus chain AA [auth E] Focus chain CA [auth E] Focus chain F [auth A] Focus chain G [auth A] Focus chain I [auth A] Focus chain J [auth A] Focus chain K [auth A] Focus chain M [auth B] Focus chain N [auth B] Focus chain Q [auth C] Focus chain S [auth C] Focus chain W [auth D] Focus chain X [auth D] Focus chain Y [auth D] Interactions & Density Focus chain AA [auth E] Focus chain CA [auth E] Focus chain F [auth A] Focus chain G [auth A] Focus chain I [auth A] Focus chain J [auth A] Focus chain K [auth A] Focus chain M [auth B] Focus chain N [auth B] Focus chain Q [auth C] Focus chain S [auth C] Focus chain W [auth D] Focus chain X [auth D] Focus chain Y [auth D]
OLA Query on OLA Download Ideal Coordinates CCD File SDF format, chain U [auth D] MOL2 format, chain U [auth D] mmCIF format, chain U [auth D]	U [auth D]	OLEIC ACID C₁₈ H₃₄ O₂ ZQPPMHVWECSIRJ-KTKRTIGZSA-N		Interactions Focus chain U [auth D] Interactions & Density Focus chain U [auth D]
PO4 Query on PO4 Download Ideal Coordinates CCD File SDF format, chain BA [auth E] SDF format, chain H [auth A] SDF format, chain O [auth B] SDF format, chain R [auth C] SDF format, chain V [auth D] MOL2 format, chain BA [auth E] MOL2 format, chain H [auth A] MOL2 format, chain O [auth B] MOL2 format, chain R [auth C] MOL2 format, chain V [auth D] mmCIF format, chain BA [auth E] mmCIF format, chain H [auth A] mmCIF format, chain O [auth B] mmCIF format, chain R [auth C] mmCIF format, chain V [auth D]	BA [auth E], H [auth A], O [auth B], R [auth C], V [auth D]	PHOSPHATE ION O₄ P NBIIXXVUZAFLBC-UHFFFAOYSA-K		Interactions Focus chain BA [auth E] Focus chain H [auth A] Focus chain O [auth B] Focus chain R [auth C] Focus chain V [auth D] Interactions & Density Focus chain BA [auth E] Focus chain H [auth A] Focus chain O [auth B] Focus chain R [auth C] Focus chain V [auth D]