8R97 | pdb_00008r97

Crystal structure of the cryorhodopsin CryoR2 at pH 4.6, type B crystals, non-illuminated state

PDB DOI: https://doi.org/10.2210/pdb8R97/pdb

Classification: MEMBRANE PROTEIN
Organism(s): Subtercola sp.
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: 3.00 Å
R-Value Free:
0.301 (Depositor), 0.254 (DCC)
R-Value Work:
0.266 (Depositor)
R-Value Observed:
0.268 (Depositor)

Starting Model: experimental
View more details

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: 362.01 kDa
Atom Count: 21,953
Modeled Residue Count: 2,874
Deposited Residue Count: 3,270
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
cryorhodopsin CryoR2	A B C D E A, B, C, D, E, F [auth H], G, H [auth F], I, J [auth K]	327	Subtercola sp.	Mutation(s): 0

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 CB [auth I] SDF format, chain EA [auth D] SDF format, chain HB [auth K] SDF format, chain IA [auth E] SDF format, chain MA [auth H] SDF format, chain P [auth A] SDF format, chain SA [auth G] SDF format, chain V [auth B] SDF format, chain YA [auth F] SDF format, chain Z [auth C] MOL2 format, chain CB [auth I] MOL2 format, chain EA [auth D] MOL2 format, chain HB [auth K] MOL2 format, chain IA [auth E] MOL2 format, chain MA [auth H] MOL2 format, chain P [auth A] MOL2 format, chain SA [auth G] MOL2 format, chain V [auth B] MOL2 format, chain YA [auth F] MOL2 format, chain Z [auth C] mmCIF format, chain CB [auth I] mmCIF format, chain EA [auth D] mmCIF format, chain HB [auth K] mmCIF format, chain IA [auth E] mmCIF format, chain MA [auth H] mmCIF format, chain P [auth A] mmCIF format, chain SA [auth G] mmCIF format, chain V [auth B] mmCIF format, chain YA [auth F] mmCIF format, chain Z [auth C]	CB [auth I] EA [auth D] HB [auth K] IA [auth E] MA [auth H] CB [auth I], EA [auth D], HB [auth K], IA [auth E], MA [auth H], P [auth A], SA [auth G], V [auth B], YA [auth F], Z [auth C]	RETINAL C₂₀ H₂₈ O NCYCYZXNIZJOKI-OVSJKPMPSA-N		Interactions Focus chain CB [auth I] Focus chain EA [auth D] Focus chain HB [auth K] Focus chain IA [auth E] Focus chain MA [auth H] Focus chain P [auth A] Focus chain SA [auth G] Focus chain V [auth B] Focus chain YA [auth F] Focus chain Z [auth C] Interactions & Density Focus chain CB [auth I] Focus chain EA [auth D] Focus chain HB [auth K] Focus chain IA [auth E] Focus chain MA [auth H] Focus chain P [auth A] Focus chain SA [auth G] Focus chain V [auth B] Focus chain YA [auth F] Focus chain Z [auth C]
LFA Query on LFA Download:Ideal Coordinates CCD File SDF format, chain AB [auth I] SDF format, chain BA [auth D] SDF format, chain CA [auth D] SDF format, chain DB [auth K] SDF format, chain EB [auth K] SDF format, chain FA [auth E] SDF format, chain FB [auth K] SDF format, chain GA [auth E] SDF format, chain JA [auth H] SDF format, chain K [auth A] SDF format, chain KA [auth H] SDF format, chain L [auth A] SDF format, chain M [auth A] SDF format, chain N [auth A] SDF format, chain NA [auth G] SDF format, chain OA [auth G] SDF format, chain PA [auth G] SDF format, chain Q [auth B] SDF format, chain QA [auth G] SDF format, chain R [auth B] SDF format, chain S [auth B] SDF format, chain T [auth B] SDF format, chain TA [auth F] SDF format, chain UA [auth F] SDF format, chain VA [auth F] SDF format, chain W [auth C] SDF format, chain WA [auth F] SDF format, chain X [auth C] MOL2 format, chain AB [auth I] MOL2 format, chain BA [auth D] MOL2 format, chain CA [auth D] MOL2 format, chain DB [auth K] MOL2 format, chain EB [auth K] MOL2 format, chain FA [auth E] MOL2 format, chain FB [auth K] MOL2 format, chain GA [auth E] MOL2 format, chain JA [auth H] MOL2 format, chain K [auth A] MOL2 format, chain KA [auth H] MOL2 format, chain L [auth A] MOL2 format, chain M [auth A] MOL2 format, chain N [auth A] MOL2 format, chain NA [auth G] MOL2 format, chain OA [auth G] MOL2 format, chain PA [auth G] MOL2 format, chain Q [auth B] MOL2 format, chain QA [auth G] MOL2 format, chain R [auth B] MOL2 format, chain S [auth B] MOL2 format, chain T [auth B] MOL2 format, chain TA [auth F] MOL2 format, chain UA [auth F] MOL2 format, chain VA [auth F] MOL2 format, chain W [auth C] MOL2 format, chain WA [auth F] MOL2 format, chain X [auth C] mmCIF format, chain AB [auth I] mmCIF format, chain BA [auth D] mmCIF format, chain CA [auth D] mmCIF format, chain DB [auth K] mmCIF format, chain EB [auth K] mmCIF format, chain FA [auth E] mmCIF format, chain FB [auth K] mmCIF format, chain GA [auth E] mmCIF format, chain JA [auth H] mmCIF format, chain K [auth A] mmCIF format, chain KA [auth H] mmCIF format, chain L [auth A] mmCIF format, chain M [auth A] mmCIF format, chain N [auth A] mmCIF format, chain NA [auth G] mmCIF format, chain OA [auth G] mmCIF format, chain PA [auth G] mmCIF format, chain Q [auth B] mmCIF format, chain QA [auth G] mmCIF format, chain R [auth B] mmCIF format, chain S [auth B] mmCIF format, chain T [auth B] mmCIF format, chain TA [auth F] mmCIF format, chain UA [auth F] mmCIF format, chain VA [auth F] mmCIF format, chain W [auth C] mmCIF format, chain WA [auth F] mmCIF format, chain X [auth C]	AB [auth I] BA [auth D] CA [auth D] DB [auth K] EB [auth K] AB [auth I], BA [auth D], CA [auth D], DB [auth K], EB [auth K], FA [auth E], FB [auth K], GA [auth E], JA [auth H], K [auth A], KA [auth H], L [auth A], M [auth A], N [auth A], NA [auth G], OA [auth G], PA [auth G], Q [auth B], QA [auth G], R [auth B], S [auth B], T [auth B], TA [auth F], UA [auth F], VA [auth F], W [auth C], WA [auth F], X [auth C]	EICOSANE C₂₀ H₄₂ CBFCDTFDPHXCNY-UHFFFAOYSA-N		Interactions Focus chain AB [auth I] Focus chain BA [auth D] Focus chain CA [auth D] Focus chain DB [auth K] Focus chain EB [auth K] Focus chain FA [auth E] Focus chain FB [auth K] Focus chain GA [auth E] Focus chain JA [auth H] Focus chain K [auth A] Focus chain KA [auth H] Focus chain L [auth A] Focus chain M [auth A] Focus chain N [auth A] Focus chain NA [auth G] Focus chain OA [auth G] Focus chain PA [auth G] Focus chain Q [auth B] Focus chain QA [auth G] Focus chain R [auth B] Focus chain S [auth B] Focus chain T [auth B] Focus chain TA [auth F] Focus chain UA [auth F] Focus chain VA [auth F] Focus chain W [auth C] Focus chain WA [auth F] Focus chain X [auth C] Interactions & Density Focus chain AB [auth I] Focus chain BA [auth D] Focus chain CA [auth D] Focus chain DB [auth K] Focus chain EB [auth K] Focus chain FA [auth E] Focus chain FB [auth K] Focus chain GA [auth E] Focus chain JA [auth H] Focus chain K [auth A] Focus chain KA [auth H] Focus chain L [auth A] Focus chain M [auth A] Focus chain N [auth A] Focus chain NA [auth G] Focus chain OA [auth G] Focus chain PA [auth G] Focus chain Q [auth B] Focus chain QA [auth G] Focus chain R [auth B] Focus chain S [auth B] Focus chain T [auth B] Focus chain TA [auth F] Focus chain UA [auth F] Focus chain VA [auth F] Focus chain W [auth C] Focus chain WA [auth F] Focus chain X [auth C]
OLA Query on OLA Download:Ideal Coordinates CCD File SDF format, chain AA [auth D] SDF format, chain ZA [auth I] MOL2 format, chain AA [auth D] MOL2 format, chain ZA [auth I] mmCIF format, chain AA [auth D] mmCIF format, chain ZA [auth I]	AA [auth D], ZA [auth I]	OLEIC ACID C₁₈ H₃₄ O₂ ZQPPMHVWECSIRJ-KTKRTIGZSA-N		Interactions Focus chain AA [auth D] Focus chain ZA [auth I] Interactions & Density Focus chain AA [auth D] Focus chain ZA [auth I]
PO4 Query on PO4 Download:Ideal Coordinates CCD File SDF format, chain BB [auth I] SDF format, chain DA [auth D] SDF format, chain GB [auth K] SDF format, chain HA [auth E] SDF format, chain LA [auth H] SDF format, chain O [auth A] SDF format, chain RA [auth G] SDF format, chain U [auth B] SDF format, chain XA [auth F] SDF format, chain Y [auth C] MOL2 format, chain BB [auth I] MOL2 format, chain DA [auth D] MOL2 format, chain GB [auth K] MOL2 format, chain HA [auth E] MOL2 format, chain LA [auth H] MOL2 format, chain O [auth A] MOL2 format, chain RA [auth G] MOL2 format, chain U [auth B] MOL2 format, chain XA [auth F] MOL2 format, chain Y [auth C] mmCIF format, chain BB [auth I] mmCIF format, chain DA [auth D] mmCIF format, chain GB [auth K] mmCIF format, chain HA [auth E] mmCIF format, chain LA [auth H] mmCIF format, chain O [auth A] mmCIF format, chain RA [auth G] mmCIF format, chain U [auth B] mmCIF format, chain XA [auth F] mmCIF format, chain Y [auth C]	BB [auth I] DA [auth D] GB [auth K] HA [auth E] LA [auth H] BB [auth I], DA [auth D], GB [auth K], HA [auth E], LA [auth H], O [auth A], RA [auth G], U [auth B], XA [auth F], Y [auth C]	PHOSPHATE ION O₄ P NBIIXXVUZAFLBC-UHFFFAOYSA-K		Interactions Focus chain BB [auth I] Focus chain DA [auth D] Focus chain GB [auth K] Focus chain HA [auth E] Focus chain LA [auth H] Focus chain O [auth A] Focus chain RA [auth G] Focus chain U [auth B] Focus chain XA [auth F] Focus chain Y [auth C] Interactions & Density Focus chain BB [auth I] Focus chain DA [auth D] Focus chain GB [auth K] Focus chain HA [auth E] Focus chain LA [auth H] Focus chain O [auth A] Focus chain RA [auth G] Focus chain U [auth B] Focus chain XA [auth F] Focus chain Y [auth C]