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
Membrane Protein: Yes PDBTM

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

Validation slider image for 8R96

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:

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
cryorhodopsin	A, B, C, D, E	327	Subtercola endophyticus	Mutation(s): 0 Membrane Entity: Yes
UniProt
Find proteins for A0ABF7PQ03 (Subtercola endophyticus) Explore A0ABF7PQ03 Go to UniProtKB: A0ABF7PQ03
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	A0ABF7PQ03
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 Z [auth D] SDF format, chain T [auth C] SDF format, chain P [auth B] MOL2 format, chain DA [auth E] MOL2 format, chain L [auth A] MOL2 format, chain Z [auth D] MOL2 format, chain T [auth C] MOL2 format, chain P [auth B] mmCIF format, chain DA [auth E] mmCIF format, chain L [auth A] mmCIF format, chain Z [auth D] mmCIF format, chain T [auth C] mmCIF format, chain P [auth B]	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 F [auth A] SDF format, chain G [auth A] SDF format, chain J [auth A] SDF format, chain K [auth A] SDF format, chain N [auth B] SDF format, chain S [auth C] SDF format, chain Y [auth D] SDF format, chain X [auth D] SDF format, chain W [auth D] SDF format, chain Q [auth C] SDF format, chain M [auth B] SDF format, chain I [auth A] SDF format, chain CA [auth E] SDF format, chain AA [auth E] MOL2 format, chain F [auth A] MOL2 format, chain G [auth A] MOL2 format, chain J [auth A] MOL2 format, chain K [auth A] MOL2 format, chain N [auth B] MOL2 format, chain S [auth C] MOL2 format, chain Y [auth D] MOL2 format, chain X [auth D] MOL2 format, chain W [auth D] MOL2 format, chain Q [auth C] MOL2 format, chain M [auth B] MOL2 format, chain I [auth A] MOL2 format, chain CA [auth E] MOL2 format, chain AA [auth E] mmCIF format, chain F [auth A] mmCIF format, chain G [auth A] mmCIF format, chain J [auth A] mmCIF format, chain K [auth A] mmCIF format, chain N [auth B] mmCIF format, chain S [auth C] mmCIF format, chain Y [auth D] mmCIF format, chain X [auth D] mmCIF format, chain W [auth D] mmCIF format, chain Q [auth C] mmCIF format, chain M [auth B] mmCIF format, chain I [auth A] mmCIF format, chain CA [auth E] mmCIF format, chain AA [auth E]	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 V [auth D] SDF format, chain R [auth C] SDF format, chain O [auth B] SDF format, chain H [auth A] SDF format, chain BA [auth E] MOL2 format, chain V [auth D] MOL2 format, chain R [auth C] MOL2 format, chain O [auth B] MOL2 format, chain H [auth A] MOL2 format, chain BA [auth E] mmCIF format, chain V [auth D] mmCIF format, chain R [auth C] mmCIF format, chain O [auth B] mmCIF format, chain H [auth A] mmCIF format, chain BA [auth E]	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]

Experimental Data & Validation

Experimental Data

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)

Space Group: C 2 2 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 85.565	α = 90
b = 295.665	β = 90
c = 185.5	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
STARANISO	data scaling
MOLREP	phasing
XDS	data reduction

Structure Validation

View Full Validation Report

Ligand Structure Quality Assessment

View more in-depth experimental data

Entry History

& Funding Information

Deposition Data

Released Date: 2024-12-11

Deposition Author(s):

Funding Organization	Location	Grant Number
EIPOD fellowship under Marie Sklodowska-Curie Actions COFUND	Germany	847543

Revision History (Full details and data files)

Version 1.0: 2024-12-11
Type: Initial release

RCSB PDB is hosted by

RCSB PDB is a member of

RCSB Partners
Nucleic Acid Knowledgebase

CoreTrustSeal

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.