6GUY

Room temperature structure of Archaerhodopsin-3 via LCP extruder using synchrotron radiation

PDB DOI: https://doi.org/10.2210/pdb6GUY/pdb

Classification: PROTON TRANSPORT
Organism(s): Halorubrum sodomense
Mutation(s): Yes
Membrane Protein: Yes PDBTMMemProtMD

Deposited: 2018-06-19 Released: 2019-10-09
Deposition Author(s): Moraes, I., Judge, P.J., Axford, D., Bada Juarez, J.F., Vinals, J., Watts, A.
Funding Organization(s): Wellcome Trust, Biotechnology and Biological Sciences Research Council

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.20 Å
R-Value Free: 0.252
R-Value Work: 0.223
R-Value Observed: 0.226

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 2.2 of the entry. See complete history.

Literature

Room temperature structure of Archaerhodopsin-3 via LCP extruder using synchrotron radiation

Bada Juarez, J.F., Judge, P.J., Vinals, J., Axford, D., Birch, J., Aller, P., Butryn, A., Owen, R.L., Sherrell, D.A., Beale, J.H., Orville, A.M., Watts, A., Moraes, I.

To be published.

Macromolecule Content

Total Structure Weight: 28.39 kDa
Atom Count: 2,099
Modelled Residue Count: 241
Deposited Residue Count: 241
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Archaerhodopsin-3	A	241	Halorubrum sodomense	Mutation(s): 1 Membrane Entity: Yes
UniProt
Find proteins for P96787 (Halorubrum sodomense) Explore P96787 Go to UniProtKB: P96787
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P96787
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 6 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 B [auth A] MOL2 format, chain B [auth A] mmCIF format, chain B [auth A]	B [auth A]	RETINAL C₂₀ H₂₈ O NCYCYZXNIZJOKI-OVSJKPMPSA-N		Interactions Focus chain B [auth A] Interactions & Density Focus chain B [auth A]
R16 Query on R16 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 L [auth A] 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 L [auth A] 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 L [auth A]	C [auth A], D [auth A], E [auth A], F [auth A], L [auth A]	HEXADECANE C₁₆ H₃₄ DCAYPVUWAIABOU-UHFFFAOYSA-N		Interactions Focus chain C [auth A] Focus chain D [auth A] Focus chain E [auth A] Focus chain F [auth A] Focus chain L [auth A] Interactions & Density Focus chain C [auth A] Focus chain D [auth A] Focus chain E [auth A] Focus chain F [auth A] Focus chain L [auth A]
DD9 Query on DD9 Download Ideal Coordinates CCD File SDF format, chain G [auth A] SDF format, chain H [auth A] SDF format, chain I [auth A] SDF format, chain J [auth A] SDF format, chain K [auth A] MOL2 format, chain G [auth A] MOL2 format, chain H [auth A] MOL2 format, chain I [auth A] MOL2 format, chain J [auth A] MOL2 format, chain K [auth A] mmCIF format, chain G [auth A] mmCIF format, chain H [auth A] mmCIF format, chain I [auth A] mmCIF format, chain J [auth A] mmCIF format, chain K [auth A]	G [auth A], H [auth A], I [auth A], J [auth A], K [auth A]	nonane C₉ H₂₀ BKIMMITUMNQMOS-UHFFFAOYSA-N		Interactions Focus chain G [auth A] Focus chain H [auth A] Focus chain I [auth A] Focus chain J [auth A] Focus chain K [auth A] Interactions & Density Focus chain G [auth A] Focus chain H [auth A] Focus chain I [auth A] Focus chain J [auth A] Focus chain K [auth A]
CA Query on CA Download Ideal Coordinates CCD File SDF format, chain M [auth A] MOL2 format, chain M [auth A] mmCIF format, chain M [auth A]	M [auth A]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N		Interactions Focus chain M [auth A] Interactions & Density Focus chain M [auth A]
CL Query on CL Download Ideal Coordinates CCD File SDF format, chain O [auth A] SDF format, chain P [auth A] SDF format, chain Q [auth A] MOL2 format, chain O [auth A] MOL2 format, chain P [auth A] MOL2 format, chain Q [auth A] mmCIF format, chain O [auth A] mmCIF format, chain P [auth A] mmCIF format, chain Q [auth A]	O [auth A], P [auth A], Q [auth A]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain O [auth A] Focus chain P [auth A] Focus chain Q [auth A] Interactions & Density Focus chain O [auth A] Focus chain P [auth A] Focus chain Q [auth A]
NA Query on NA Download Ideal Coordinates CCD File SDF format, chain N [auth A] MOL2 format, chain N [auth A] mmCIF format, chain N [auth A]	N [auth A]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N		Interactions Focus chain N [auth A] Interactions & Density Focus chain N [auth A]

Modified Residues 1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
PCA Query on PCA	A	L-PEPTIDE LINKING	C₅ H₇ N O₃		GLN

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.20 Å
R-Value Free: 0.252
R-Value Work: 0.223
R-Value Observed: 0.226
Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 46.294	α = 90
b = 48.271	β = 90
c = 104.902	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
DIALS	data reduction
cctbx.prime	data scaling
PHASER	phasing
PDB_EXTRACT	data extraction

Structure Validation

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Ligand Structure Quality Assessment

Entry History & Funding Information

Deposition Data

Released Date: 2019-10-09

Deposition Author(s):

Funding Organization	Location	Grant Number
Wellcome Trust	United Kingdom	202892/Z/16/Z
Biotechnology and Biological Sciences Research Council	United Kingdom	BB/N006011/1

Revision History (Full details and data files)

Version 1.0: 2019-10-09
Type: Initial release
Version 2.0: 2020-03-11
Changes: Polymer sequence
Version 2.1: 2024-01-17
Changes: Data collection, Database references, Derived calculations, Refinement description
Version 2.2: 2024-10-23
Changes: Structure summary