6YT4 | pdb_00006yt4

Crystal structure of the N112A mutant of the light-driven sodium pump KR2 in the pentameric form, pH 8.0

PDB DOI: https://doi.org/10.2210/pdb6YT4/pdb

Classification: MEMBRANE PROTEIN
Organism(s): Dokdonia eikasta
Expression System: Escherichia coli
Mutation(s): Yes
Membrane Protein: Yes PDBTM MemProtMD

Deposited: 2020-04-23 Released: 2020-06-17
Deposition Author(s): Kovalev, K., Maliar, N., Astashkin, R., Gordeliy, V.
Funding Organization(s): Russian Foundation for Basic Research

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.40 Å
R-Value Free:
0.217 (Depositor), 0.224 (DCC)
R-Value Work:
0.186 (Depositor), 0.198 (DCC)
R-Value Observed:
0.188 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

This is version 1.3 of the entry. See complete history.

Literature

Crystal Structure of the N112A Mutant of the Light-Driven Sodium Pump KR2

Maliar, N., Kovalev, K., Baeken, C., Balandin, T., Astashkin, R., Rulev, M., Alekseev, A., Ilyinsky, N., Rogachev, A., Chupin, V., Dolgikh, D., Kirpichnikov, M., Gordeliy, V.

(2020) Crystals (Basel)

DOI: https://doi.org/10.3390/cryst10060496

Macromolecule Content

Total Structure Weight: 180.06 kDa
Atom Count: 11,860
Modeled Residue Count: 1,349
Deposited Residue Count: 1,440
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Sodium pumping rhodopsin	A, B, C [auth D], D [auth E], E [auth C]	288	Dokdonia eikasta	Mutation(s): 1 Gene Names: NaR Membrane Entity: Yes
UniProt
Find proteins for N0DKS8 (Dokdonia eikasta) Explore N0DKS8 Go to UniProtKB: N0DKS8
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	N0DKS8
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 6 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
OLC Query on OLC Download:Ideal Coordinates CCD File SDF format, chain F [auth A] SDF format, chain IB [auth C] SDF format, chain JA [auth D] SDF format, chain R [auth B] SDF format, chain VA [auth E] MOL2 format, chain F [auth A] MOL2 format, chain IB [auth C] MOL2 format, chain JA [auth D] MOL2 format, chain R [auth B] MOL2 format, chain VA [auth E] mmCIF format, chain F [auth A] mmCIF format, chain IB [auth C] mmCIF format, chain JA [auth D] mmCIF format, chain R [auth B] mmCIF format, chain VA [auth E]	F [auth A], IB [auth C], JA [auth D], R [auth B], VA [auth E]	(2R)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate C₂₁ H₄₀ O₄ RZRNAYUHWVFMIP-GDCKJWNLSA-N		Interactions Focus chain F [auth A] Focus chain IB [auth C] Focus chain JA [auth D] Focus chain R [auth B] Focus chain VA [auth E] Interactions & Density Focus chain F [auth A] Focus chain IB [auth C] Focus chain JA [auth D] Focus chain R [auth B] Focus chain VA [auth E]
BOG Query on BOG Download:Ideal Coordinates CCD File SDF format, chain AA [auth B] SDF format, chain DB [auth E] SDF format, chain MA [auth D] SDF format, chain N [auth A] SDF format, chain OB [auth C] MOL2 format, chain AA [auth B] MOL2 format, chain DB [auth E] MOL2 format, chain MA [auth D] MOL2 format, chain N [auth A] MOL2 format, chain OB [auth C] mmCIF format, chain AA [auth B] mmCIF format, chain DB [auth E] mmCIF format, chain MA [auth D] mmCIF format, chain N [auth A] mmCIF format, chain OB [auth C]	AA [auth B], DB [auth E], MA [auth D], N [auth A], OB [auth C]	octyl beta-D-glucopyranoside C₁₄ H₂₈ O₆ HEGSGKPQLMEBJL-RKQHYHRCSA-N		Interactions Focus chain AA [auth B] Focus chain DB [auth E] Focus chain MA [auth D] Focus chain N [auth A] Focus chain OB [auth C] Interactions & Density Focus chain AA [auth B] Focus chain DB [auth E] Focus chain MA [auth D] Focus chain N [auth A] Focus chain OB [auth C]
RET Query on RET Download:Ideal Coordinates CCD File SDF format, chain BA [auth B] SDF format, chain FB [auth E] SDF format, chain O [auth A] SDF format, chain PB [auth C] SDF format, chain QA [auth D] MOL2 format, chain BA [auth B] MOL2 format, chain FB [auth E] MOL2 format, chain O [auth A] MOL2 format, chain PB [auth C] MOL2 format, chain QA [auth D] mmCIF format, chain BA [auth B] mmCIF format, chain FB [auth E] mmCIF format, chain O [auth A] mmCIF format, chain PB [auth C] mmCIF format, chain QA [auth D]	BA [auth B], FB [auth E], O [auth A], PB [auth C], QA [auth D]	RETINAL C₂₀ H₂₈ O NCYCYZXNIZJOKI-OVSJKPMPSA-N		Interactions Focus chain BA [auth B] Focus chain FB [auth E] Focus chain O [auth A] Focus chain PB [auth C] Focus chain QA [auth D] Interactions & Density Focus chain BA [auth B] Focus chain FB [auth E] Focus chain O [auth A] Focus chain PB [auth C] Focus chain QA [auth D]
LFA Query on LFA Download:Ideal Coordinates CCD File SDF format, chain AB [auth E] SDF format, chain BB [auth E] SDF format, chain CA [auth B] SDF format, chain GA [auth D] SDF format, chain H [auth A] SDF format, chain IA [auth D] SDF format, chain JB [auth C] SDF format, chain K [auth A] SDF format, chain KB [auth C] SDF format, chain LA [auth D] SDF format, chain LB [auth C] SDF format, chain MB [auth C] SDF format, chain NB [auth C] SDF format, chain OA [auth D] SDF format, chain PA [auth D] SDF format, chain S [auth B] SDF format, chain SA [auth E] SDF format, chain T [auth B] SDF format, chain TA [auth E] SDF format, chain U [auth B] SDF format, chain W [auth B] SDF format, chain X [auth B] SDF format, chain XA [auth E] SDF format, chain ZA [auth E] SDF format, chain J [auth A] SDF format, chain HA [auth D] SDF format, chain FA [auth D] SDF format, chain EB [auth E] MOL2 format, chain AB [auth E] MOL2 format, chain BB [auth E] MOL2 format, chain CA [auth B] MOL2 format, chain GA [auth D] MOL2 format, chain H [auth A] MOL2 format, chain IA [auth D] MOL2 format, chain JB [auth C] MOL2 format, chain K [auth A] MOL2 format, chain KB [auth C] MOL2 format, chain LA [auth D] MOL2 format, chain LB [auth C] MOL2 format, chain MB [auth C] MOL2 format, chain NB [auth C] MOL2 format, chain OA [auth D] MOL2 format, chain PA [auth D] MOL2 format, chain S [auth B] MOL2 format, chain SA [auth E] MOL2 format, chain T [auth B] MOL2 format, chain TA [auth E] MOL2 format, chain U [auth B] MOL2 format, chain W [auth B] MOL2 format, chain X [auth B] MOL2 format, chain XA [auth E] MOL2 format, chain ZA [auth E] MOL2 format, chain J [auth A] MOL2 format, chain HA [auth D] MOL2 format, chain FA [auth D] MOL2 format, chain EB [auth E] mmCIF format, chain AB [auth E] mmCIF format, chain BB [auth E] mmCIF format, chain CA [auth B] mmCIF format, chain GA [auth D] mmCIF format, chain H [auth A] mmCIF format, chain IA [auth D] mmCIF format, chain JB [auth C] mmCIF format, chain K [auth A] mmCIF format, chain KB [auth C] mmCIF format, chain LA [auth D] mmCIF format, chain LB [auth C] mmCIF format, chain MB [auth C] mmCIF format, chain NB [auth C] mmCIF format, chain OA [auth D] mmCIF format, chain PA [auth D] mmCIF format, chain S [auth B] mmCIF format, chain SA [auth E] mmCIF format, chain T [auth B] mmCIF format, chain TA [auth E] mmCIF format, chain U [auth B] mmCIF format, chain W [auth B] mmCIF format, chain X [auth B] mmCIF format, chain XA [auth E] mmCIF format, chain ZA [auth E] mmCIF format, chain J [auth A] mmCIF format, chain HA [auth D] mmCIF format, chain FA [auth D] mmCIF format, chain EB [auth E]	AB [auth E] BB [auth E] CA [auth B] EB [auth E] FA [auth D] AB [auth E], BB [auth E], CA [auth B], EB [auth E], FA [auth D], GA [auth D], H [auth A], HA [auth D], IA [auth D], J [auth A], JB [auth C], K [auth A], KB [auth C], LA [auth D], LB [auth C], MB [auth C], NB [auth C], OA [auth D], PA [auth D], S [auth B], SA [auth E], T [auth B], TA [auth E], U [auth B], W [auth B], X [auth B], XA [auth E], ZA [auth E]	EICOSANE C₂₀ H₄₂ CBFCDTFDPHXCNY-UHFFFAOYSA-N		Interactions Focus chain AB [auth E] Focus chain BB [auth E] Focus chain CA [auth B] Focus chain EB [auth E] Focus chain FA [auth D] Focus chain GA [auth D] Focus chain H [auth A] Focus chain HA [auth D] Focus chain IA [auth D] Focus chain J [auth A] Focus chain JB [auth C] Focus chain K [auth A] Focus chain KB [auth C] Focus chain LA [auth D] Focus chain LB [auth C] Focus chain MB [auth C] Focus chain NB [auth C] Focus chain OA [auth D] Focus chain PA [auth D] Focus chain S [auth B] Focus chain SA [auth E] Focus chain T [auth B] Focus chain TA [auth E] Focus chain U [auth B] Focus chain W [auth B] Focus chain X [auth B] Focus chain XA [auth E] Focus chain ZA [auth E] Interactions & Density Focus chain AB [auth E] Focus chain BB [auth E] Focus chain CA [auth B] Focus chain EB [auth E] Focus chain FA [auth D] Focus chain GA [auth D] Focus chain H [auth A] Focus chain HA [auth D] Focus chain IA [auth D] Focus chain J [auth A] Focus chain JB [auth C] Focus chain K [auth A] Focus chain KB [auth C] Focus chain LA [auth D] Focus chain LB [auth C] Focus chain MB [auth C] Focus chain NB [auth C] Focus chain OA [auth D] Focus chain PA [auth D] Focus chain S [auth B] Focus chain SA [auth E] Focus chain T [auth B] Focus chain TA [auth E] Focus chain U [auth B] Focus chain W [auth B] Focus chain X [auth B] Focus chain XA [auth E] Focus chain ZA [auth E]
OLA Query on OLA Download:Ideal Coordinates CCD File SDF format, chain CB [auth E] SDF format, chain DA [auth B] SDF format, chain G [auth A] SDF format, chain HB [auth C] SDF format, chain I [auth A] SDF format, chain L [auth A] SDF format, chain NA [auth D] SDF format, chain UA [auth E] SDF format, chain V [auth B] SDF format, chain WA [auth E] SDF format, chain Y [auth B] SDF format, chain Z [auth B] SDF format, chain YA [auth E] SDF format, chain P [auth A] SDF format, chain M [auth A] SDF format, chain KA [auth D] MOL2 format, chain CB [auth E] MOL2 format, chain DA [auth B] MOL2 format, chain G [auth A] MOL2 format, chain HB [auth C] MOL2 format, chain I [auth A] MOL2 format, chain L [auth A] MOL2 format, chain NA [auth D] MOL2 format, chain UA [auth E] MOL2 format, chain V [auth B] MOL2 format, chain WA [auth E] MOL2 format, chain Y [auth B] MOL2 format, chain Z [auth B] MOL2 format, chain YA [auth E] MOL2 format, chain P [auth A] MOL2 format, chain M [auth A] MOL2 format, chain KA [auth D] mmCIF format, chain CB [auth E] mmCIF format, chain DA [auth B] mmCIF format, chain G [auth A] mmCIF format, chain HB [auth C] mmCIF format, chain I [auth A] mmCIF format, chain L [auth A] mmCIF format, chain NA [auth D] mmCIF format, chain UA [auth E] mmCIF format, chain V [auth B] mmCIF format, chain WA [auth E] mmCIF format, chain Y [auth B] mmCIF format, chain Z [auth B] mmCIF format, chain YA [auth E] mmCIF format, chain P [auth A] mmCIF format, chain M [auth A] mmCIF format, chain KA [auth D]	CB [auth E] DA [auth B] G [auth A] HB [auth C] I [auth A] CB [auth E], DA [auth B], G [auth A], HB [auth C], I [auth A], KA [auth D], L [auth A], M [auth A], NA [auth D], P [auth A], UA [auth E], V [auth B], WA [auth E], Y [auth B], YA [auth E], Z [auth B]	OLEIC ACID C₁₈ H₃₄ O₂ ZQPPMHVWECSIRJ-KTKRTIGZSA-N		Interactions Focus chain CB [auth E] Focus chain DA [auth B] Focus chain G [auth A] Focus chain HB [auth C] Focus chain I [auth A] Focus chain KA [auth D] Focus chain L [auth A] Focus chain M [auth A] Focus chain NA [auth D] Focus chain P [auth A] Focus chain UA [auth E] Focus chain V [auth B] Focus chain WA [auth E] Focus chain Y [auth B] Focus chain YA [auth E] Focus chain Z [auth B] Interactions & Density Focus chain CB [auth E] Focus chain DA [auth B] Focus chain G [auth A] Focus chain HB [auth C] Focus chain I [auth A] Focus chain KA [auth D] Focus chain L [auth A] Focus chain M [auth A] Focus chain NA [auth D] Focus chain P [auth A] Focus chain UA [auth E] Focus chain V [auth B] Focus chain WA [auth E] Focus chain Y [auth B] Focus chain YA [auth E] Focus chain Z [auth B]
NA (Subject of Investigation/LOI) Query on NA Download:Ideal Coordinates CCD File SDF format, chain EA [auth B] SDF format, chain GB [auth E] SDF format, chain Q [auth A] SDF format, chain RA [auth D] SDF format, chain QB [auth C] MOL2 format, chain EA [auth B] MOL2 format, chain GB [auth E] MOL2 format, chain Q [auth A] MOL2 format, chain RA [auth D] MOL2 format, chain QB [auth C] mmCIF format, chain EA [auth B] mmCIF format, chain GB [auth E] mmCIF format, chain Q [auth A] mmCIF format, chain RA [auth D] mmCIF format, chain QB [auth C]	EA [auth B], GB [auth E], Q [auth A], QB [auth C], RA [auth D]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N		Interactions Focus chain EA [auth B] Focus chain GB [auth E] Focus chain Q [auth A] Focus chain QB [auth C] Focus chain RA [auth D] Interactions & Density Focus chain EA [auth B] Focus chain GB [auth E] Focus chain Q [auth A] Focus chain QB [auth C] Focus chain RA [auth D]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.40 Å
R-Value Free: 0.217 (Depositor), 0.224 (DCC)
R-Value Work: 0.186 (Depositor), 0.198 (DCC)
R-Value Observed: 0.188 (Depositor)

Space Group: C 2 2 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 129.84	α = 90
b = 239.7	β = 90
c = 134.58	γ = 90

Software Package:

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

Structure Validation

View Full Validation Report

View more in-depth experimental data

Entry History

& Funding Information

Deposition Data

Released Date: 2020-06-17

Deposition Author(s):

Funding Organization	Location	Grant Number
Russian Foundation for Basic Research	Russian Federation	17-00-00164
Russian Foundation for Basic Research	Russian Federation	17-00-00165
Russian Foundation for Basic Research	Russian Federation	17-00-00167

Revision History (Full details and data files)

Version 1.0: 2020-06-17
Type: Initial release
Version 1.1: 2020-07-29
Type: Remediation
Reason: Carbohydrate remediation
Changes: Data collection, Derived calculations, Structure summary
Version 1.2: 2024-01-24
Changes: Data collection, Database references, Refinement description, Structure summary
Version 1.3: 2024-11-20
Changes: Structure summary