4Y9H | pdb_00004y9h

The 1.43 angstrom crystal structure of bacteriorhodopsin crystallized from bicelles

PDB DOI: https://doi.org/10.2210/pdb4Y9H/pdb

Classification: LIPID BINDING PROTEIN
Organism(s): Halobacterium salinarum R1
Mutation(s): No
Membrane Protein: Yes PDBTM MemProtMD

Deposited: 2015-02-17 Released: 2016-02-17
Deposition Author(s): Saiki, H., Sugiyama, S., Kakinouchi, K., Kawatake, S., Hanashima, S., Matsumori, N., Murata, M.
Funding Organization(s): JSPS KAKENHI

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.43 Å
R-Value Free:
0.221 (Depositor), 0.227 (DCC)
R-Value Work:
0.199 (Depositor), 0.207 (DCC)
R-Value Observed:
0.201 (Depositor)

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.2 of the entry. See complete history.

Literature

The 1.43 angstrom crystal structure of bacteriorhodopsin crystallized from bicelles

Saiki, H., Sugiyama, S., Kakinouchi, K., Kawatake, S., Hanashima, S., Matsumori, N., Murata, M.

To be published.

Macromolecule Content

Total Structure Weight: 27.53 kDa
Atom Count: 2,109
Modeled Residue Count: 226
Deposited Residue Count: 226
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Bacteriorhodopsin	A	226	Halobacterium salinarum R1	Mutation(s): 0 Membrane Entity: Yes
UniProt
Find proteins for B0R5N9 (Halobacterium salinarum (strain ATCC 29341 / DSM 671 / R1)) Explore B0R5N9 Go to UniProtKB: B0R5N9
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	B0R5N9
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 7 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
RET 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 J [auth A] MOL2 format, chain J [auth A] mmCIF format, chain J [auth A]	J [auth A]	HEXADECANE C₁₆ H₃₄ DCAYPVUWAIABOU-UHFFFAOYSA-N		Interactions Focus chain J [auth A] Interactions & Density Focus chain J [auth A]
D12 Query on D12 Download:Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain F [auth A] SDF format, chain G [auth A] SDF format, chain L [auth A] SDF format, chain M [auth A] SDF format, chain O [auth A] SDF format, chain P [auth A] SDF format, chain Q [auth A] MOL2 format, chain E [auth A] MOL2 format, chain F [auth A] MOL2 format, chain G [auth A] MOL2 format, chain L [auth A] MOL2 format, chain M [auth A] MOL2 format, chain O [auth A] MOL2 format, chain P [auth A] MOL2 format, chain Q [auth A] mmCIF format, chain E [auth A] mmCIF format, chain F [auth A] mmCIF format, chain G [auth A] mmCIF format, chain L [auth A] mmCIF format, chain M [auth A] mmCIF format, chain O [auth A] mmCIF format, chain P [auth A] mmCIF format, chain Q [auth A]	E [auth A] F [auth A] G [auth A] L [auth A] M [auth A] E [auth A], F [auth A], G [auth A], L [auth A], M [auth A], O [auth A], P [auth A], Q [auth A]	DODECANE C₁₂ H₂₆ SNRUBQQJIBEYMU-UHFFFAOYSA-N		Interactions Focus chain E [auth A] Focus chain F [auth A] Focus chain G [auth A] Focus chain L [auth A] Focus chain M [auth A] Focus chain O [auth A] Focus chain P [auth A] Focus chain Q [auth A] Interactions & Density Focus chain E [auth A] Focus chain F [auth A] Focus chain G [auth A] Focus chain L [auth A] Focus chain M [auth A] Focus chain O [auth A] Focus chain P [auth A] Focus chain Q [auth A]
D10 Query on D10 Download:Ideal Coordinates CCD File SDF format, chain R [auth A] SDF format, chain K [auth A] SDF format, chain I [auth A] SDF format, chain H [auth A] MOL2 format, chain R [auth A] MOL2 format, chain K [auth A] MOL2 format, chain I [auth A] MOL2 format, chain H [auth A] mmCIF format, chain R [auth A] mmCIF format, chain K [auth A] mmCIF format, chain I [auth A] mmCIF format, chain H [auth A]	H [auth A], I [auth A], K [auth A], R [auth A]	DECANE C₁₀ H₂₂ DIOQZVSQGTUSAI-UHFFFAOYSA-N		Interactions Focus chain H [auth A] Focus chain I [auth A] Focus chain K [auth A] Focus chain R [auth A] Interactions & Density Focus chain H [auth A] Focus chain I [auth A] Focus chain K [auth A] Focus chain R [auth A]
DD9 Query on DD9 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]	nonane C₉ H₂₀ BKIMMITUMNQMOS-UHFFFAOYSA-N		Interactions Focus chain N [auth A] Interactions & Density Focus chain N [auth A]
HP6 Query on HP6 Download:Ideal Coordinates CCD File SDF format, chain D [auth A] MOL2 format, chain D [auth A] mmCIF format, chain D [auth A]	D [auth A]	HEPTANE C₇ H₁₆ IMNFDUFMRHMDMM-UHFFFAOYSA-N		Interactions Focus chain D [auth A] Interactions & Density Focus chain D [auth A]
PO4 Query on PO4 Download:Ideal Coordinates CCD File SDF format, chain C [auth A] MOL2 format, chain C [auth A] mmCIF format, chain C [auth A]	C [auth A]	PHOSPHATE ION O₄ P NBIIXXVUZAFLBC-UHFFFAOYSA-K		Interactions Focus chain C [auth A] Interactions & Density Focus chain C [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.43 Å
R-Value Free: 0.221 (Depositor), 0.227 (DCC)
R-Value Work: 0.199 (Depositor), 0.207 (DCC)
R-Value Observed: 0.201 (Depositor)

Space Group: C 2 2 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 45.215	α = 90
b = 102.794	β = 90
c = 128.337	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
HKL-2000	data reduction
HKL-2000	data scaling
REFMAC	phasing

Structure Validation

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Ligand Structure Quality Assessment

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Entry History

& Funding Information

Deposition Data

Released Date: 2016-02-17

Deposition Author(s):

Funding Organization	Location	Grant Number
JSPS KAKENHI	Japan	25286051
JSPS KAKENHI	Japan	25650051

Revision History (Full details and data files)

Version 1.0: 2016-02-17
Type: Initial release
Version 1.1: 2020-02-05
Changes: Data collection, Database references, Derived calculations
Version 1.2: 2024-03-20
Changes: Data collection, Database references