SAXSdb — 9h1w

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1. Protein Identity and Related Structures Protein Identity & Related Structures

Sensory rhodopsin-2

Natronomonas pharaonis

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein monomer	Monomer	Protein 1	RETINAL × 1 CHLORIDE ION × 1 octyl beta-D-glucopyranoside × 8 [(Z)-octadec-9-enyl] (2R)-2,3-bis(oxidanyl)propanoate × 6 water × 1	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	BACS2_NATPH
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–239； UniProt 1–239

The page prioritizes protein identity, the current assembly, associated components, oligomeric state and cross-PDB links. Chain mapping and sequence ranges are retained as data evidence. Internal IDs, import timestamps and assembly operation expressions are maintenance fields and are not shown here.

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2. Structure Basics 2. Structure Basics

Entry ID entry_id	9h1w
Deposition date deposition_date	2024-10-10
Last revision last_revision	2025-04-30
Structure title title	Grouped 150-240 ms dark structure of sensory rhodopsin-II solved by serial millisecond crystallography
Keywords keywords	;SRII, serial millisecond crystallography, sensory rhodopsin, sensory rhodopsin II, SMX, SSX, Time-resolved crystallography, TRX, SIGNALING PROTEIN ;; SIGNALING PROTEIN
Experimental Method method	X-RAY DIFFRACTION

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3. Official assembly/model SAXS Official SAXS Profiles

This page reads only the latest assembly calculations. Every curve maps to an explicit PDB entry, official biological assembly and coordinate model.

9h1w__assembly_1__model_1

Assembly 1 · Model 1 · CRYSOL 4.1.3-1-20251215 (887e7ef)

Download this curve (.dat)

9h1w__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

9h1w__assembly_1__model_1 | P(r) · Pending

P(r) will be calculated and displayed separately for the same assembly/model.

Rg（Guinier）	19.11 Å
Rg (electron density)	17.89 Å
Total Rg	19.34 Å
Atom count	1918
Residues	212
Excluded volume	36683 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`9h1w__assembly_1__model_1`	monomeric （1）	Success	4.1.3-1-20251215 (887e7ef)	View Download

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4. Crystallography and Experiment 4. Crystallography & Experiment

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5. Entities and Polymers Entities & Polymers (6)

Entity 1 Entity 1 polymer

Description description	Sensory rhodopsin-2
Molecular weight formula_weight	26666.1 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A
Atom count atom_count	1951

MVGLTTLFWLGAIGMLVGTLAFAWAGRDAGSGERRYYVTLVGISGIAAVAYVVMALGVGWVPVAERTVFAPRYIDWILTTPLIVYFLGLLAGLDSREFGIVITLNTVVMLAGFAGAMVPGIERYALFGMGAVAFLGLVYYLVGPMTESASQRSSGIKSLYVRLRNLTVILWAIYPFIWLLGPPGVALLTPTVDVALIVYLDLVTKVGFGFIALDAAATLRAEHGESLAGVDTDAPAVADENSHHHHHHH

Source Source

Source organism organism	Natronomonas pharaonis
NCBI taxonomy ID ncbi_taxonomy_id	2257
Host organism host_organism	Escherichia coli

Entity 2 Entity 2 non-polymer

Description description	RETINAL
Molecular weight formula_weight	284.4 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 3 Entity 3 non-polymer

Description description	CHLORIDE ION
Molecular weight formula_weight	35.5 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 4 Entity 4 non-polymer

Description description	octyl beta-D-glucopyranoside
Molecular weight formula_weight	292.4 kDa
Source method src_method	syn
Copy count entity_count	8

Entity 5 Entity 5 non-polymer

Description description	[(Z)-octadec-9-enyl] (2R)-2,3-bis(oxidanyl)propanoate
Molecular weight formula_weight	356.5 kDa
Source method src_method	syn
Copy count entity_count	6

Entity 6 Entity 6 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	33

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Unit-cell length a length_a	89.750 Å
Unit-cell length b length_b	131.750 Å
Unit-cell length c length_c	51.000 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	90.00 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	8

Space group space_group	C 2 2 21
Space-group number int_tables_number	20
Crystal system crystal_system	orthorhombic

Resolution resolution	2.200 Å
Low-resolution limit resolution_low	44.880 Å
R factor r_factor	0.2158
R_work r_work	0.2157
R_free r_free	0.2185

Grouped 150-240 ms dark structure of sensory rhodopsin-II solved by serial millisecond crystallography

1. Protein Identity and Related Structures Protein Identity & Related Structures

Sensory rhodopsin-2

State in the Current Structure

Other States of the Same Protein in the Database

2. Structure Basics 2. Structure Basics

3. Official assembly/model SAXS Official SAXS Profiles

9h1w__assembly_1__model_1

9h1w__assembly_1__model_1 | I(q)

9h1w__assembly_1__model_1 | P(r) · Pending

4. Crystallography and Experiment 4. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

Diffraction experiment Diffraction

5. Entities and Polymers Entities & Polymers (6)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 non-polymer

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 non-polymer

Entity 5 Entity 5 non-polymer

Entity 6 Entity 6 water

7. Citations (1)

Grouped 150-240 ms dark structure of sensory rhodopsin-II solved by serial millisecond crystallography

1. Protein Identity and Related Structures Protein Identity & Related Structures

Sensory rhodopsin-2

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

2. Structure Basics 2. Structure Basics

3. Official assembly/model SAXS Official SAXS Profiles

9h1w__assembly_1__model_1

9h1w__assembly_1__model_1 | I(q)

9h1w__assembly_1__model_1 | P(r) · Pending

4. Crystallography and Experiment 4. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

Diffraction experiment Diffraction

5. Entities and Polymers Entities & Polymers (6)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 non-polymer

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 non-polymer

Entity 5 Entity 5 non-polymer

Entity 6 Entity 6 water

7. Citations (1)