SAXSdb — 8e1k

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

Photoactive yellow protein

Halorhodospira halophila

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein monomer	Monomer	Protein 1	;4'-HYDROXYCINNAMIC ACID ; × 1 water × 1	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	PYP_HALHA
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–125； UniProt 1–125

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	8e1k
Deposition date deposition_date	2022-08-10
Structure title title	Crystal structure of photoactive yellow protein (PYP); F96oCNF M100Q construct
Keywords keywords	PHOTORECEPTOR, 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.

8e1k__assembly_1__model_1

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

Download this curve (.dat)

8e1k__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

8e1k__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	14.84 Å
Rg (electron density)	13.20 Å
Total Rg	14.59 Å
Atom count	982
Residues	123
Excluded volume	17340 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`8e1k__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 (3)

Entity 1 Entity 1 polymer

Description description	Photoactive yellow protein
Molecular weight formula_weight	13910.5 kDa
Mutation mutation	M100Q
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	1291

MEHVAFGSEDIENTLAKMDDGQLDGLAFGAIQLDGDGNILQYNAAEGDITGRDPKQVIGKNFFKDVAPCTDSPEFYGKFKEGVASGNLNTMFEYTXDYQQTPTKVKVHMKKALSGDSYWVFVKRV

Source Source

Source organism organism	Halorhodospira halophila
NCBI taxonomy ID ncbi_taxonomy_id	1053
Host organism host_organism	Escherichia coli str. K-12 substr. DH10B

Entity 2 Entity 2 non-polymer

Description description	;4'-HYDROXYCINNAMIC ACID ;
Molecular weight formula_weight	164.2 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 3 Entity 3 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	99

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Unit-cell length a length_a	66.362 Å
Unit-cell length b length_b	66.362 Å
Unit-cell length c length_c	40.574 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	90.00 °
Unit-cell angle γ angle_gamma	120.00 °
Molecules per unit cell Z z_pdb	6

Space group space_group	P 63
Space-group number int_tables_number	173
Crystal system crystal_system	—

Resolution resolution	1.020 Å
Low-resolution limit resolution_low	33.180 Å
R factor r_factor	0.1480
R_work r_work	0.1470
R_free r_free	0.1610

Crystal structure of photoactive yellow protein (PYP); F96oCNF M100Q construct

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

Photoactive yellow protein

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

8e1k__assembly_1__model_1

8e1k__assembly_1__model_1 | I(q)

8e1k__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 (3)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 non-polymer

Entity 3 Entity 3 water

7. Citations (1)

Crystal structure of photoactive yellow protein (PYP); F96oCNF M100Q construct

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

Photoactive yellow protein

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

8e1k__assembly_1__model_1

8e1k__assembly_1__model_1 | I(q)

8e1k__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 (3)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 non-polymer

Entity 3 Entity 3 water

7. Citations (1)