SAXSdb — 4j89

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

Green fluorescent protein

Aequorea victoria

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein monomer	Monomer	Protein 1	SULFATE ION × 2 1,2-ETHANEDIOL × 13 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL × 1 water × 1	Consistent with protein count
2	Protein monomer	Monomer	Protein 1	SULFATE ION × 3 1,2-ETHANEDIOL × 10 water × 1	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	GFP_AEQVI
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 3–237； UniProt 2–238 Author chain B； PDBConstruct 3–237； UniProt 2–238

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	4j89
Deposition date deposition_date	2013-02-14
Structure title title	Different photochemical events of a genetically encoded aryl azide define and modulate GFP fluorescence
Keywords keywords	beta-barrel, fluorescent protein, chromophore by cyclisation, p-azido-L-phenylalanine, cytosol; FLUORESCENT 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.

4j89__assembly_2__model_1

Assembly 2 · Model 1 · CRYSOL 4.1.3-1-20251215 (887e7ef)

Download this curve (.dat)

4j89__assembly_2__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

4j89__assembly_2__model_1 | P(r) · Pending

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

Rg（Guinier）	18.35 Å
Rg (electron density)	17.09 Å
Total Rg	18.16 Å
Atom count	1859
Residues	226
Excluded volume	32918 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`4j89__assembly_1__model_1`	monomeric （1）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`4j89__assembly_2__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 (5)

Entity 1 Entity 1 polymer

Description description	Green fluorescent protein
Molecular weight formula_weight	27870.4 kDa
Mutation mutation	S30R, Y39N, Q80R, F99S, N105T, F145Y, M153T, V163A, A171V, A206V
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B
Atom count atom_count	4074

MVSKGEELFTGVVPILVELDGDVNGHKFSVRGEGEGDATNGKLTLKFICTTGKLPVPWPTLVTTLXVQCFSRYPDHMKRHDFFKSAMPEGYVQERTISFKDDGTYKTRAEVKFEGDTLVNRIELKGIDFKEDGNILGHKLEYNFNSHNVYITADKQKNGIKANFKIRHNVEDGSVQLADHYQQNTPIGDGPVLLPDNHYLSTQSVLSKDPNEKRDHMVLLEFVTAAGITHGMDELYKGSHHHHHH

Source Source

Source organism organism	Aequorea victoria
Common name common_name	Jellyfish
NCBI taxonomy ID ncbi_taxonomy_id	6100
Host organism host_organism	Escherichia coli

Entity 2 Entity 2 non-polymer

Description description	SULFATE ION
Molecular weight formula_weight	96.1 kDa
Source method src_method	syn
Copy count entity_count	5

Entity 3 Entity 3 non-polymer

Description description	1,2-ETHANEDIOL
Molecular weight formula_weight	62.1 kDa
Source method src_method	syn
Copy count entity_count	23

Entity 4 Entity 4 non-polymer

Description description	2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL
Molecular weight formula_weight	122.1 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 5 Entity 5 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	283

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6. Fold Classification (SCOP + CATH) 5 domains

SCOP 2.08 (3 domains)

Domain ID domain_id	d4j89a1
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.22 — GFP-like
Superfamily Superfamily superfamily	d.22.1 — GFP-like
Family Family family	d.22.1.1 — Fluorescent proteins

Domain ID domain_id	d4j89a2
Class class	l — Artifacts
Fold Fold fold	l.1 — Tags
Superfamily Superfamily superfamily	l.1.1 — Tags
Family Family family	l.1.1.1 — Tags

Domain ID domain_id	d4j89b_
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.22 — GFP-like
Superfamily Superfamily superfamily	d.22.1 — GFP-like
Family Family family	d.22.1.1 — Fluorescent proteins

CATH v4.4 (2 domains)

Domain ID domain_id	4j89A00
Class class	2 — Mainly Beta
Architecture architecture	40 — Beta Barrel
Topology topology	155 — Green Fluorescent Protein
Homologous superfamily homologous superfamily	10 — Green fluorescent protein

Domain ID domain_id	4j89B00
Class class	2 — Mainly Beta
Architecture architecture	40 — Beta Barrel
Topology topology	155 — Green Fluorescent Protein
Homologous superfamily homologous superfamily	10 — Green fluorescent protein

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Unit-cell length a length_a	52.370 Å
Unit-cell length b length_b	98.110 Å
Unit-cell length c length_c	102.910 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	P 21 21 21
Space-group number int_tables_number	19
Crystal system crystal_system	—

Resolution resolution	2.100 Å
Low-resolution limit resolution_low	51.460 Å
R factor r_factor	0.1850
R_work r_work	0.1820
R_free r_free	0.2420

Different photochemical events of a genetically encoded aryl azide define and modulate GFP fluorescence

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

Green fluorescent 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

4j89__assembly_2__model_1

4j89__assembly_2__model_1 | I(q)

4j89__assembly_2__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 (5)

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 water

6. Fold Classification (SCOP + CATH) 5 domains

SCOP 2.08 (3 domains)

CATH v4.4 (2 domains)

7. Citations (1)

Different photochemical events of a genetically encoded aryl azide define and modulate GFP fluorescence

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

Green fluorescent 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

4j89__assembly_2__model_1

4j89__assembly_2__model_1 | I(q)

4j89__assembly_2__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 (5)

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 water

6. Fold Classification (SCOP + CATH) 5 domains

SCOP 2.08 (3 domains)

CATH v4.4 (2 domains)

7. Citations (1)