SAXSdb — 4jgf

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

Gamma-crystallin D

Homo sapiens

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein monomer	Monomer	Protein 1	water × 1	Consistent with protein count
2	Protein monomer	Monomer	Protein 1	water × 1	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	CRGD_HUMAN
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–171； UniProt 2–172 Author chain B； PDBConstruct 1–171； UniProt 2–172

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	4jgf
Deposition date deposition_date	2013-03-01
Structure title title	Crystal Structure of the Cataract-Causing P23T gamma D-Crystallin Mutant
Keywords keywords	STRUCTURAL PROTEIN; STRUCTURAL 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.

4jgf__assembly_1__model_1

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

Download this curve (.dat)

4jgf__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

4jgf__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	17.87 Å
Rg (electron density)	16.70 Å
Total Rg	17.59 Å
Atom count	1433
Residues	171
Excluded volume	24830 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`4jgf__assembly_1__model_1`	monomeric （1）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`4jgf__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 (2)

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6. Fold Classification (SCOP + CATH) 6 domains

SCOP 2.08 (2 domains)

Domain ID domain_id	d4jgfa_
Class class	b — All beta proteins
Fold Fold fold	b.11 — gamma-Crystallin-like
Superfamily Superfamily superfamily	b.11.1 — gamma-Crystallin-like
Family Family family	b.11.1.0 — automated matches

Domain ID domain_id	d4jgfb_
Class class	b — All beta proteins
Fold Fold fold	b.11 — gamma-Crystallin-like
Superfamily Superfamily superfamily	b.11.1 — gamma-Crystallin-like
Family Family family	b.11.1.0 — automated matches

CATH v4.4 (4 domains)

Domain ID domain_id	4jgfA01
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	20 — Gamma-B Crystallin; domain 1
Homologous superfamily homologous superfamily	10 — Crystallins

Domain ID domain_id	4jgfA02
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	20 — Gamma-B Crystallin; domain 1
Homologous superfamily homologous superfamily	10 — Crystallins

Domain ID domain_id	4jgfB01
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	20 — Gamma-B Crystallin; domain 1
Homologous superfamily homologous superfamily	10 — Crystallins

Domain ID domain_id	4jgfB02
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	20 — Gamma-B Crystallin; domain 1
Homologous superfamily homologous superfamily	10 — Crystallins

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Unit-cell length a length_a	37.550 Å
Unit-cell length b length_b	101.931 Å
Unit-cell length c length_c	41.371 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	96.54 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	4

Space group space_group	P 1 21 1
Space-group number int_tables_number	4
Crystal system crystal_system	—

Resolution resolution	2.500 Å
Low-resolution limit resolution_low	32.010 Å
R factor r_factor	0.2335
R_work r_work	0.2277
R_free r_free	0.2835

Description description	Gamma-crystallin D
Molecular weight formula_weight	20404.7 kDa
Mutation mutation	P23T
Source method src_method	man
Copy count entity_count	2

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B
Atom count atom_count	2871

Crystal Structure of the Cataract-Causing P23T gamma D-Crystallin Mutant

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

Gamma-crystallin D

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

4jgf__assembly_1__model_1

4jgf__assembly_1__model_1 | I(q)

4jgf__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 (2)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 water

6. Fold Classification (SCOP + CATH) 6 domains

SCOP 2.08 (2 domains)

CATH v4.4 (4 domains)

7. Citations (1)

Source organism organism	Homo sapiens
Common name common_name	human
NCBI taxonomy ID ncbi_taxonomy_id	9606
Host organism host_organism	Escherichia coli

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	5

Crystal Structure of the Cataract-Causing P23T gamma D-Crystallin Mutant

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

Gamma-crystallin D

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

4jgf__assembly_1__model_1

4jgf__assembly_1__model_1 | I(q)

4jgf__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 (2)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 water

6. Fold Classification (SCOP + CATH) 6 domains

SCOP 2.08 (2 domains)

CATH v4.4 (4 domains)

7. Citations (1)