SAXSdb — 1hdf

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

SPHERULIN 3A

PHYSARUM POLYCEPHALUM

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein homooligomer	Homooligomer	Protein 4	CALCIUM ION × 8 water × 4	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	SR3A_PHYPO
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–102； UniProt 2–103 Author chain B； PDBConstruct 1–102； UniProt 2–103

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	1hdf
Deposition date deposition_date	2000-11-13
Structure title title	Evolution of the eye lens beta-gamma-crystallin domain fold
Keywords keywords	STRUCTURAL PROTEIN, CRYSTALLINS, EYE LENS, DOMAIN INTERACTIONS, SPHERULIN 3A, TYROSINE CORNER; 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.

1hdf__assembly_1__model_1

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

Download this curve (.dat)

1hdf__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

1hdf__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	23.24 Å
Rg (electron density)	22.07 Å
Total Rg	22.86 Å
Atom count	3096
Residues	396
Excluded volume	55008 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`1hdf__assembly_1__model_1`	tetrameric （4）	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	SPHERULIN 3A
Molecular weight formula_weight	11230.3 kDa
Mutation mutation	YES
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	1675

SVCKGVSGNPAKGEVFLYKHVNFQGDSWKVTGNVYDFRSVSGLNDVVSSVKVGPNTKAFIFKDDRFNGNFIRLEESSQVTDLTTRNLNDAISSMIVATFESA

Source Source

Source organism organism	PHYSARUM POLYCEPHALUM
NCBI taxonomy ID ncbi_taxonomy_id	5791
Host organism host_organism	ESCHERICHIA COLI

Entity 2 Entity 2 non-polymer

Description description	CALCIUM ION
Molecular weight formula_weight	40.1 kDa
Source method src_method	syn
Copy count entity_count	4

Entity 3 Entity 3 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	127

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6. Fold Classification (SCOP + CATH) 4 domains

SCOP 2.08 (2 domains)

Domain ID domain_id	d1hdfa_
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.11.1.1 — Crystallins/Ca-binding development proteins

Domain ID domain_id	d1hdfb_
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.11.1.1 — Crystallins/Ca-binding development proteins

CATH v4.4 (2 domains)

Domain ID domain_id	1hdfA00
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	1hdfB00
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	41.350 Å
Unit-cell length b length_b	41.350 Å
Unit-cell length c length_c	213.640 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	16

Space group space_group	P 43 21 2
Space-group number int_tables_number	96
Crystal system crystal_system	—

Resolution resolution	2.350 Å
Low-resolution limit resolution_low	20.000 Å
R factor r_factor	0.2390
R_work r_work	0.2390
R_free r_free	—

Evolution of the eye lens beta-gamma-crystallin domain fold

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

SPHERULIN 3A

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

1hdf__assembly_1__model_1

1hdf__assembly_1__model_1 | I(q)

1hdf__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

6. Fold Classification (SCOP + CATH) 4 domains

SCOP 2.08 (2 domains)

CATH v4.4 (2 domains)

7. Citations (1)

Evolution of the eye lens beta-gamma-crystallin domain fold

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

SPHERULIN 3A

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

1hdf__assembly_1__model_1

1hdf__assembly_1__model_1 | I(q)

1hdf__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

6. Fold Classification (SCOP + CATH) 4 domains

SCOP 2.08 (2 domains)

CATH v4.4 (2 domains)

7. Citations (1)