SAXSdb — 1a5d

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

GAMMAE CRYSTALLIN

OrganismNot specified

State in the Current Structure

Assembly	Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Associated Components	Method and Experimental Conditions	Structure Quality
1	Protein monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count	Chain A； UniProt 1–173	Not recorded	No other associated polymer	X-RAY DIFFRACTION X-ray crystallization conditions：pH 7；pH 7.0	Resolution 2.30 Å
2	Protein monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count	Chain B； UniProt 1–173	Not recorded	No other associated polymer	X-RAY DIFFRACTION X-ray crystallization conditions：pH 7；pH 7.0	Resolution 2.30 Å

Other States of the Same Protein in the Database

Each row is a biological assembly of the same UniProt protein in another PDB entry. The “Difference from current entry” column identifies evidence-level differences; no tag means the currently parsed fields agree.

Other PDB	Difference from Current Entry 1A5D	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
1ZGT Structure of hydrogenated rat gamma E crystallin in H2O Deposited 2005-04-22	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1–173（173 aa）	Not recorded	ACT ACETATE ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.4；293 K；PEG 3350, magnesium Actetate, pH 7.4, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 1.45 Å R-free 0.254
1ZIE Hydrogenated gammaE crystallin in D2O solvent Deposited 2005-04-27	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1–173（173 aa）	Not recorded	ACT ACETATE ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.4；293 K；PEG 3350, Magnesium Acetate, D2O, pH 7.4, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 1.44 Å R-free 0.220
1ZIQ Deuterated gammaE crystallin in D2O solvent Deposited 2005-04-27	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1–173（173 aa）	Not recorded	ACT ACETATE ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.4；293 K；PEG 3350, Magnesium Acetate, D2O, pH 7.4, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 1.72 Å R-free 0.225
1ZIR Deuterated gammaE crystallin in H2O solvent Deposited 2005-04-27	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1–173（173 aa）	Not recorded	ACT ACETATE ION × 3	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.7；293 K；PEG 3350, Magnesium acetate, H2O, pH 7.7, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 1.36 Å R-free 0.211

4 other PDB entries and 4 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	CRGE_RAT
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–173； UniProt 1–173 Author chain B； PDBConstruct 1–173； UniProt 1–173

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	1a5d
Deposition date deposition_date	1998-02-12
Structure title title	GAMMAE CRYSTALLIN FROM RAT LENS
Keywords keywords	EYE LENS PROTEIN; EYE LENS PROTEIN
Experimental Method method	X-RAY DIFFRACTION

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3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

Radius of gyration Rg (Guinier) rg_guinier	31.39 Å
Radius of gyration Rg (electron density) rg_electron	31.09 Å
Forward intensity I(0) i0	31814700.00
Molecular weight molecular_weight	42161.0 kDa
Excluded volume excluded_volume	51485 Å³
Envelope volume envelope_volume	65777 Å³
Hydration-shell volume shell_volume	18618 Å³
Envelope diameter envelope_diameter	106.6 Å
Shell Rg shell_rg	36.33 Å
Envelope Rg envelope_rg	30.40 Å
Shape Rg shape_rg	31.09 Å
Total Rg total_rg	31.50 Å
Total atoms total_atoms	2973
Residues n_residues	346
Spherical-harmonic order n_harmonics	20
q range q_range	— – 0.5000 Å⁻¹
Data points n_points	101
Shell type shell_type	directional
Solvent electron density solvent_density	0.3340 e/Å³
Shell contrast contrast_shell	0.0300 e/Å³
CRYSOL version crysol_version	4.1.3

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4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

Maximum dimension Dmax dmax	102.8 Å
Rg (real space) rg_real	31.81 Å
Rg uncertainty (real space) rg_real_error	0.99 Å
I(0) (real space) i0_real	3.1810e+07
I(0) uncertainty (real space) i0_real_error	5.1850e+05
Rg (reciprocal space) rg_reciprocal	31.64 Å
I(0) (reciprocal space) i0_reciprocal	31810000.0000
Solution quality estimate total_estimate	0.7305
Solution quality rating solution_quality	REASONABLE a REASONABLE solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	20.6 Å
Skewness Skewness skewness	0.427
Kurtosis Kurtosis kurtosis	-0.745
Angular range angular_range	— – 0.2500 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	4214000.0000
Real-space data points n_real_points	51
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.566; Stabil: 0.998; Sysdev: 1.000; Positv: 1.000; Valcen: 0.376; Smooth: 0.425

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (2)

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7. Fold Classification (SCOP + CATH) 8 domains

SCOP 2.08 (4 domains)

Domain ID domain_id	d1a5da1
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	d1a5da2
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	d1a5db1
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	d1a5db2
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 (4 domains)

Domain ID domain_id	1a5dA01
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	1a5dA02
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	1a5dB01
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	1a5dB02
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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8. Citations (1)

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Unit-cell length a length_a	37.760 Å
Unit-cell length b length_b	43.710 Å
Unit-cell length c length_c	107.440 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	108.54 °
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	2.300 Å
Low-resolution limit resolution_low	8.000 Å
R factor r_factor	0.1680
R_work r_work	0.1680
R_free r_free	—

Description description	GAMMAE CRYSTALLIN
Molecular weight formula_weight	21163.6 kDa
Source method src_method	nat
Copy count entity_count	2

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B
Atom count atom_count	3230

GAMMAE CRYSTALLIN FROM RAT LENS

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

GAMMAE CRYSTALLIN

State in the Current Structure

Other States of the Same Protein in the Database

SAXS scattering curve SAXS Profile

P(r) Distance Distribution P(r) Distribution

2. Structure Basics 2. Structure Basics

3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

5. Crystallography and Experiment 5. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

Diffraction experiment Diffraction

6. Entities and Polymers Entities & Polymers (2)

Entity 1 Entity 1 polymer

Polymer Polymer

Entity 2 Entity 2 water

7. Fold Classification (SCOP + CATH) 8 domains

SCOP 2.08 (4 domains)

CATH v4.4 (4 domains)

8. Citations (1)

9. Files and Curves (10)

Files (7)

Curves (3)

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	257

fit	/app/data/saxs_computation/a5/1a5d/1a5d.fit
pddf	/app/data/pr_computation/a5/1a5d/1a5d.pr.out
profile	/app/data/saxs_computation/a5/1a5d/1a5d.dat