SAXSdb — 1zir

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

Gamma crystallin E

Rattus norvegicus

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	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

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 1ZIR	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
1A5D GAMMAE CRYSTALLIN FROM RAT LENS Deposited 1998-02-12	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	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions pH 7；pH 7.0	Resolution 2.30 Å
1A5D GAMMAE CRYSTALLIN FROM RAT LENS Deposited 1998-02-12	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain B 1–173（173 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions pH 7；pH 7.0	Resolution 2.30 Å
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

4 other PDB entries and 5 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

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	1zir
Deposition date deposition_date	2005-04-27
Structure title title	Deuterated gammaE crystallin in H2O solvent
Keywords keywords	4 Greek key motifs, STRUCTURAL PROTEIN; STRUCTURAL 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	17.66 Å
Radius of gyration Rg (electron density) rg_electron	16.52 Å
Forward intensity I(0) i0	8751200.00
Molecular weight molecular_weight	20417.0 kDa
Excluded volume excluded_volume	24844 Å³
Envelope volume envelope_volume	28208 Å³
Hydration-shell volume shell_volume	14716 Å³
Envelope diameter envelope_diameter	58.3 Å
Shell Rg shell_rg	22.01 Å
Envelope Rg envelope_rg	16.71 Å
Shape Rg shape_rg	16.53 Å
Total Rg total_rg	17.39 Å
Total atoms total_atoms	1443
Residues n_residues	173
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	61.4 Å
Rg (real space) rg_real	17.63 Å
Rg uncertainty (real space) rg_real_error	0.50 Å
I(0) (real space) i0_real	8.7510e+06
I(0) uncertainty (real space) i0_real_error	1.0970e+05
Rg (reciprocal space) rg_reciprocal	17.64 Å
I(0) (reciprocal space) i0_reciprocal	8751000.0000
Solution quality estimate total_estimate	0.7782
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	56.5 Å
Skewness Skewness skewness	0.338
Kurtosis Kurtosis kurtosis	-0.314
Angular range angular_range	— – 0.4500 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	1934000.0000
Real-space data points n_real_points	76
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.718; Stabil: 0.999; Sysdev: 1.000; Positv: 1.000; Valcen: 0.961; Smooth: 0.000

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (3)

Entity 1 Entity 1 polymer

Description description	Gamma crystallin E
Molecular weight formula_weight	21163.6 kDa
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	1771

GKITFYEDRGFQGRHYECSTDHSNLQPYFSRCNSVRVDSGCWMLYEQPNFTGCQYFLRRGDYPDYQQWMGFSDSVRSCRLIPHSSSHRIRIYEREDYRGQMVEITDDCPHLQDRFHFSDFHSFHVMEGYWVLYEMPNYRGRQYLLRPGEYRRYHDWGAMNARVGSLRRIMDFY

来源 Source

来源生物 organism	Rattus norvegicus
通用名 common_name	Norway rat
NCBI Class编号 ncbi_taxonomy_id	10116
宿主生物 host_organism	Escherichia coli BL21(DE3)

Entity 2 Entity 2 non-polymer

Description description	ACETATE ION
Molecular weight formula_weight	59.0 kDa
Source method src_method	syn
Copy count entity_count	3

Entity 3 Entity 3 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	147

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7. Fold Classification (SCOP + CATH) 4 domains

SCOP 2.08 (2 domains)

Domain ID domain_id	d1zira1
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	d1zira2
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	1zirA01
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	1zirA02
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	37.530 Å
Unit-cell length b length_b	43.320 Å
Unit-cell length c length_c	101.610 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	4

Space group space_group	P 21 21 21
Space-group number int_tables_number	19
Crystal system crystal_system	—

Resolution resolution	1.360 Å
Low-resolution limit resolution_low	50.640 Å
R factor r_factor	0.1820
R_work r_work	0.1800
R_free r_free	0.2110

fit	/app/data/saxs_computation/zi/1zir/1zir.fit
pddf	/app/data/pr_computation/zi/1zir/1zir.pr.out
profile	/app/data/saxs_computation/zi/1zir/1zir.dat

Deuterated gammaE crystallin in H2O solvent

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

Gamma crystallin E

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