SAXSdb — 1iej

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

OVOTRANSFERRIN

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 20–351	Fragment：N-TERMINAL DOMAIN(RESIDUES 20-351)	FE FE (III) ION × 1 CO3 CARBONATE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 5.9；293 K；PEG6000, pH 5.9, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 1.65 Å R-free 0.242

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 1IEJ	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
1AIV APO OVOTRANSFERRIN Deposited 1997-04-28	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Other combination Monomer；Protein × 1 PDB declaration: monomeric	Chain A 20–705（686 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions pH 5.9；pH 5.9	Resolution 3.00 Å R-free 0.265
1IQ7 Ovotransferrin, C-Terminal Lobe, Apo Form Deposited 2001-07-06	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 361–705（345 aa） Fragment：C-TERMINAL LOBE	Not recorded	NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1 SO4 SULFATE ION × 1	X-RAY DIFFRACTION mmCIF provides none of the parsed conditions	Resolution 2.30 Å R-free 0.239
1JL4 CRYSTAL STRUCTURE OF THE HUMAN CD4 N-TERMINAL TWO DOMAIN FRAGMENT COMPLEXED TO A CLASS II MHC MOLECULE Deposited 2001-07-15	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain C 153–165（13 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8.5；297 K；17% PEG 4,000/0.2M Li2SO4/0.1M Tris, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 297K	Resolution 4.30 Å R-free 0.453
1N04 Diferric chicken serum transferrin at 2.8 A resolution. Deposited 2002-10-11	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 20–705（686 aa）	Not recorded	FUL beta-L-fucopyranose × 1 FE FE (III) ION × 2 CO3 CARBONATE ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；277 K；PEG6000, 0.02M acetate, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 277K X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；277 K；PEG4000, 20mM sodium bicarbonate, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 277K	Resolution 2.80 Å R-free 0.269
1NFT OVOTRANSFERRIN, N-TERMINAL LOBE, IRON LOADED OPEN FORM Deposited 1999-01-07	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 23–351（329 aa） Fragment：N-TERMINAL LOBE	Not recorded	SO4 SULFATE ION × 3 FE FE (III) ION × 1 NTA NITRILOTRIACETIC ACID × 1	X-RAY DIFFRACTION X-ray crystallization conditions pH 7.5；pH 7.5	Resolution 2.10 Å R-free 0.256
1NFT OVOTRANSFERRIN, N-TERMINAL LOBE, IRON LOADED OPEN FORM Deposited 1999-01-07	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein homooligomer Homooligomer；Protein × 6 PDB declaration: hexameric	Chain A 23–351（329 aa） Fragment：N-TERMINAL LOBE	Not recorded	SO4 SULFATE ION × 18 FE FE (III) ION × 6 NTA NITRILOTRIACETIC ACID × 6	X-RAY DIFFRACTION X-ray crystallization conditions pH 7.5；pH 7.5	Resolution 2.10 Å R-free 0.256
1NNT STRUCTURAL EVIDENCE FOR A PH-SENSITIVE DI-LYSINE TRIGGER IN THE HEN OVOTRANSFERRIN N-LOBE: IMPLICATIONS FOR TRANSFERRIN IRON RELEASE Deposited 1993-09-15	Different construct Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 24–351（328 aa）	Not recorded	FE FE (III) ION × 1 CO3 CARBONATE ION × 1	X-RAY DIFFRACTION mmCIF provides none of the parsed conditions	Resolution 2.30 Å
1OVT REFINED CRYSTALLOGRAPHIC STRUCTURE OF HEN OVOTRANSFERRIN AT 2.4 ANGSTROMS RESOLUTION Deposited 1995-04-28	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 20–705（686 aa）	Not recorded	FE FE (III) ION × 2 CO3 CARBONATE ION × 2	X-RAY DIFFRACTION mmCIF provides none of the parsed conditions	Resolution 2.40 Å
1RYX Crystal structure of hen serum transferrin in apo- form Deposited 2003-12-23	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 20–705（686 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.9；277 K；18-23% PEG 6000 in 0.02M sodium acetate buffer, pH 5.9, VAPOR DIFFUSION, HANGING DROP, temperature 277K	Resolution 3.50 Å R-free 0.341
1TFA OVOTRANSFERRIN, N-TERMINAL LOBE, APO FORM Deposited 1999-01-07	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 23–351（329 aa） Fragment：N-TERMINAL LOBE	Not recorded	SO4 SULFATE ION × 4	X-RAY DIFFRACTION X-ray crystallization conditions pH 6；pH 6.0	Resolution 1.90 Å R-free 0.243
2D3I Crystal Structure of Aluminum-Bound Ovotransferrin at 2.15 Angstrom Resolution Deposited 2005-09-28	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 20–705（686 aa）	Not recorded	AL ALUMINUM ION × 2 BCT BICARBONATE ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8；277 K；PEG400, pH 8.0, VAPOR DIFFUSION, SITTING DROP, temperature 277K	Resolution 2.15 Å R-free 0.243
8FEI CryoEM structure of Conalbumin from chicken egg white (sigma-Cas 1391-06-6) Deposited 2022-12-06	Different construct Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1–705（705 aa）	Not recorded	FE FE (III) ION × 2	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5；PBS cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.00 Å

11 other PDB entries and 12 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	TRFE_CHICK
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–332； UniProt 20–351

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	1iej
Deposition date deposition_date	2001-04-10
Structure title title	OVOTRANSFERRIN, N-TERMINAL LOBE, HOLO FORM, AT 1.65 A RESOLUTION
Keywords keywords	transferrin, iron, ovotransferrin, METAL BINDING PROTEIN; METAL BINDING 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	20.35 Å
Radius of gyration Rg (electron density) rg_electron	19.29 Å
Forward intensity I(0) i0	23411100.00
Molecular weight molecular_weight	36345.0 kDa
Excluded volume excluded_volume	45211 Å³
Envelope volume envelope_volume	51357 Å³
Hydration-shell volume shell_volume	21849 Å³
Envelope diameter envelope_diameter	67.7 Å
Shell Rg shell_rg	26.04 Å
Envelope Rg envelope_rg	19.53 Å
Shape Rg shape_rg	19.28 Å
Total Rg total_rg	20.18 Å
Total atoms total_atoms	2550
Residues n_residues	329
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	65.6 Å
Rg (real space) rg_real	20.26 Å
Rg uncertainty (real space) rg_real_error	0.33 Å
I(0) (real space) i0_real	2.3410e+07
I(0) uncertainty (real space) i0_real_error	2.9210e+05
Rg (reciprocal space) rg_reciprocal	20.28 Å
I(0) (reciprocal space) i0_reciprocal	23410000.0000
Solution quality estimate total_estimate	0.8864
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	24.4 Å
Skewness Skewness skewness	0.237
Kurtosis Kurtosis kurtosis	-0.353
Angular range angular_range	— – 0.3900 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	5269000.0000
Real-space data points n_real_points	71
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.857; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.994; Smooth: 0.955

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (4)

Entity 1 Entity 1 polymer

Description description	OVOTRANSFERRIN
Molecular weight formula_weight	36542.3 kDa
Source method src_method	nat
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A
Atom count atom_count	2827

APPKSVIRWCTISSPEEKKCNNLRDLTQQERISLTCVQKATYLDCIKAIANNEADAITLDGGQVFEAGLAPYKLKPIAAEVYEHTEGSTTSYYAVAVVKKGTEFTVNDLQGKTSCHTGLGRSAGWNIPIGTLLHRGAIEWEGIESGSVEQAVAKFFSASCVPGATIEQKLCRQCKGDPKTKCARNAPYSGYSGAFHCLKDGKGDVAFVKHTTVNENAPDQKDEYELLCLDGSRQPVDNYKTCNWARVAAHAVVARDDNKVEDIWSFLSKAQSDFGVDTKSDFHLFGPPGKKDPVLKDLLFKDSAIMLKRVPSLMDSQLYLGFEYYSAIQSMR

Entity 2 Entity 2 non-polymer

Description description	FE (III) ION
Molecular weight formula_weight	55.8 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 3 Entity 3 non-polymer

Description description	CARBONATE ION
Molecular weight formula_weight	60.0 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 4 Entity 4 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	256

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7. Fold Classification (SCOP + CATH) 3 domains

SCOP 2.08 (1 domains)

Domain ID domain_id	d1ieja_
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.94 — Periplasmic binding protein-like II
Superfamily Superfamily superfamily	c.94.1 — Periplasmic binding protein-like II
Family Family family	c.94.1.2 — Transferrin

CATH v4.4 (2 domains)

Domain ID domain_id	1iejA01
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	190 — D-Maltodextrin-Binding Protein; domain 2
Homologous superfamily homologous superfamily	10 — Periplasmic binding protein-like II

Domain ID domain_id	1iejA02
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	190 — D-Maltodextrin-Binding Protein; domain 2
Homologous superfamily homologous superfamily	10 — Periplasmic binding protein-like II

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8. Citations (1)

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Unit-cell length a length_a	46.460 Å
Unit-cell length b length_b	85.950 Å
Unit-cell length c length_c	76.100 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	1.650 Å
Low-resolution limit resolution_low	10.000 Å
R factor r_factor	—
R_work r_work	0.1730
R_free r_free	0.2420

fit	/app/data/saxs_computation/ie/1iej/1iej.fit
pddf	/app/data/pr_computation/ie/1iej/1iej.pr.out
profile	/app/data/saxs_computation/ie/1iej/1iej.dat

OVOTRANSFERRIN, N-TERMINAL LOBE, HOLO FORM, AT 1.65 A RESOLUTION

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

OVOTRANSFERRIN

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