SAXSdb — 1nnt

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

OVOTRANSFERRIN

Gallus gallus

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 24–351	Not recorded	FE FE (III) ION × 1 CO3 CARBONATE ION × 1	X-RAY DIFFRACTION mmCIF provides none of the parsed experimental conditions	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 1NNT	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
1IEJ OVOTRANSFERRIN, N-TERMINAL LOBE, HOLO FORM, AT 1.65 A RESOLUTION Deposited 2001-04-10	Different construct Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 20–351（332 aa） Fragment：N-TERMINAL DOMAIN(RESIDUES 20-351)	Not recorded	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
1IQ7 Ovotransferrin, C-Terminal Lobe, Apo Form Deposited 2001-07-06	Different construct Different ligand/ion 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
1OVT REFINED CRYSTALLOGRAPHIC STRUCTURE OF HEN OVOTRANSFERRIN AT 2.4 ANGSTROMS RESOLUTION Deposited 1995-04-28	Different construct Different ligand/ion 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 1–328； UniProt 24–351

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	1nnt
Deposition date deposition_date	1993-09-15
Structure title title	STRUCTURAL EVIDENCE FOR A PH-SENSITIVE DI-LYSINE TRIGGER IN THE HEN OVOTRANSFERRIN N-LOBE: IMPLICATIONS FOR TRANSFERRIN IRON RELEASE
Keywords keywords	IRON TRANSPORT PROTEIN; IRON TRANSPORT 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	20.42 Å
Radius of gyration Rg (electron density) rg_electron	19.32 Å
Forward intensity I(0) i0	23459300.00
Molecular weight molecular_weight	36174.0 kDa
Excluded volume excluded_volume	44951 Å³
Envelope volume envelope_volume	51625 Å³
Hydration-shell volume shell_volume	21932 Å³
Envelope diameter envelope_diameter	67.4 Å
Shell Rg shell_rg	26.09 Å
Envelope Rg envelope_rg	19.54 Å
Shape Rg shape_rg	19.31 Å
Total Rg total_rg	20.23 Å
Total atoms total_atoms	2538
Residues n_residues	328
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	65.9 Å
Rg (real space) rg_real	20.33 Å
Rg uncertainty (real space) rg_real_error	0.35 Å
I(0) (real space) i0_real	2.3460e+07
I(0) uncertainty (real space) i0_real_error	2.7360e+05
Rg (reciprocal space) rg_reciprocal	20.35 Å
I(0) (reciprocal space) i0_reciprocal	23460000.0000
Solution quality estimate total_estimate	0.8874
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	24.5 Å
Skewness Skewness skewness	0.234
Kurtosis Kurtosis kurtosis	-0.354
Angular range angular_range	— – 0.3900 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	5171000.0000
Real-space data points n_real_points	71
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.856; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.994; Smooth: 0.970

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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	36105.8 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	2646

SVIRWCTISSPEEKKCNNLRDLTQQERISLTCVQKATYLDCIKAIANNEADAISLDGGQAFEAGLAPYKLKPIAAEVYEHTEGSTTSYYAVAVVKKGTEFTVNDLQGKTSCHTGLGRSAGWNIPIGTLLHRGAIEWEGIESGSVEQAVAKFFSASCVPGATIEQKLCRQCKGDPKTKCARNAPYSGYSGAFHCLKDGKGDVAFVKHTTVNENAPDQKDEYELLCLDGSRQPVDNYKTCNWARVAAHAVVARDDNKVEDIWSFLSKAQSDFGVDTKSDFHLFGPPGKKDPVLKDLLFKDSAIMLKRVPSLMDSQLYLGFEYYSAIQSMR

来源 Source

来源生物 organism	Gallus gallus
通用名 common_name	chicken
NCBI Class编号 ncbi_taxonomy_id	9031

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	108

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7. Fold Classification (SCOP + CATH) 3 domains

SCOP 2.08 (1 domains)

Domain ID domain_id	d1nnta_
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	1nntA01
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	1nntA02
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	46.940 Å
Unit-cell length b length_b	91.790 Å
Unit-cell length c length_c	75.820 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	2.300 Å
Low-resolution limit resolution_low	— Å
R factor r_factor	0.1600
R_work r_work	0.1600
R_free r_free	—

fit	/app/data/saxs_computation/nn/1nnt/1nnt.fit
pddf	/app/data/pr_computation/nn/1nnt/1nnt.pr.out
profile	/app/data/saxs_computation/nn/1nnt/1nnt.dat

STRUCTURAL EVIDENCE FOR A PH-SENSITIVE DI-LYSINE TRIGGER IN THE HEN OVOTRANSFERRIN N-LOBE: IMPLICATIONS FOR TRANSFERRIN IRON RELEASE