SAXSdb — 3t7l

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

Zinc finger FYVE domain-containing protein 16

Homo sapiens

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 733–820	Fragment：FYVE domain (UNP residues 733-820)	ZN ZINC ION × 2 EDO 1,2-ETHANEDIOL × 1	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, SITTING DROP；pH 7.5；277.15 K；20% PEG 3350, 0.2 M NaNO3, 10% Ethylene glycol, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 277.15K	Resolution 1.09 Å R-free 0.154

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 3T7L	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
5MK0 Crystal structure of the His Domain Protein Tyrosine Phosphatase (HD-PTP/PTPN23) Bro1 domain (Endofin peptide complex) Deposited 2016-12-02	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain B 1–22（22 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；277 K；0.2 M Ammonium tartrate dibasic, 20% PEG3350 and 0.1 M MMT buffer pH 9.0, 25% PEG1500	Resolution 1.76 Å R-free 0.193
5MK0 Crystal structure of the His Domain Protein Tyrosine Phosphatase (HD-PTP/PTPN23) Bro1 domain (Endofin peptide complex) Deposited 2016-12-02	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain D 1–22（22 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；277 K；0.2 M Ammonium tartrate dibasic, 20% PEG3350 and 0.1 M MMT buffer pH 9.0, 25% PEG1500	Resolution 1.76 Å R-free 0.193

1 other PDB entries and 2 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	ZFY16_HUMAN
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 3–90； UniProt 733–820

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	3t7l
Deposition date deposition_date	2011-07-30
Structure title title	Crystal structure of the FYVE domain of endofin (ZFYVE16) at 1.1A resolution
Keywords keywords	structural genomics consortium, SGC, zinc finger, LIPID BINDING PROTEIN, TRANSPORT PROTEIN; 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	13.07 Å
Radius of gyration Rg (electron density) rg_electron	12.26 Å
Forward intensity I(0) i0	1838930.00
Molecular weight molecular_weight	8596.0 kDa
Excluded volume excluded_volume	10491 Å³
Envelope volume envelope_volume	12008 Å³
Hydration-shell volume shell_volume	8693 Å³
Envelope diameter envelope_diameter	43.1 Å
Shell Rg shell_rg	17.49 Å
Envelope Rg envelope_rg	12.79 Å
Shape Rg shape_rg	12.33 Å
Total Rg total_rg	13.31 Å
Total atoms total_atoms	587
Residues n_residues	74
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	45.0 Å
Rg (real space) rg_real	13.08 Å
Rg uncertainty (real space) rg_real_error	0.30 Å
I(0) (real space) i0_real	1.8390e+06
I(0) uncertainty (real space) i0_real_error	1.9000e+04
Rg (reciprocal space) rg_reciprocal	13.08 Å
I(0) (reciprocal space) i0_reciprocal	1839000.0000
Solution quality estimate total_estimate	0.7851
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	14.3 Å
Skewness Skewness skewness	0.386
Kurtosis Kurtosis kurtosis	-0.208
Angular range angular_range	— – 0.5000 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	560500.0000
Real-space data points n_real_points	80
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.752; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.947; Smooth: 0.000

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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	Zinc finger FYVE domain-containing protein 16
Molecular weight formula_weight	10244.1 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	745

SMEGLVLGQKQPTWVPDSEAPNCMNCQVKFTFTKRRHHCRACGKVFCGVCCNRKCKLQYLEKEARVCVVCYETISKAQAFERMMSPTGSN

来源 Source

来源生物 organism	Homo sapiens
通用名 common_name	human
NCBI Class编号 ncbi_taxonomy_id	9606
宿主生物 host_organism	Escherichia coli

Entity 2 Entity 2 non-polymer

Description description	ZINC ION
Molecular weight formula_weight	65.4 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 3 Entity 3 non-polymer

Description description	1,2-ETHANEDIOL
Molecular weight formula_weight	62.1 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	86

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7. Fold Classification (SCOP + CATH) 2 domains

SCOP 2.08 (1 domains)

Domain ID domain_id	d3t7la_
Class class	g — Small proteins
Fold Fold fold	g.50 — FYVE/PHD zinc finger
Superfamily Superfamily superfamily	g.50.1 — FYVE/PHD zinc finger
Family Family family	g.50.1.0 — automated matches

CATH v4.4 (1 domains)

Domain ID domain_id	3t7lA00
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	40 — Herpes Virus-1
Homologous superfamily homologous superfamily	10 — Zinc/RING finger domain, C3HC4 (zinc finger)

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8. Citations (1)

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Unit-cell length a length_a	42.944 Å
Unit-cell length b length_b	42.944 Å
Unit-cell length c length_c	76.879 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	8

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

Resolution resolution	1.090 Å
Low-resolution limit resolution_low	22.010 Å
R factor r_factor	0.1424
R_work r_work	0.1418
R_free r_free	0.1542

fit	/app/data/saxs_computation/t7/3t7l/3t7l.fit
pddf	/app/data/pr_computation/t7/3t7l/3t7l.pr.out
profile	/app/data/saxs_computation/t7/3t7l/3t7l.dat

Crystal structure of the FYVE domain of endofin (ZFYVE16) at 1.1A resolution

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

Zinc finger FYVE domain-containing protein 16

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