SAXSdb — 3n0a

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

Tyrosine-protein phosphatase auxilin

Bos taurus

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 40–400	Fragment：UNP residues 40-400	CA CALCIUM ION × 1 CL CHLORIDE ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 7.5；293 K；15.5% PEG 4000, 0.1 M HEPES, pH 7.5, 0.01 M CaCl2, 0.8 M NaCl, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 2.20 Å R-free 0.200

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 3N0A	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
1N4C NMR Structure of the J-Domain and Clathrin Substrate Binding Domain of Bovine Auxilin Deposited 2002-10-30	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 737–910（174 aa） Fragment：Residues (737-845), J-Domain	Not recorded	No recorded non-water small molecule	SOLUTION NMR NMR measurement conditions pH 4.5；300 K；Ionic strength (raw mmCIF value) 60mM NaCl；Pressure ambient NMR sample composition 1.5mM Auxilin (20kD C-terminal construct) U-15N \| 90% H20, 10% D2O NMR sample composition 1.5mM Auxilin (20kD C-terminal construct) U-15N,13C \| 90% H2O/10% D2O	Resolution not provided
1NZ6 Crystal Structure of Auxilin J-Domain Deposited 2003-02-16	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 810–910（101 aa） Fragment：J-Domain	Non-standard monomer：Yes (specific site not provided by mmCIF)	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions microbatch under oil；pH 8；277 K；PEG 8000, Tris-Cl, TCEP, Glycerol, pH 8.0, microbatch under oil, temperature 277K	Resolution 2.50 Å R-free 0.268
1NZ6 Crystal Structure of Auxilin J-Domain Deposited 2003-02-16	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain B 810–910（101 aa） Fragment：J-Domain	Non-standard monomer：Yes (specific site not provided by mmCIF)	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions microbatch under oil；pH 8；277 K；PEG 8000, Tris-Cl, TCEP, Glycerol, pH 8.0, microbatch under oil, temperature 277K	Resolution 2.50 Å R-free 0.268
1XI5 Clathrin D6 coat with auxilin J-domain Deposited 2004-09-21	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 216 PDB declaration: 216-MERIC	Chain J 797–910（114 aa） Fragment：residues 797-910 Chain K 797–910（114 aa） Fragment：residues 797-910 Chain L 797–910（114 aa） Fragment：residues 797-910 Chain M 797–910（114 aa） Fragment：residues 797-910 Chain N 797–910（114 aa） Fragment：residues 797-910 Chain O 797–910（114 aa） Fragment：residues 797-910 Chain P 797–910（114 aa） Fragment：residues 797-910 Chain Q 797–910（114 aa） Fragment：residues 797-910 Chain R 797–910（114 aa） Fragment：residues 797-910	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer 20MM HEPES；pH 7；20MM HEPES cryo-EM vitrification conditions Cryogen ETHANE；VITRIFIED	Resolution 12.00 Å
1XI5 Clathrin D6 coat with auxilin J-domain Deposited 2004-09-21	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 18 PDB declaration: octadecameric	Chain J 797–910（114 aa） Fragment：residues 797-910 Chain K 797–910（114 aa） Fragment：residues 797-910 Chain L 797–910（114 aa） Fragment：residues 797-910 Chain M 797–910（114 aa） Fragment：residues 797-910 Chain N 797–910（114 aa） Fragment：residues 797-910 Chain O 797–910（114 aa） Fragment：residues 797-910 Chain P 797–910（114 aa） Fragment：residues 797-910 Chain Q 797–910（114 aa） Fragment：residues 797-910 Chain R 797–910（114 aa） Fragment：residues 797-910	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer 20MM HEPES；pH 7；20MM HEPES cryo-EM vitrification conditions Cryogen ETHANE；VITRIFIED	Resolution 12.00 Å
1XI5 Clathrin D6 coat with auxilin J-domain Deposited 2004-09-21	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 3 Protein heterocomplex Heteromer；Protein × 18 PDB declaration: octadecameric	Chain J 797–910（114 aa） Fragment：residues 797-910 Chain K 797–910（114 aa） Fragment：residues 797-910 Chain L 797–910（114 aa） Fragment：residues 797-910 Chain M 797–910（114 aa） Fragment：residues 797-910 Chain N 797–910（114 aa） Fragment：residues 797-910 Chain O 797–910（114 aa） Fragment：residues 797-910 Chain P 797–910（114 aa） Fragment：residues 797-910 Chain Q 797–910（114 aa） Fragment：residues 797-910 Chain R 797–910（114 aa） Fragment：residues 797-910	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer 20MM HEPES；pH 7；20MM HEPES cryo-EM vitrification conditions Cryogen ETHANE；VITRIFIED	Resolution 12.00 Å
2QWN Crystal structure of disulfide-bond-crosslinked complex of bovine hsc70 (1-386aa)R171C and bovine Auxilin (810-910aa)D876C in the ADP*Pi state Deposited 2007-08-10	Different construct Different mutation/modification 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 812–905（94 aa）	Mutation：D876C	PO4 PHOSPHATE ION × 1 NA SODIUM ION × 2 MG MAGNESIUM ION × 1 ADP ADENOSINE-5'-DIPHOSPHATE × 1	X-RAY DIFFRACTION X-ray crystallization conditions microbatch under oil；pH 8；289 K；PEG3350, Ammonium Acetate, pH 8.0, microbatch under oil, temperature 289K	Resolution 2.40 Å R-free 0.279
2QWO Crystal structure of disulfide-bond-crosslinked complex of bovine hsc70 (1-394aa)R171C and bovine Auxilin (810-910aa)D876C in the ADP*Pi form #1 Deposited 2007-08-10	Different construct Different mutation/modification 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 813–904（92 aa）	Mutation：D876C	PO4 PHOSPHATE ION × 1 NA SODIUM ION × 2 MG MAGNESIUM ION × 1 ADP ADENOSINE-5'-DIPHOSPHATE × 1 ACY ACETIC ACID × 1 GOL GLYCEROL × 2	X-RAY DIFFRACTION X-ray crystallization conditions microbatch under oil；pH 8.5；289 K；PEG3350, Ammonium Acetate, pH 8.5, microbatch under oil, temperature 289K	Resolution 1.70 Å R-free 0.222
2QWP Crystal structure of disulfide-bond-crosslinked complex of bovine hsc70 (1-394aa)R171C and bovine Auxilin (810-910aa)D876C in the ADP*Pi form #2 Deposited 2007-08-10	Different construct Different mutation/modification 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 813–904（92 aa）	Mutation：D876C	PO4 PHOSPHATE ION × 1 NA SODIUM ION × 2 MG MAGNESIUM ION × 1 ADP ADENOSINE-5'-DIPHOSPHATE × 1 ACY ACETIC ACID × 1 GOL GLYCEROL × 2	X-RAY DIFFRACTION X-ray crystallization conditions microbatch under oil；pH 8.5；289 K；PEG3350, Ammonium Acetate, pH 8.5, microbatch under oil, temperature 289K	Resolution 1.75 Å R-free 0.243
2QWQ Crystal structure of disulfide-bond-crosslinked complex of bovine hsc70 (1-394aa)R171C and bovine Auxilin (810-910aa)D876C in the AMPPNP hydrolyzed form Deposited 2007-08-10	Different construct Different mutation/modification 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 813–904（92 aa）	Mutation：D876C	PO4 PHOSPHATE ION × 1 ADP ADENOSINE-5'-DIPHOSPHATE × 1 ACY ACETIC ACID × 1 GOL GLYCEROL × 2	X-RAY DIFFRACTION X-ray crystallization conditions microbatch under oil；pH 8.5；289 K；PEG3350, Ammonium Acetate, pH 8.5, microbatch under oil, temperature 289K	Resolution 2.21 Å R-free 0.295
2QWR Crystal structure of disulfide-bond-crosslinked complex of bovine hsc70 (1-394aa)R171C and bovine Auxilin (810-910aa)D876C in the AMPPNP intact form Deposited 2007-08-10	Different construct Different mutation/modification 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 813–904（92 aa）	Mutation：D876C	ANP PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER × 1 ACY ACETIC ACID × 1 GOL GLYCEROL × 2	X-RAY DIFFRACTION X-ray crystallization conditions microbatch under oil；pH 8.5；289 K；PEG3350, Ammonium Acetate, pH 8.5, microbatch under oil, temperature 289K	Resolution 2.21 Å R-free 0.294

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

View Construct and Data Evidence

UniProt name	AUXI_BOVIN
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–361； UniProt 40–400

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	3n0a
Deposition date deposition_date	2010-05-13
Structure title title	Crystal structure of auxilin (40-400)
Keywords keywords	phosphatase-like domain, C2 domain, Hydrolase; HYDROLASE
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	23.37 Å
Radius of gyration Rg (electron density) rg_electron	22.29 Å
Forward intensity I(0) i0	24639200.00
Molecular weight molecular_weight	38620.0 kDa
Excluded volume excluded_volume	48641 Å³
Envelope volume envelope_volume	58274 Å³
Hydration-shell volume shell_volume	22169 Å³
Envelope diameter envelope_diameter	76.7 Å
Shell Rg shell_rg	28.76 Å
Envelope Rg envelope_rg	22.50 Å
Shape Rg shape_rg	22.28 Å
Total Rg total_rg	23.16 Å
Total atoms total_atoms	2714
Residues n_residues	335
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	74.3 Å
Rg (real space) rg_real	23.34 Å
Rg uncertainty (real space) rg_real_error	0.48 Å
I(0) (real space) i0_real	2.4640e+07
I(0) uncertainty (real space) i0_real_error	3.8590e+05
Rg (reciprocal space) rg_reciprocal	23.35 Å
I(0) (reciprocal space) i0_reciprocal	24640000.0000
Solution quality estimate total_estimate	0.9050
Solution quality rating solution_quality	EXCELLENT a EXCELLENT solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	24.0 Å
Skewness Skewness skewness	0.269
Kurtosis Kurtosis kurtosis	-0.570
Angular range angular_range	— – 0.3400 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	6007000.0000
Real-space data points n_real_points	66
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.926; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.989; Smooth: 0.993

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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	Tyrosine-protein phosphatase auxilin
Molecular weight formula_weight	41444.5 kDa
EC 编号 ec_number	3.1.3.48
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	2927

DTLKDTSSRVIQSVTSYTKGDLDFTYVTSRIIVMSFPLDSVDIGFRNQVDDIRSFLDSRHLDHYTVYNLSPKSYRTAKFHSRVSECSWPIRQAPSLHNLFAVCRNMYNWLLQNPKNVCVVHCLDGRAASSILVGAMFIFCNLYSTPGPAVRLLYAKRPGIGLSPSHRRYLGYMCDLLADKPYRPHFKPLTIKSITVSPVPFFNKQRNGCRPYCDVLIGETKIYTTCADFERMKEYRVQDGKIFIPLSITVQGDVVVSMYHLRSTIGSRLQAKVTNTQIFQLQFHTGFIPLDTTVLKFTKPELDACDVPEKYPQLFQVTLDVELQPHDKVMELTPPWEHYCTKDVNPSILFSSHQEHQDTLV

来源 Source

来源生物 organism	Bos taurus
通用名 common_name	bovine,cow,domestic cattle,domestic cow
NCBI Class编号 ncbi_taxonomy_id	9913

Entity 2 Entity 2 non-polymer

Description description	CALCIUM ION
Molecular weight formula_weight	40.1 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 3 Entity 3 non-polymer

Description description	CHLORIDE ION
Molecular weight formula_weight	35.5 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 4 Entity 4 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	213

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7. Fold Classification (SCOP + CATH) 2 domains

CATH v4.4 (2 domains)

Domain ID domain_id	3n0aA01
Class class	3 — Alpha Beta
Architecture architecture	90 — Alpha-Beta Complex
Topology topology	190 — Protein-Tyrosine Phosphatase; Chain A
Homologous superfamily homologous superfamily	10 — Protein tyrosine phosphatase superfamily

Domain ID domain_id	3n0aA02
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	1110 —

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8. Citations (1)

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Unit-cell length a length_a	137.925 Å
Unit-cell length b length_b	137.925 Å
Unit-cell length c length_c	51.327 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	90.00 °
Unit-cell angle γ angle_gamma	120.00 °
Molecules per unit cell Z z_pdb	6

Space group space_group	P 32 2 1
Space-group number int_tables_number	154
Crystal system crystal_system	—

Resolution resolution	2.200 Å
Low-resolution limit resolution_low	33.900 Å
R factor r_factor	0.1734
R_work r_work	0.1720
R_free r_free	0.1995

fit	/app/data/saxs_computation/n0/3n0a/3n0a.fit
pddf	/app/data/pr_computation/n0/3n0a/3n0a.pr.out
profile	/app/data/saxs_computation/n0/3n0a/3n0a.dat

Crystal structure of auxilin (40-400)

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

Tyrosine-protein phosphatase auxilin

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