SAXSdb — 6tpu

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

Receptor-type tyrosine-protein phosphatase F

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 513–706	Not recorded	CL CHLORIDE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION；pH 7；277 K；1.8 M Ammonium citrate tribasic pH 7.0	Resolution 1.55 Å R-free 0.193
2	Protein monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count	Chain B； UniProt 513–706	Not recorded	CL CHLORIDE ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION；pH 7；277 K；1.8 M Ammonium citrate tribasic pH 7.0	Resolution 1.55 Å R-free 0.193

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 6TPU	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
1LAR CRYSTAL STRUCTURE OF THE TANDEM PHOSPHATASE DOMAINS OF RPTP LAR Deposited 1999-04-20	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 1323–1897（575 aa） Fragment：PHOSPHATASE	Mutation：P1307M	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions pH 8；pH 8.0	Resolution 2.00 Å R-free 0.274
1LAR CRYSTAL STRUCTURE OF THE TANDEM PHOSPHATASE DOMAINS OF RPTP LAR Deposited 1999-04-20	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 1323–1897（575 aa） Fragment：PHOSPHATASE	Mutation：P1307M	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions pH 8；pH 8.0	Resolution 2.00 Å R-free 0.274
2DJU Solution structures of the fn3 domain of human receptor-type tyrosine-protein phosphatase F Deposited 2006-04-05	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 309–401（93 aa） Fragment：Fibronectin type III domain	Not recorded	No recorded non-water small molecule	SOLUTION NMR NMR measurement conditions pH 7；298 K；Ionic strength (raw mmCIF value) 120mM；Pressure ambient NMR sample composition 1mM fn3 domain U-15N, 13C; 20mM d-Tris HCl; 100mM NaCl; 1mM d-DTT; 0.02% NaN3; 90% H2O, 10% D2O \| 90% H2O/10% D2O	Resolution not provided
2DN7 Solution structures of the 6th fn3 domain of human receptor-type tyrosine-protein phosphatase F Deposited 2006-04-25	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 811–904（94 aa） Fragment：Fibronectin type III domain	Not recorded	No recorded non-water small molecule	SOLUTION NMR NMR measurement conditions pH 7；296 K；Ionic strength (raw mmCIF value) 120mM；Pressure ambient NMR sample composition 1mM fn3 domain U-15N,13C; 20mM d-Tris HCl; 100mM NaCl; 1mM d-DTT; 0.02% NaN3; 10% D2O \| 90% H2O/10% D2O	Resolution not provided
2EDY Solution structures of the fn3 domain of human receptor-type tyrosine-protein phosphatase F Deposited 2007-02-15	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 905–1000（96 aa） Fragment：Fibronectin type III domain	Not recorded	No recorded non-water small molecule	SOLUTION NMR NMR measurement conditions pH 7；298 K；Ionic strength (raw mmCIF value) 120mM；Pressure ambient NMR sample composition 1mM fn3 domain U-15N, 13C; 20mM d-Tris HCl; 100mM NaCl; 1mM d-DTT; 0.02% NaN3; 90% H2O, 10% D2O \| 90% H2O/10% D2O	Resolution not provided
2YD5 Crystal structure of the N-terminal Ig1-2 module of Human Receptor Protein Tyrosine Phosphatase LAR Deposited 2011-03-17	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 29–231（203 aa） Fragment：IG1-2, RESIDUES 29-231	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions pH 5.6；0.1 M SODIUM ACETATE TRIHYDRATE, 20% ISOPROPANOL, 20% (W/V) PEG 4000, 0.25 MM HEPARIN DP10, PH 5.6 .	Resolution 2.20 Å R-free 0.233
2YD8 Crystal structure of the N-terminal Ig1-2 module of Human Receptor Protein Tyrosine Phosphatase LAR in complex with sucrose octasulphate Deposited 2011-03-18	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 29–231（203 aa） Fragment：IG1-2, RESIDUES 29-231	Not recorded	YYJ 1,3,4,6-tetra-O-sulfo-beta-D-fructofuranose × 1	X-RAY DIFFRACTION X-ray crystallization conditions pH 6；0.1 M MES, 30% PEG 6000, PH 6.0 .	Resolution 2.05 Å R-free 0.227
4N5U Crystal structure of the 4th FN3 domain of human Protein Tyrosine phosphatase, receptor type F [PSI-NYSGRC-006240] Deposited 2013-10-10	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 601–705（105 aa） Fragment：Fibronectin type-III 4 domain, residues 601-705	Not recorded	SO4 SULFATE ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 10.5；298 K；Protein (20 mM Hepes, pH 7.5, 150 mM NaCl, 5% glycerol, Reservoir (0.2M Lithium Sulfate, 0.1M CAPS, 1.2M NaH2PO4/0.8M K2HPO4), Cryoprotection (2M Li2SO4), VAPOR DIFFUSION, SITTING DROP, temperature 298K	Resolution 1.46 Å R-free 0.198
6KR4 Crystal structure of the liprin-alpha3_SAM123/LAR_D1D2 complex Deposited 2019-08-20	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 A 1332–1907（576 aa）	Not recorded	PG4 TETRAETHYLENE GLYCOL × 1 PO4 PHOSPHATE ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.5；296 K；50mM Tris-HCl, 200mM NaCl, 1mM ethylenediaminetetraacetic acid, 1mM dithiothreitol	Resolution 2.85 Å R-free 0.230
6KR4 Crystal structure of the liprin-alpha3_SAM123/LAR_D1D2 complex Deposited 2019-08-20	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 B 1332–1907（576 aa）	Not recorded	PG4 TETRAETHYLENE GLYCOL × 1 PO4 PHOSPHATE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.5；296 K；50mM Tris-HCl, 200mM NaCl, 1mM ethylenediaminetetraacetic acid, 1mM dithiothreitol	Resolution 2.85 Å R-free 0.230
6KR4 Crystal structure of the liprin-alpha3_SAM123/LAR_D1D2 complex Deposited 2019-08-20	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 3 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain C 1332–1907（576 aa）	Not recorded	PG4 TETRAETHYLENE GLYCOL × 1 PO4 PHOSPHATE ION × 1 PGE TRIETHYLENE GLYCOL × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.5；296 K；50mM Tris-HCl, 200mM NaCl, 1mM ethylenediaminetetraacetic acid, 1mM dithiothreitol	Resolution 2.85 Å R-free 0.230
6KR4 Crystal structure of the liprin-alpha3_SAM123/LAR_D1D2 complex Deposited 2019-08-20	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 4 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain D 1332–1907（576 aa）	Not recorded	PO4 PHOSPHATE ION × 1 PGE TRIETHYLENE GLYCOL × 1 P6G HEXAETHYLENE GLYCOL × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.5；296 K；50mM Tris-HCl, 200mM NaCl, 1mM ethylenediaminetetraacetic acid, 1mM dithiothreitol	Resolution 2.85 Å R-free 0.230
6TPT Crystal structures of FNIII domain three and four of the human leucocyte common antigen-related protein, LAR Deposited 2019-12-14	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 512–706（195 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION；pH 6.5；277 K；0.2 M Sodium fluoride, 0.1 M Bis-tris propane pH 6.5, and 20% PEG3350	Resolution 3.20 Å R-free 0.269
6TPV Crystal structures of FNIII domain one and two of the human leucocyte common antigen-related protein, LAR Deposited 2019-12-14	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 319–512（194 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8.3；277 K；0.2 M Sodium citrate tribasic dihydrate pH 8.3, 20 % PEG 3,350	Resolution 1.80 Å R-free 0.220
6TPV Crystal structures of FNIII domain one and two of the human leucocyte common antigen-related protein, LAR Deposited 2019-12-14	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain B 319–512（194 aa）	Not recorded	IMD IMIDAZOLE × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8.3；277 K；0.2 M Sodium citrate tribasic dihydrate pH 8.3, 20 % PEG 3,350	Resolution 1.80 Å R-free 0.220
6TPW Crystal structures of FNIII domain one through four of the human leucocyte common antigen-related protein ( LAR) Deposited 2019-12-14	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 319–706（388 aa）	Not recorded	SO4 SULFATE ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions EVAPORATION；277 K；0.2 M Ammonium sulfate and 30% PEG8000	Resolution 2.90 Å R-free 0.301

11 other PDB entries and 16 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	PTPRF_HUMAN
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 2–195； UniProt 513–706 Author chain B； PDBConstruct 2–195； UniProt 513–706

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	6tpu
Deposition date deposition_date	2019-12-14
Structure title title	Crystal structures of FNIII domain three and four of the human leucocyte common antigen-related protein, LAR
Keywords keywords	Fibronectin type-III, adhesion protein, CELL ADHESION; CELL ADHESION
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	28.18 Å
Radius of gyration Rg (electron density) rg_electron	27.90 Å
Forward intensity I(0) i0	33623600.00
Molecular weight molecular_weight	43412.0 kDa
Excluded volume excluded_volume	53648 Å³
Envelope volume envelope_volume	68694 Å³
Hydration-shell volume shell_volume	22375 Å³
Envelope diameter envelope_diameter	100.9 Å
Shell Rg shell_rg	32.07 Å
Envelope Rg envelope_rg	28.08 Å
Shape Rg shape_rg	27.85 Å
Total Rg total_rg	28.50 Å
Total atoms total_atoms	3059
Residues n_residues	387
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	95.8 Å
Rg (real space) rg_real	28.38 Å
Rg uncertainty (real space) rg_real_error	0.98 Å
I(0) (real space) i0_real	3.3620e+07
I(0) uncertainty (real space) i0_real_error	5.4980e+05
Rg (reciprocal space) rg_reciprocal	28.32 Å
I(0) (reciprocal space) i0_reciprocal	33620000.0000
Solution quality estimate total_estimate	0.8587
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	34.2 Å
Skewness Skewness skewness	0.459
Kurtosis Kurtosis kurtosis	-0.251
Angular range angular_range	— – 0.2800 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	3249000.0000
Real-space data points n_real_points	57
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.861; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.832; Smooth: 0.745

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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	Receptor-type tyrosine-protein phosphatase F
Molecular weight formula_weight	21862.1 kDa
EC 编号 ec_number	3.1.3.48
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B
Atom count atom_count	3616

GAQPADFQAEVESDTRIQLSWLLPPQERIIMYELVYWAAEDEDQQHKVTFDPTSSYTLEDLKPDTLYRFQLAARSDMGVGVFTPTIEARTAQSTPSAPPQKVMCVSMGSTTVRVSWVPPPADSRNGVITQYSVAYEAVDGEDRGRHVVDGISREHSSWDLVGLEKWTEYRVWVRAHTDVGPGPESSPVLVRTDED

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	CHLORIDE ION
Molecular weight formula_weight	35.5 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	467

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7. Fold Classification (SCOP + CATH) 9 domains

SCOP 2.08 (5 domains)

Domain ID domain_id	d6tpua1
Class class	b — All beta proteins
Fold Fold fold	b.1 — Immunoglobulin-like beta-sandwich
Superfamily Superfamily superfamily	b.1.2 — Fibronectin type III
Family Family family	b.1.2.0 — automated matches

Domain ID domain_id	d6tpua2
Class class	b — All beta proteins
Fold Fold fold	b.1 — Immunoglobulin-like beta-sandwich
Superfamily Superfamily superfamily	b.1.2 — Fibronectin type III
Family Family family	b.1.2.0 — automated matches

Domain ID domain_id	d6tpua3
Class class	l — Artifacts
Fold Fold fold	l.1 — Tags
Superfamily Superfamily superfamily	l.1.1 — Tags
Family Family family	l.1.1.1 — Tags

Domain ID domain_id	d6tpub1
Class class	b — All beta proteins
Fold Fold fold	b.1 — Immunoglobulin-like beta-sandwich
Superfamily Superfamily superfamily	b.1.2 — Fibronectin type III
Family Family family	b.1.2.0 — automated matches

Domain ID domain_id	d6tpub2
Class class	b — All beta proteins
Fold Fold fold	b.1 — Immunoglobulin-like beta-sandwich
Superfamily Superfamily superfamily	b.1.2 — Fibronectin type III
Family Family family	b.1.2.0 — automated matches

CATH v4.4 (4 domains)

Domain ID domain_id	6tpuA01
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	10 — Immunoglobulins

Domain ID domain_id	6tpuA02
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	10 — Immunoglobulins

Domain ID domain_id	6tpuB01
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	10 — Immunoglobulins

Domain ID domain_id	6tpuB02
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	10 — Immunoglobulins

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8. Citations (1)

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Unit-cell length a length_a	85.290 Å
Unit-cell length b length_b	105.100 Å
Unit-cell length c length_c	62.000 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	135.56 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	8

Space group space_group	C 1 2 1
Space-group number int_tables_number	5
Crystal system crystal_system	—

Resolution resolution	1.550 Å
Low-resolution limit resolution_low	43.410 Å
R factor r_factor	0.1664
R_work r_work	0.1654
R_free r_free	0.1933

fit	/app/data/saxs_computation/tp/6tpu/6tpu.fit
pddf	/app/data/pr_computation/tp/6tpu/6tpu.pr.out
profile	/app/data/saxs_computation/tp/6tpu/6tpu.dat

Crystal structures of FNIII domain three and four of the human leucocyte common antigen-related protein, LAR

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

Receptor-type tyrosine-protein phosphatase F

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