SAXSdb — 1d2a

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

TYROSINE PHOSPHATASE

Saccharomyces cerevisiae

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 2–161	Mutation：C13A	PO4 PHOSPHATE ION × 1 CL CHLORIDE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, SITTING DROP；pH 7；293 K；PEG 3400, Bis-TRIS, sodium chloride, sodium phosphate, adenine, pH 7.0, VAPOR DIFFUSION, SITTING DROP, temperature 293.0K	Resolution 1.90 Å R-free 0.243
2	Protein monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count	Chain B； UniProt 2–161	Mutation：C13A	PO4 PHOSPHATE ION × 1 ADE ADENINE × 1	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, SITTING DROP；pH 7；293 K；PEG 3400, Bis-TRIS, sodium chloride, sodium phosphate, adenine, pH 7.0, VAPOR DIFFUSION, SITTING DROP, temperature 293.0K	Resolution 1.90 Å R-free 0.243

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 1D2A	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
1D1P CRYSTAL STRUCTURE OF A YEAST LOW MOLECULAR WEIGHT PROTEIN TYROSINE PHOSPHATASE (LTP1) Deposited 1999-09-20	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 2–161（160 aa）	Not recorded	EPE 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7；298 K；PEG 3400, HEPES, sodium chloride, pH 7.0, VAPOR DIFFUSION, SITTING DROP, temperature 298.0K	Resolution 2.20 Å R-free 0.235
1D1P CRYSTAL STRUCTURE OF A YEAST LOW MOLECULAR WEIGHT PROTEIN TYROSINE PHOSPHATASE (LTP1) Deposited 1999-09-20	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 2–161（160 aa）	Not recorded	EPE 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7；298 K；PEG 3400, HEPES, sodium chloride, pH 7.0, VAPOR DIFFUSION, SITTING DROP, temperature 298.0K	Resolution 2.20 Å R-free 0.235
1D1Q CRYSTAL STRUCTURE OF A YEAST LOW MOLECULAR WEIGHT PROTEIN TYROSINE PHOSPHATASE (LTP1) COMPLEXED WITH THE SUBSTRATE PNPP Deposited 1999-09-20	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1–161（161 aa）	Mutation：C13A	4NP 4-NITROPHENYL PHOSPHATE × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7；293 K；PEG 3400, Bis-TRIS, sodium chloride para-nitrophenyl phosphate, pH 7.0, VAPOR DIFFUSION, SITTING DROP, temperature 293.0K	Resolution 1.70 Å R-free 0.215
1D1Q CRYSTAL STRUCTURE OF A YEAST LOW MOLECULAR WEIGHT PROTEIN TYROSINE PHOSPHATASE (LTP1) COMPLEXED WITH THE SUBSTRATE PNPP Deposited 1999-09-20	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain B 1–161（161 aa）	Mutation：C13A	PO4 PHOSPHATE ION × 1 GOL GLYCEROL × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7；293 K；PEG 3400, Bis-TRIS, sodium chloride para-nitrophenyl phosphate, pH 7.0, VAPOR DIFFUSION, SITTING DROP, temperature 293.0K	Resolution 1.70 Å R-free 0.215

2 other PDB entries and 4 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	PPAL_YEAST
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–160； UniProt 2–161 Author chain B； PDBConstruct 1–160； UniProt 2–161

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	1d2a
Deposition date deposition_date	1999-09-22
Structure title title	CRYSTAL STRUCTURE OF A YEAST LOW MOLECULAR WEIGHT PROTEIN TYROSINE PHOSPHATASE (LTP1) COMPLEXED WITH THE ACTIVATOR ADENINE
Keywords keywords	BETA-ALPHA-BETA, TYROSINE PHOSPHATASE, LTP1, 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	23.70 Å
Radius of gyration Rg (electron density) rg_electron	23.27 Å
Forward intensity I(0) i0	23240100.00
Molecular weight molecular_weight	36441.0 kDa
Excluded volume excluded_volume	45410 Å³
Envelope volume envelope_volume	53061 Å³
Hydration-shell volume shell_volume	20064 Å³
Envelope diameter envelope_diameter	81.0 Å
Shell Rg shell_rg	28.89 Å
Envelope Rg envelope_rg	23.37 Å
Shape Rg shape_rg	23.26 Å
Total Rg total_rg	23.99 Å
Total atoms total_atoms	2569
Residues n_residues	312
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	80.5 Å
Rg (real space) rg_real	23.85 Å
Rg uncertainty (real space) rg_real_error	0.70 Å
I(0) (real space) i0_real	2.3240e+07
I(0) uncertainty (real space) i0_real_error	3.6100e+05
Rg (reciprocal space) rg_reciprocal	23.82 Å
I(0) (reciprocal space) i0_reciprocal	23240000.0000
Solution quality estimate total_estimate	0.6515
Solution quality rating solution_quality	REASONABLE a REASONABLE solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	22.6 Å
Skewness Skewness skewness	0.475
Kurtosis Kurtosis kurtosis	-0.414
Angular range angular_range	— – 0.3350 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	5074000.0000
Real-space data points n_real_points	65
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.747; Stabil: 1.000; Sysdev: 0.154; Positv: 1.000; Valcen: 0.797; Smooth: 0.966

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (5)

Entity 1 Entity 1 polymer

Description description	TYROSINE PHOSPHATASE
Molecular weight formula_weight	18540.0 kDa
EC 编号 ec_number	3.1.3.48
Mutation mutation	C13A
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	2869

TIEKPKISVAFIALGNFCRSPMAEAIFKHEVEKANLENRFNKIDSFGTSNYHVGESPDHRTVSICKQHGVKINHKGKQIKTKHFDEYDYIIGMDESNINNLKKIQPEGSKAKVCLFGDWNTNDGTVQTIIEDPWYGDIQDFEYNFKQITYFSKQFLKKEL

来源 Source

来源生物 organism	Saccharomyces cerevisiae
通用名 common_name	;baker's yeast ;
NCBI Class编号 ncbi_taxonomy_id	4932
宿主生物 host_organism	Escherichia coli

Entity 2 Entity 2 non-polymer

Description description	PHOSPHATE ION
Molecular weight formula_weight	95.0 kDa
Source method src_method	syn
Copy count entity_count	2

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	1

Entity 4 Entity 4 non-polymer

Description description	ADENINE
Molecular weight formula_weight	135.1 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 5 Entity 5 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	300

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7. Fold Classification (SCOP + CATH) 4 domains

SCOP 2.08 (2 domains)

Domain ID domain_id	d1d2aa_
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.44 — Phosphotyrosine protein phosphatases I-like
Superfamily Superfamily superfamily	c.44.1 — Phosphotyrosine protein phosphatases I
Family Family family	c.44.1.1 — Low-molecular-weight phosphotyrosine protein phosphatases

Domain ID domain_id	d1d2ab_
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.44 — Phosphotyrosine protein phosphatases I-like
Superfamily Superfamily superfamily	c.44.1 — Phosphotyrosine protein phosphatases I
Family Family family	c.44.1.1 — Low-molecular-weight phosphotyrosine protein phosphatases

CATH v4.4 (2 domains)

Domain ID domain_id	1d2aA00
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	2300 — Response regulator

Domain ID domain_id	1d2aB00
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	2300 — Response regulator

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8. Citations (3)

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Unit-cell length a length_a	51.492 Å
Unit-cell length b length_b	63.272 Å
Unit-cell length c length_c	97.590 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 21 21 21
Space-group number int_tables_number	19
Crystal system crystal_system	—

Resolution resolution	1.900 Å
Low-resolution limit resolution_low	12.000 Å
R factor r_factor	0.1820
R_work r_work	0.1820
R_free r_free	0.2430

fit	/app/data/saxs_computation/d2/1d2a/1d2a.fit
pddf	/app/data/pr_computation/d2/1d2a/1d2a.pr.out
profile	/app/data/saxs_computation/d2/1d2a/1d2a.dat

CRYSTAL STRUCTURE OF A YEAST LOW MOLECULAR WEIGHT PROTEIN TYROSINE PHOSPHATASE (LTP1) COMPLEXED WITH THE ACTIVATOR ADENINE

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

TYROSINE PHOSPHATASE

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