2q47

Ensemble refinement of the protein crystal structure of a putative phosphoprotein phosphatase from Arabidopsis thaliana gene At1g05000

Method: X-RAY DIFFRACTION

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

Probable tyrosine-protein phosphatase At1g05000

Arabidopsis thaliana

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein homooligomer	Homooligomer	Protein 2	SULFATE ION × 4 water × 2	Consistent with protein count
2	Protein homooligomer	Homooligomer	Protein 6	SULFATE ION × 12 water × 6	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	Y1500_ARATH
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–151； UniProt 52–202 Author chain B； PDBConstruct 1–151； UniProt 52–202

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	2q47
Deposition date deposition_date	2007-05-31
Structure title title	Ensemble refinement of the protein crystal structure of a putative phosphoprotein phosphatase from Arabidopsis thaliana gene At1g05000
Keywords keywords	;Ensemble Refinement, Refinement Methodology Development, AT1G05000, phosphoprotein phosphatase, Structural Genomics, Protein Structure Initiative, PSI, Center for Eukaryotic Structural Genomics, CESG, UNKNOWN FUNCTION ;; STRUCTURAL GENOMICS, UNKNOWN FUNCTION
Experimental Method method	X-RAY DIFFRACTION

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3. Official assembly/model SAXS Official SAXS Profiles

This page reads only the latest assembly calculations. Every curve maps to an explicit PDB entry, official biological assembly and coordinate model.

2q47__assembly_2__model_2

Assembly 2 · Model 2 · CRYSOL 4.1.3-1-20251215 (887e7ef)

Download this curve (.dat)

2q47__assembly_2__model_2 | I(q)

100 plotted points; both axes use logarithmic scales.

2q47__assembly_2__model_2 | P(r) · Pending

P(r) will be calculated and displayed separately for the same assembly/model.

Rg（Guinier）	28.75 Å
Rg (electron density)	27.92 Å
Total Rg	28.73 Å
Atom count	7404
Residues	888
Excluded volume	132760 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`2q47__assembly_1__model_1`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
1	2	`2q47__assembly_1__model_2`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
1	3	`2q47__assembly_1__model_3`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
1	4	`2q47__assembly_1__model_4`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
1	5	`2q47__assembly_1__model_5`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
1	6	`2q47__assembly_1__model_6`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
1	7	`2q47__assembly_1__model_7`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
1	8	`2q47__assembly_1__model_8`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
1	9	`2q47__assembly_1__model_9`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
1	10	`2q47__assembly_1__model_10`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
1	11	`2q47__assembly_1__model_11`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
1	12	`2q47__assembly_1__model_12`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
1	13	`2q47__assembly_1__model_13`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
1	14	`2q47__assembly_1__model_14`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
1	15	`2q47__assembly_1__model_15`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
1	16	`2q47__assembly_1__model_16`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`2q47__assembly_2__model_1`	hexameric （6）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	2	`2q47__assembly_2__model_2`	hexameric （6）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	3	`2q47__assembly_2__model_3`	hexameric （6）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	4	`2q47__assembly_2__model_4`	hexameric （6）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	5	`2q47__assembly_2__model_5`	hexameric （6）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	6	`2q47__assembly_2__model_6`	hexameric （6）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	7	`2q47__assembly_2__model_7`	hexameric （6）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	8	`2q47__assembly_2__model_8`	hexameric （6）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	9	`2q47__assembly_2__model_9`	hexameric （6）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	10	`2q47__assembly_2__model_10`	hexameric （6）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	11	`2q47__assembly_2__model_11`	hexameric （6）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	12	`2q47__assembly_2__model_12`	hexameric （6）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	13	`2q47__assembly_2__model_13`	hexameric （6）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	14	`2q47__assembly_2__model_14`	hexameric （6）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	15	`2q47__assembly_2__model_15`	hexameric （6）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	16	`2q47__assembly_2__model_16`	hexameric （6）	Success	4.1.3-1-20251215 (887e7ef)	View Download

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4. Crystallography and Experiment 4. Crystallography & Experiment

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5. Entities and Polymers Entities & Polymers (3)

Entity 1 Entity 1 polymer

Description description	Probable tyrosine-protein phosphatase At1g05000
Molecular weight formula_weight	17540.0 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	40448

HLIPPLNFSMVDNGIFRSGFPDSANFSFLQTLGLRSIIYLCPEPYPESNLQFLKSNGIRLFQFGIEGNKEPFVNIPDHKIRMALKVLLDEKNHPVLIHCKRGKHRTGCLVGCLRKLQKWCLTSIFDEYQRFAAAKARVSDQRFMEIFDVSS

Source Source

Source organism organism	Arabidopsis thaliana
Common name common_name	thale cress
NCBI taxonomy ID ncbi_taxonomy_id	3702
Host organism host_organism	Escherichia coli

Entity 2 Entity 2 non-polymer

Description description	SULFATE ION
Molecular weight formula_weight	96.1 kDa
Source method src_method	syn
Copy count entity_count	4

Entity 3 Entity 3 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	60

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6. Fold Classification (SCOP + CATH) 4 domains

SCOP 2.08 (2 domains)

Domain ID domain_id	d2q47a1
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.45 — (Phosphotyrosine protein) phosphatases II
Superfamily Superfamily superfamily	c.45.1 — (Phosphotyrosine protein) phosphatases II
Family Family family	c.45.1.1 — Dual specificity phosphatase-like

Domain ID domain_id	d2q47b1
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.45 — (Phosphotyrosine protein) phosphatases II
Superfamily Superfamily superfamily	c.45.1 — (Phosphotyrosine protein) phosphatases II
Family Family family	c.45.1.1 — Dual specificity phosphatase-like

CATH v4.4 (2 domains)

Domain ID domain_id	2q47A00
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	2q47B00
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

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Unit-cell length a length_a	124.483 Å
Unit-cell length b length_b	124.483 Å
Unit-cell length c length_c	124.483 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	24

Space group space_group	P 21 3
Space-group number int_tables_number	198
Crystal system crystal_system	—

Resolution resolution	3.300 Å
Low-resolution limit resolution_low	41.500 Å
R factor r_factor	0.1600
R_work r_work	0.1600
R_free r_free	0.2340

Ensemble refinement of the protein crystal structure of a putative phosphoprotein phosphatase from Arabidopsis thaliana gene At1g05000

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

Probable tyrosine-protein phosphatase At1g05000

State in the Current Structure

Other States of the Same Protein in the Database

2. Structure Basics 2. Structure Basics

3. Official assembly/model SAXS Official SAXS Profiles

2q47__assembly_2__model_2

2q47__assembly_2__model_2 | I(q)

2q47__assembly_2__model_2 | P(r) · Pending

4. Crystallography and Experiment 4. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

5. Entities and Polymers Entities & Polymers (3)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 non-polymer

Entity 3 Entity 3 water

6. Fold Classification (SCOP + CATH) 4 domains

SCOP 2.08 (2 domains)

CATH v4.4 (2 domains)

7. Citations (1)

Ensemble refinement of the protein crystal structure of a putative phosphoprotein phosphatase from Arabidopsis thaliana gene At1g05000

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

Probable tyrosine-protein phosphatase At1g05000

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

2. Structure Basics 2. Structure Basics

3. Official assembly/model SAXS Official SAXS Profiles

2q47__assembly_2__model_2

2q47__assembly_2__model_2 | I(q)

2q47__assembly_2__model_2 | P(r) · Pending

4. Crystallography and Experiment 4. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

5. Entities and Polymers Entities & Polymers (3)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 non-polymer

Entity 3 Entity 3 water

6. Fold Classification (SCOP + CATH) 4 domains

SCOP 2.08 (2 domains)

CATH v4.4 (2 domains)

7. Citations (1)