SAXSdb — 2r25

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

Phosphorelay intermediate protein YPD1

Saccharomyces cerevisiae

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 2	Osmosensing histidine protein kinase SLN1 × 1 （P39928） MAGNESIUM ION × 1 SODIUM ION × 1 BERYLLIUM TRIFLUORIDE ION × 1 water × 2	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	YPD1_YEAST
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–167； UniProt 1–167

Osmosensing histidine protein kinase SLN1

Saccharomyces cerevisiae

UniProt P39928

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 2	Phosphorelay intermediate protein YPD1 × 1 （Q07688） MAGNESIUM ION × 1 SODIUM ION × 1 BERYLLIUM TRIFLUORIDE ION × 1 water × 2	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	SLN1_YEAST
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain B； PDBConstruct 1–133； UniProt 1086–1218

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	2r25
Deposition date deposition_date	2007-08-24
Structure title title	Complex of YPD1 and SLN1-R1 with bound Mg2+ and BeF3-
Keywords keywords	;alpha5-beta5, response regulator, four helix bundle, histidine phosphotransfer (HPt) protein, histidine kinase (HK), Cytoplasm, Nucleus, Phosphorylation, Two-component regulatory system, Glycoprotein, Magnesium, Membrane, Metal-binding, Transferase, Transmembrane, Signaling PROTEIN-Transferase COMPLEX ;; Signaling PROTEIN/Transferase
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.

2r25__assembly_1__model_1

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

Download this curve (.dat)

2r25__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

2r25__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	21.34 Å
Rg (electron density)	20.29 Å
Total Rg	21.16 Å
Atom count	2383
Residues	299
Excluded volume	42685 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`2r25__assembly_1__model_1`	dimeric （2）	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 (6)

Entity 1 Entity 1 polymer

Description description	Phosphorelay intermediate protein YPD1
Molecular weight formula_weight	19187.7 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	2723

MSTIPSEIINWTILNEIISMDDDDSDFSKGLIIQFIDQAQTTFAQMQRQLDGEKNLTELDNLGHFLKGSSAALGLQRIAWVCERIQNLGRKMEHFFPNKTELVNTLSDKSIINGINIDEDDEEIKIQVDDKDENSIYLILIAKALNQSRLEFKLARIELSKYYNTNL

Source Source

Source organism organism	Saccharomyces cerevisiae
Common name common_name	;baker's yeast ;
NCBI taxonomy ID ncbi_taxonomy_id	4932
Host organism host_organism	Escherichia coli

Entity 2 Entity 2 polymer

Description description	Osmosensing histidine protein kinase SLN1
Molecular weight formula_weight	14950.3 kDa
EC 编号 ec_number	2.7.13.3
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	B

TSVKILVVEDNHVNQEVIKRMLNLEGIENIELACDGQEAFDKVKELTSKGENYNMIFMDVQMPKVDGLLSTKMIRRDLGYTSPIVALTAFADDSNIKECLESGMNGFLSKPIKRPKLKTILTEFCAAYQGKKN

Source Source

Source organism organism	Saccharomyces cerevisiae
Common name common_name	;baker's yeast ;
NCBI taxonomy ID ncbi_taxonomy_id	4932
Host organism host_organism	Escherichia coli

Entity 3 Entity 3 non-polymer

Description description	MAGNESIUM ION
Molecular weight formula_weight	24.3 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 4 Entity 4 non-polymer

Description description	SODIUM ION
Molecular weight formula_weight	23.0 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 5 Entity 5 non-polymer

Description description	BERYLLIUM TRIFLUORIDE ION
Molecular weight formula_weight	66.0 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 6 Entity 6 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	238

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6. Fold Classification (SCOP + CATH) 4 domains

SCOP 2.08 (2 domains)

Domain ID domain_id	d2r25a_
Class class	a — All alpha proteins
Fold Fold fold	a.24 — Four-helical up-and-down bundle
Superfamily Superfamily superfamily	a.24.10 — Histidine-containing phosphotransfer domain, HPT domain
Family Family family	a.24.10.2 — Phosphorelay protein-like

Domain ID domain_id	d2r25b_
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.23 — Flavodoxin-like
Superfamily Superfamily superfamily	c.23.1 — CheY-like
Family Family family	c.23.1.1 — CheY-related

CATH v4.4 (2 domains)

Domain ID domain_id	2r25A00
Class class	1 — Mainly Alpha
Architecture architecture	20 — Up-down Bundle
Topology topology	120 — Four Helix Bundle (Hemerythrin (Met), subunit A)
Homologous superfamily homologous superfamily	160 — HPT domain

Domain ID domain_id	2r25B00
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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Unit-cell length a length_a	52.013 Å
Unit-cell length b length_b	75.544 Å
Unit-cell length c length_c	98.392 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	4

Space group space_group	P 21 21 21
Space-group number int_tables_number	19
Crystal system crystal_system	—

Resolution resolution	1.700 Å
Low-resolution limit resolution_low	17.750 Å
R factor r_factor	0.1990
R_work r_work	0.1960
R_free r_free	0.2400

Complex of YPD1 and SLN1-R1 with bound Mg2+ and BeF3-

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

Phosphorelay intermediate protein YPD1

State in the Current Structure

Other States of the Same Protein in the Database

Osmosensing histidine protein kinase SLN1

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

2r25__assembly_1__model_1

2r25__assembly_1__model_1 | I(q)

2r25__assembly_1__model_1 | P(r) · Pending

4. Crystallography and Experiment 4. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

Diffraction experiment Diffraction

5. Entities and Polymers Entities & Polymers (6)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 polymer

Polymer Polymer

Source Source

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 non-polymer

Entity 5 Entity 5 non-polymer

Entity 6 Entity 6 water

6. Fold Classification (SCOP + CATH) 4 domains

SCOP 2.08 (2 domains)

CATH v4.4 (2 domains)

7. Citations (1)

Complex of YPD1 and SLN1-R1 with bound Mg2+ and BeF3-

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

Phosphorelay intermediate protein YPD1

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

Osmosensing histidine protein kinase SLN1

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

2r25__assembly_1__model_1

2r25__assembly_1__model_1 | I(q)

2r25__assembly_1__model_1 | P(r) · Pending

4. Crystallography and Experiment 4. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

Diffraction experiment Diffraction

5. Entities and Polymers Entities & Polymers (6)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 polymer

Polymer Polymer

Source Source

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 non-polymer

Entity 5 Entity 5 non-polymer

Entity 6 Entity 6 water

6. Fold Classification (SCOP + CATH) 4 domains

SCOP 2.08 (2 domains)

CATH v4.4 (2 domains)

7. Citations (1)