6m7w

Role of the highly conserved G68 residue in the yeast phosphorelay protein Ypd1: implications for interactions between histidine phosphotransfer (HPt) and response regulator proteins

Method: X-RAY DIFFRACTION

▼

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

Phosphorelay intermediate protein YPD1

Saccharomyces cerevisiae (strain ATCC 204508 / S288c)

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein monomer	Monomer	Protein 1	water × 1	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

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.

▼

2. Structure Basics 2. Structure Basics

Entry ID entry_id	6m7w
Deposition date deposition_date	2018-08-21
Structure title title	Role of the highly conserved G68 residue in the yeast phosphorelay protein Ypd1: implications for interactions between histidine phosphotransfer (HPt) and response regulator proteins
Keywords keywords	G68Q mutant, HPt, yeast phosphorelay, TRANSFERASE; TRANSFERASE
Experimental Method method	X-RAY DIFFRACTION

▼

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.

6m7w__assembly_1__model_1

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

Download this curve (.dat)

6m7w__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

6m7w__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	17.74 Å
Rg (electron density)	16.50 Å
Total Rg	17.47 Å
Atom count	1344
Residues	166
Excluded volume	23906 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`6m7w__assembly_1__model_1`	monomeric （1）	Success	4.1.3-1-20251215 (887e7ef)	View Download

▶

4. Crystallography and Experiment 4. Crystallography & Experiment

▶

5. Entities and Polymers Entities & Polymers (2)

▼

6. Fold Classification (SCOP + CATH) 2 domains

SCOP 2.08 (1 domains)

Domain ID domain_id	d6m7wa_
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

CATH v4.4 (1 domains)

Domain ID domain_id	6m7wA00
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

▶

Unit-cell length a length_a	76.724 Å
Unit-cell length b length_b	76.724 Å
Unit-cell length c length_c	66.788 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 31 2 1
Space-group number int_tables_number	152
Crystal system crystal_system	—

Resolution resolution	1.980 Å
Low-resolution limit resolution_low	47.104 Å
R factor r_factor	0.1813
R_work r_work	0.1783
R_free r_free	0.2074

Description description	Phosphorelay intermediate protein YPD1
Molecular weight formula_weight	19258.7 kDa
Mutation mutation	G68Q
Source method src_method	man
Copy count entity_count	1

Polymer type type	polypeptide(L)
Chain IDs strand_id	A
Atom count atom_count	1528

Role of the highly conserved G68 residue in the yeast phosphorelay protein Ypd1: implications for interactions between histidine phosphotransfer (HPt) and response regulator proteins

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

2. Structure Basics 2. Structure Basics

3. Official assembly/model SAXS Official SAXS Profiles

6m7w__assembly_1__model_1

6m7w__assembly_1__model_1 | I(q)

6m7w__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 (2)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 water

6. Fold Classification (SCOP + CATH) 2 domains

SCOP 2.08 (1 domains)

CATH v4.4 (1 domains)

7. Citations (4)

Source organism organism	Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
Common name common_name	;Baker's yeast ;
NCBI taxonomy ID ncbi_taxonomy_id	559292
Host organism host_organism	Escherichia coli

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	165

Role of the highly conserved G68 residue in the yeast phosphorelay protein Ypd1: implications for interactions between histidine phosphotransfer (HPt) and response regulator proteins

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

2. Structure Basics 2. Structure Basics

3. Official assembly/model SAXS Official SAXS Profiles

6m7w__assembly_1__model_1

6m7w__assembly_1__model_1 | I(q)

6m7w__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 (2)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 water

6. Fold Classification (SCOP + CATH) 2 domains

SCOP 2.08 (1 domains)

CATH v4.4 (1 domains)

7. Citations (4)