SAXSdb — 1c02

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

PHOSPHOTRANSFERASE YPD1P

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 homooligomer Homooligomer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count	Chain A； UniProt 2–167 Chain B； UniProt 2–167	Not recorded	No other associated polymer	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 7.36；297 K；AMMONIUM SULFATE, LITHIUM SULFATE, HEPES, PEG 400, pH 7.36, VAPOR DIFFUSION, HANGING DROP, temperature 297.0K	Resolution 1.80 Å R-free 0.247

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 1C02	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
1C03 CRYSTAL STRUCTURE OF YPD1P (TRICLINIC FORM) Deposited 1999-07-14	Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1–167（167 aa）	Mutation：C-TERMINAL 6 HIS-TAG	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.36；297 K；PEG 400, ammonium sulfate, Hepes, Li2SO4, pH 7.36, VAPOR DIFFUSION, HANGING DROP, temperature 297K	Resolution 2.30 Å R-free 0.248
1C03 CRYSTAL STRUCTURE OF YPD1P (TRICLINIC FORM) Deposited 1999-07-14	Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain B 1–167（167 aa）	Mutation：C-TERMINAL 6 HIS-TAG	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.36；297 K；PEG 400, ammonium sulfate, Hepes, Li2SO4, pH 7.36, VAPOR DIFFUSION, HANGING DROP, temperature 297K	Resolution 2.30 Å R-free 0.248
1C03 CRYSTAL STRUCTURE OF YPD1P (TRICLINIC FORM) Deposited 1999-07-14	Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 3 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain C 1–167（167 aa）	Mutation：C-TERMINAL 6 HIS-TAG	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.36；297 K；PEG 400, ammonium sulfate, Hepes, Li2SO4, pH 7.36, VAPOR DIFFUSION, HANGING DROP, temperature 297K	Resolution 2.30 Å R-free 0.248
1C03 CRYSTAL STRUCTURE OF YPD1P (TRICLINIC FORM) Deposited 1999-07-14	Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 4 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain D 1–167（167 aa）	Mutation：C-TERMINAL 6 HIS-TAG	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.36；297 K；PEG 400, ammonium sulfate, Hepes, Li2SO4, pH 7.36, VAPOR DIFFUSION, HANGING DROP, temperature 297K	Resolution 2.30 Å R-free 0.248
1OXB Complex between YPD1 and SLN1 response regulator domain in space group P2(1)2(1)2(1) Deposited 2003-04-01	Different construct Different mutation/modification 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 2–167（166 aa）	Not recorded	SO4 SULFATE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.3；296 K；ammonium sulfate, sodium acetate, BeCl2, NaF, pH 5.3, VAPOR DIFFUSION, HANGING DROP, temperature 296K	Resolution 2.30 Å R-free 0.266
1OXK Complex between YPD1 and SLN1 response regulator domain in space group P3(2) Deposited 2003-04-02	Different construct Different mutation/modification 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 2–167（166 aa） Fragment：YPD1	Not recorded	SO4 SULFATE ION × 3	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.3；296 K；ammonium sulfate, sodium acetate, BeCl2, NaF, MnCl2, pH 5.3, VAPOR DIFFUSION, HANGING DROP, temperature 296K	Resolution 2.10 Å R-free 0.258
1OXK Complex between YPD1 and SLN1 response regulator domain in space group P3(2) Deposited 2003-04-02	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain C 2–167（166 aa） Fragment：YPD1	Not recorded	SO4 SULFATE ION × 3	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.3；296 K；ammonium sulfate, sodium acetate, BeCl2, NaF, MnCl2, pH 5.3, VAPOR DIFFUSION, HANGING DROP, temperature 296K	Resolution 2.10 Å R-free 0.258
1OXK Complex between YPD1 and SLN1 response regulator domain in space group P3(2) Deposited 2003-04-02	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 3 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain E 2–167（166 aa） Fragment：YPD1	Not recorded	SO4 SULFATE ION × 3	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.3；296 K；ammonium sulfate, sodium acetate, BeCl2, NaF, MnCl2, pH 5.3, VAPOR DIFFUSION, HANGING DROP, temperature 296K	Resolution 2.10 Å R-free 0.258
1OXK Complex between YPD1 and SLN1 response regulator domain in space group P3(2) Deposited 2003-04-02	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 4 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain G 2–167（166 aa） Fragment：YPD1	Not recorded	SO4 SULFATE ION × 3	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.3；296 K；ammonium sulfate, sodium acetate, BeCl2, NaF, MnCl2, pH 5.3, VAPOR DIFFUSION, HANGING DROP, temperature 296K	Resolution 2.10 Å R-free 0.258
1OXK Complex between YPD1 and SLN1 response regulator domain in space group P3(2) Deposited 2003-04-02	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 5 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain I 2–167（166 aa） Fragment：YPD1	Not recorded	SO4 SULFATE ION × 3	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.3；296 K；ammonium sulfate, sodium acetate, BeCl2, NaF, MnCl2, pH 5.3, VAPOR DIFFUSION, HANGING DROP, temperature 296K	Resolution 2.10 Å R-free 0.258
1OXK Complex between YPD1 and SLN1 response regulator domain in space group P3(2) Deposited 2003-04-02	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 6 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain K 2–167（166 aa） Fragment：YPD1	Not recorded	SO4 SULFATE ION × 3	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.3；296 K；ammonium sulfate, sodium acetate, BeCl2, NaF, MnCl2, pH 5.3, VAPOR DIFFUSION, HANGING DROP, temperature 296K	Resolution 2.10 Å R-free 0.258
1OXK Complex between YPD1 and SLN1 response regulator domain in space group P3(2) Deposited 2003-04-02	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 7 Protein heterocomplex Heteromer；Protein × 8 PDB declaration: octameric	Chain A 2–167（166 aa） Fragment：YPD1 Chain C 2–167（166 aa） Fragment：YPD1 Chain E 2–167（166 aa） Fragment：YPD1 Chain I 2–167（166 aa） Fragment：YPD1	Not recorded	SO4 SULFATE ION × 12	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.3；296 K；ammonium sulfate, sodium acetate, BeCl2, NaF, MnCl2, pH 5.3, VAPOR DIFFUSION, HANGING DROP, temperature 296K	Resolution 2.10 Å R-free 0.258
1QSP CRYSTAL STRUCTURE OF THE YEAST PHOSPHORELAY PROTEIN YPD1 Deposited 1999-06-22	Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 3–167（165 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5；298 K；PEG 4000, SODIUM ACETATE AMMONIUM ACETATE, BETA-MERCAPTOETHANOL, pH 5.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K	Resolution 2.70 Å R-free 0.254
1QSP CRYSTAL STRUCTURE OF THE YEAST PHOSPHORELAY PROTEIN YPD1 Deposited 1999-06-22	Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain B 3–167（165 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5；298 K；PEG 4000, SODIUM ACETATE AMMONIUM ACETATE, BETA-MERCAPTOETHANOL, pH 5.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K	Resolution 2.70 Å R-free 0.254
2R25 Complex of YPD1 and SLN1-R1 with bound Mg2+ and BeF3- Deposited 2007-08-24	Different construct Different mutation/modification 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 1–167（167 aa）	Not recorded	MG MAGNESIUM ION × 1 NA SODIUM ION × 1 BEF BERYLLIUM TRIFLUORIDE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions pH 5.6；295 K；2.2 M ammonium sulfate, 50 mM sodium acetate, VAPOR DIFFUSION, HANGING DROP, temperature 295K, pH 5.60	Resolution 1.70 Å R-free 0.240
5KBX Co-crystal structure of the Saccharomyces cerevisiae histidine phosphotransfer signaling protein Ypd1 and the receiver domain of its downstream response regulator Ssk1 Deposited 2016-06-03	Different construct Different mutation/modification 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 1–167（167 aa）	Not recorded	GOL GLYCEROL × 3 PO4 PHOSPHATE ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 10.5；296 K；0.2 M lithium sulfate, 0.1 M CAPS/NaOH pH 10.5, 1.2 M NaH2PO4/0.8 M K2HPO4	Resolution 2.80 Å R-free 0.279
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 Deposited 2018-08-21	Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1–167（167 aa）	Mutation：G68Q	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5；296 K；0.1 M sodium acetate (pH 5.0), 0.2M ammonium acetate and 25-30% PEG 4000	Resolution 1.98 Å R-free 0.207

7 other PDB entries and 17 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	Q07688_YEAST
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–166； UniProt 2–167 Author chain B； PDBConstruct 1–166； UniProt 2–167

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.

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2. Structure Basics 2. Structure Basics

Entry ID entry_id	1c02
Deposition date deposition_date	1999-07-14
Structure title title	CRYSTAL STRUCTURE OF YEAST YPD1P
Keywords keywords	HELIX-BUNDLE, TRANSFERASE; TRANSFERASE
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	23.66 Å
Radius of gyration Rg (electron density) rg_electron	22.86 Å
Forward intensity I(0) i0	24821600.00
Molecular weight molecular_weight	38053.0 kDa
Excluded volume excluded_volume	47645 Å³
Envelope volume envelope_volume	57527 Å³
Hydration-shell volume shell_volume	21807 Å³
Envelope diameter envelope_diameter	88.1 Å
Shell Rg shell_rg	28.86 Å
Envelope Rg envelope_rg	23.13 Å
Shape Rg shape_rg	22.85 Å
Total Rg total_rg	23.64 Å
Total atoms total_atoms	2678
Residues n_residues	332
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	83.9 Å
Rg (real space) rg_real	23.72 Å
Rg uncertainty (real space) rg_real_error	0.70 Å
I(0) (real space) i0_real	2.4820e+07
I(0) uncertainty (real space) i0_real_error	3.9200e+05
Rg (reciprocal space) rg_reciprocal	23.71 Å
I(0) (reciprocal space) i0_reciprocal	24820000.0000
Solution quality estimate total_estimate	0.6089
Solution quality rating solution_quality	REASONABLE a REASONABLE solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	24.9 Å
Skewness Skewness skewness	0.416
Kurtosis Kurtosis kurtosis	-0.321
Angular range angular_range	— – 0.3350 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	8046000.0000
Real-space data points n_real_points	65
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.734; Stabil: 1.000; Sysdev: 0.286; Positv: 1.000; Valcen: 0.853; Smooth: 0.000

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (2)

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7. Fold Classification (SCOP + CATH) 4 domains

SCOP 2.08 (2 domains)

Domain ID domain_id	d1c02a_
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	d1c02b_
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 (2 domains)

Domain ID domain_id	1c02A00
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	1c02B00
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

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8. Citations (2)

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Unit-cell length a length_a	53.013 Å
Unit-cell length b length_b	53.013 Å
Unit-cell length c length_c	244.853 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	16

Space group space_group	P 43 21 2
Space-group number int_tables_number	96
Crystal system crystal_system	—

Resolution resolution	1.800 Å
Low-resolution limit resolution_low	8.000 Å
R factor r_factor	0.2010
R_work r_work	0.2010
R_free r_free	0.2470

Description description	PHOSPHOTRANSFERASE YPD1P
Molecular weight formula_weight	19055.5 kDa
Source method src_method	man
Copy count entity_count	2

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B
Atom count atom_count	2734

CRYSTAL STRUCTURE OF YEAST YPD1P

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

PHOSPHOTRANSFERASE YPD1P

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

6. Entities and Polymers Entities & Polymers (2)

Entity 1 Entity 1 polymer

Polymer Polymer

来源 Source

Entity 2 Entity 2 water

7. Fold Classification (SCOP + CATH) 4 domains

SCOP 2.08 (2 domains)

CATH v4.4 (2 domains)

8. Citations (2)

9. Files and Curves (10)

Files (7)

Curves (3)

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

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	56

fit	/app/data/saxs_computation/c0/1c02/1c02.fit
pddf	/app/data/pr_computation/c0/1c02/1c02.pr.out
profile	/app/data/saxs_computation/c0/1c02/1c02.dat