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	Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Associated Components	Method and Experimental Conditions	Structure Quality
1	Protein heterocomplex Heteromer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count	Chain A； UniProt 1–167	Not recorded	Osmosensing histidine protein kinase SLN1 × 1 （P39928） 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

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 2R25	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
1C02 CRYSTAL STRUCTURE OF YEAST YPD1P Deposited 1999-07-14	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 2–167（166 aa） Chain B 2–167（166 aa）	Not recorded	No recorded non-water small molecule	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
1C03 CRYSTAL STRUCTURE OF YPD1P (TRICLINIC FORM) Deposited 1999-07-14	Different mutation/modification Different oligomeric state Different ligand/ion 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 mutation/modification Different oligomeric state Different ligand/ion 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 mutation/modification Different oligomeric state Different ligand/ion 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 mutation/modification Different oligomeric state Different ligand/ion 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 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 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 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 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 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 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 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 oligomeric state Different ligand/ion 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 oligomeric state Different ligand/ion 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
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 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 mutation/modification Different oligomeric state Different ligand/ion 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	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	Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Associated Components	Method and Experimental Conditions	Structure Quality
1	Protein heterocomplex Heteromer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count	Chain B； UniProt 1086–1218	Fragment：UNP residues 1086-1218	Phosphorelay intermediate protein YPD1 × 1 （Q07688） 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

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 2R25	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
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 ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain B 1087–1220（134 aa） Fragment：C-terminal residues 1087-1220	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 ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain B 1087–1220（134 aa） Fragment：C-terminal residues 1087-1220	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 ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain D 1087–1220（134 aa） Fragment：C-terminal residues 1087-1220	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 ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 3 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain F 1087–1220（134 aa） Fragment：C-terminal residues 1087-1220	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 ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 4 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain H 1087–1220（134 aa） Fragment：C-terminal residues 1087-1220	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 ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 5 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain J 1087–1220（134 aa） Fragment：C-terminal residues 1087-1220	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 ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 6 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain L 1087–1220（134 aa） Fragment：C-terminal residues 1087-1220	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 B 1087–1220（134 aa） Fragment：C-terminal residues 1087-1220 Chain D 1087–1220（134 aa） Fragment：C-terminal residues 1087-1220 Chain F 1087–1220（134 aa） Fragment：C-terminal residues 1087-1220 Chain J 1087–1220（134 aa） Fragment：C-terminal residues 1087-1220	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

2 other PDB entries and 8 assemblies. Open the comparison page and filter oligomeric states

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. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

Radius of gyration Rg (Guinier) rg_guinier	21.34 Å
Radius of gyration Rg (electron density) rg_electron	20.29 Å
Forward intensity I(0) i0	19930800.00
Molecular weight molecular_weight	34003.0 kDa
Excluded volume excluded_volume	42685 Å³
Envelope volume envelope_volume	49880 Å³
Hydration-shell volume shell_volume	20639 Å³
Envelope diameter envelope_diameter	72.6 Å
Shell Rg shell_rg	26.69 Å
Envelope Rg envelope_rg	20.65 Å
Shape Rg shape_rg	20.29 Å
Total Rg total_rg	21.16 Å
Total atoms total_atoms	2383
Residues n_residues	299
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	73.5 Å
Rg (real space) rg_real	21.31 Å
Rg uncertainty (real space) rg_real_error	0.45 Å
I(0) (real space) i0_real	1.9930e+07
I(0) uncertainty (real space) i0_real_error	2.7400e+05
Rg (reciprocal space) rg_reciprocal	21.31 Å
I(0) (reciprocal space) i0_reciprocal	19930000.0000
Solution quality estimate total_estimate	0.8708
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	23.8 Å
Skewness Skewness skewness	0.317
Kurtosis Kurtosis kurtosis	-0.345
Angular range angular_range	— – 0.3700 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	6287000.0000
Real-space data points n_real_points	69
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.783; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.969; Smooth: 0.999

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. 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

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 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

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 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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7. 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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8. Citations (1)

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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

fit	/app/data/saxs_computation/r2/2r25/2r25.fit
pddf	/app/data/pr_computation/r2/2r25/2r25.pr.out
profile	/app/data/saxs_computation/r2/2r25/2r25.dat

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

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 (6)

Entity 1 Entity 1 polymer

Polymer Polymer

来源 Source

Entity 2 Entity 2 polymer

Polymer Polymer

来源 Source

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 non-polymer

Entity 5 Entity 5 non-polymer

Entity 6 Entity 6 water

7. Fold Classification (SCOP + CATH) 4 domains

SCOP 2.08 (2 domains)

CATH v4.4 (2 domains)

8. Citations (1)

9. Files and Curves (10)

Files (7)

Curves (3)