5kbx

Co-crystal structure of the Saccharomyces cerevisiae histidine phosphotransfer signaling protein Ypd1 and the receiver domain of its downstream response regulator Ssk1

Method: X-RAY DIFFRACTION Dmax: 77.5 Å Quality: REASONABLE

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

Phosphorelay intermediate protein YPD1

Saccharomyces cerevisiae S288C

UniProt Q07688

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 Osmolarity two-component system protein SSK1 × 1 (Q07084) 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

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.

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

Osmolarity two-component system protein SSK1

Saccharomyces cerevisiae S288C

UniProt Q07084

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 495–712 Fragment:UNP residues 495-712 Non-standard monomer:Yes (specific site not provided by mmCIF) Phosphorelay intermediate protein YPD1 × 1 (Q07688) 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

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.

No other PDB entry for the same UniProt protein was found.

View Construct and Data Evidence
UniProt name SSK1_YEAST
Isoform
PDB entities 2
Chains and sequence ranges Author chain B; PDBConstruct 1–218; UniProt 495–712

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.

SAXS scattering curve SAXS Profile

SAXS profile for 5kbx

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 5kbx
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2. Structure Basics 2. Structure Basics

Entry ID entry_id5kbx
Deposition date deposition_date2016-06-03
Structure title titleCo-crystal structure of the Saccharomyces cerevisiae histidine phosphotransfer signaling protein Ypd1 and the receiver domain of its downstream response regulator Ssk1
Keywords keywords;two-component signaling, phosphorelay, Ypd1, Ssk1, response regulator, histidine phosphotransfer protein, Saccharomyces cerevisiae, co-crystal, phosphotransfer, SIGNALING PROTEIN ;; SIGNALING PROTEIN
Experimental Method methodX-RAY DIFFRACTION

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

Radius of gyration Rg (Guinier) rg_guinier22.10
Radius of gyration Rg (electron density) rg_electron21.27
Forward intensity I(0) i019963300.00
Molecular weight molecular_weight34252.0 kDa
Excluded volume excluded_volume43104 ų
Envelope volume envelope_volume53253 ų
Hydration-shell volume shell_volume21075 ų
Envelope diameter envelope_diameter83.1
Shell Rg shell_rg27.74
Envelope Rg envelope_rg22.09
Shape Rg shape_rg21.26
Total Rg total_rg22.19
Total atoms total_atoms2396
Residues n_residues294
Spherical-harmonic order n_harmonics20
q range q_range— – 0.5000 −1
Data points n_points101
Shell type shell_typedirectional
Solvent electron density solvent_density0.3340 e/ų
Shell contrast contrast_shell0.0300 e/ų
CRYSOL version crysol_version4.1.3

4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

Maximum dimension Dmax dmax77.5
Rg (real space) rg_real22.12
Rg uncertainty (real space) rg_real_error0.77
I(0) (real space) i0_real1.9960e+07
I(0) uncertainty (real space) i0_real_error3.1500e+05
Rg (reciprocal space) rg_reciprocal22.11
I(0) (reciprocal space) i0_reciprocal19960000.0000
Solution quality estimate total_estimate0.5794
Solution quality rating solution_quality REASONABLE a REASONABLE solution
P(r) peaks n_peaks3
Primary peak position r_peak_primary24.3
Skewness Skewness skewness0.414
Kurtosis Kurtosis kurtosis-0.114
Angular range angular_range— – 0.3600 −1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha4900000.0000
Real-space data points n_real_points68
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.726; Stabil: 0.997; Sysdev: 0.145; Positv: 1.000; Valcen: 0.924; Smooth: 0.000

5. Crystallography and Experiment 5. Crystallography & Experiment

6. Entities and Polymers Entities & Polymers (5)

7. Fold Classification (SCOP + CATH) 3 domains

SCOP 2.08 (2 domains)

Domain ID domain_idd5kbxa_
Class classa — All alpha proteins
Fold Fold folda.24 — Four-helical up-and-down bundle
Superfamily Superfamily superfamilya.24.10 — Histidine-containing phosphotransfer domain, HPT domain
Family Family familya.24.10.2 — Phosphorelay protein-like
Domain ID domain_idd5kbxb_
Class classc — Alpha and beta proteins (a/b)
Fold Fold foldc.23 — Flavodoxin-like
Superfamily Superfamily superfamilyc.23.1 — CheY-like
Family Family familyc.23.1.0 — automated matches

CATH v4.4 (1 domains)

Domain ID domain_id5kbxA00
Class class1 — Mainly Alpha
Architecture architecture20 — Up-down Bundle
Topology topology120 — Four Helix Bundle (Hemerythrin (Met), subunit A)
Homologous superfamily homologous superfamily160 — HPT domain

8. Citations (3)

9. Files and Curves (10)