2pmc

Crystal Structure of CheY-Mg(2+) in Complex with CheZ(C15) Peptide solved from a P1 Crystal

Method: X-RAY DIFFRACTION Dmax: 87.7 Å Quality: GOOD

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

Chemotaxis protein cheY

Salmonella typhimurium

UniProt P0A2D5

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 2–129 Not recorded Chemotaxis protein cheZ × 1 (P07800) MG MAGNESIUM ION × 1 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, HANGING DROP;pH 6;298 K;37.5 % PEG 8000, 0.1 M ammonium thiocyanate, 0.1 M MES, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 298.0K Resolution 2.69 Å R-free 0.285
2 Protein heterocomplex Heteromer Protein × 2 PDB declaration: dimeric(2) Consistent with protein copy count Chain B; UniProt 2–129 Not recorded Chemotaxis protein cheZ × 1 (P07800) MG MAGNESIUM ION × 1 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, HANGING DROP;pH 6;298 K;37.5 % PEG 8000, 0.1 M ammonium thiocyanate, 0.1 M MES, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 298.0K Resolution 2.69 Å R-free 0.285
3 Protein monomer Monomer Protein × 1 PDB declaration: monomeric(1) Consistent with protein copy count Chain C; UniProt 2–129 Not recorded No other associated polymer X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, HANGING DROP;pH 6;298 K;37.5 % PEG 8000, 0.1 M ammonium thiocyanate, 0.1 M MES, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 298.0K Resolution 2.69 Å R-free 0.285
4 Protein monomer Monomer Protein × 1 PDB declaration: monomeric(1) Consistent with protein copy count Chain D; UniProt 2–129 Not recorded No other associated polymer X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, HANGING DROP;pH 6;298 K;37.5 % PEG 8000, 0.1 M ammonium thiocyanate, 0.1 M MES, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 298.0K Resolution 2.69 Å R-free 0.285

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.

14 other PDB entries and 21 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name CHEY_SALTY
Isoform
PDB entities 1
Chains and sequence ranges Author chain A; PDBConstruct 1–128; UniProt 2–129 Author chain B; PDBConstruct 1–128; UniProt 2–129 Author chain C; PDBConstruct 1–128; UniProt 2–129 Author chain D; PDBConstruct 1–128; UniProt 2–129

Chemotaxis protein cheZ

OrganismNot specified

UniProt P07800

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 E; UniProt 200–214 Not recorded Chemotaxis protein cheY × 1 (P0A2D5) MG MAGNESIUM ION × 1 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, HANGING DROP;pH 6;298 K;37.5 % PEG 8000, 0.1 M ammonium thiocyanate, 0.1 M MES, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 298.0K Resolution 2.69 Å R-free 0.285
2 Protein heterocomplex Heteromer Protein × 2 PDB declaration: dimeric(2) Consistent with protein copy count Chain F; UniProt 200–214 Not recorded Chemotaxis protein cheY × 1 (P0A2D5) MG MAGNESIUM ION × 1 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, HANGING DROP;pH 6;298 K;37.5 % PEG 8000, 0.1 M ammonium thiocyanate, 0.1 M MES, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 298.0K Resolution 2.69 Å R-free 0.285

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.

8 other PDB entries and 14 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name CHEZ_SALTY
Isoform
PDB entities 2
Chains and sequence ranges Author chain E; PDBConstruct 1–15; UniProt 200–214 Author chain F; PDBConstruct 1–15; UniProt 200–214

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 2pmc

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 2pmc
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2. Structure Basics 2. Structure Basics

Entry ID entry_id2pmc
Deposition date deposition_date2007-04-20
Structure title titleCrystal Structure of CheY-Mg(2+) in Complex with CheZ(C15) Peptide solved from a P1 Crystal
Keywords keywordsCHEMOTAXIS, CHEY-CHEZ PEPTIDE COMPLEX, 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_guinier27.54
Radius of gyration Rg (electron density) rg_electron26.74
Forward intensity I(0) i052063700.00
Molecular weight molecular_weight57763.0 kDa
Excluded volume excluded_volume73115 ų
Envelope volume envelope_volume92472 ų
Hydration-shell volume shell_volume29042 ų
Envelope diameter envelope_diameter93.3
Shell Rg shell_rg33.67
Envelope Rg envelope_rg26.59
Shape Rg shape_rg26.73
Total Rg total_rg27.55
Total atoms total_atoms4050
Residues n_residues528
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 dmax87.7
Rg (real space) rg_real27.44
Rg uncertainty (real space) rg_real_error0.69
I(0) (real space) i0_real5.2060e+07
I(0) uncertainty (real space) i0_real_error7.5960e+05
Rg (reciprocal space) rg_reciprocal27.48
I(0) (reciprocal space) i0_reciprocal52060000.0000
Solution quality estimate total_estimate0.8268
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary39.3
Skewness Skewness skewness0.176
Kurtosis Kurtosis kurtosis-0.545
Angular range angular_range— – 0.2900 −1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha26280000.0000
Real-space data points n_real_points59
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.915; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.999; Smooth: 0.000

5. Crystallography and Experiment 5. Crystallography & Experiment

6. Entities and Polymers Entities & Polymers (4)

7. Fold Classification (SCOP + CATH) 8 domains

SCOP 2.08 (4 domains)

Domain ID domain_idd2pmca_
Class classc — Alpha and beta proteins (a/b)
Fold Fold foldc.23 — Flavodoxin-like
Superfamily Superfamily superfamilyc.23.1 — CheY-like
Family Family familyc.23.1.1 — CheY-related
Domain ID domain_idd2pmcb_
Class classc — Alpha and beta proteins (a/b)
Fold Fold foldc.23 — Flavodoxin-like
Superfamily Superfamily superfamilyc.23.1 — CheY-like
Family Family familyc.23.1.1 — CheY-related
Domain ID domain_idd2pmcc_
Class classc — Alpha and beta proteins (a/b)
Fold Fold foldc.23 — Flavodoxin-like
Superfamily Superfamily superfamilyc.23.1 — CheY-like
Family Family familyc.23.1.1 — CheY-related
Domain ID domain_idd2pmcd_
Class classc — Alpha and beta proteins (a/b)
Fold Fold foldc.23 — Flavodoxin-like
Superfamily Superfamily superfamilyc.23.1 — CheY-like
Family Family familyc.23.1.1 — CheY-related

CATH v4.4 (4 domains)

Domain ID domain_id2pmcA00
Class class3 — Alpha Beta
Architecture architecture40 — 3-Layer(aba) Sandwich
Topology topology50 — Rossmann fold
Homologous superfamily homologous superfamily2300 — Response regulator
Domain ID domain_id2pmcB00
Class class3 — Alpha Beta
Architecture architecture40 — 3-Layer(aba) Sandwich
Topology topology50 — Rossmann fold
Homologous superfamily homologous superfamily2300 — Response regulator
Domain ID domain_id2pmcC00
Class class3 — Alpha Beta
Architecture architecture40 — 3-Layer(aba) Sandwich
Topology topology50 — Rossmann fold
Homologous superfamily homologous superfamily2300 — Response regulator
Domain ID domain_id2pmcD00
Class class3 — Alpha Beta
Architecture architecture40 — 3-Layer(aba) Sandwich
Topology topology50 — Rossmann fold
Homologous superfamily homologous superfamily2300 — Response regulator

8. Citations (1)

9. Files and Curves (10)