1u8t

Crystal structure of CheY D13K Y106W alone and in complex with a FliM peptide

Method: X-RAY DIFFRACTION Dmax: 76.5 Å Quality: EXCELLENT

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

Chemotaxis protein cheY

Escherichia coli

UniProt P06143

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 1–128 Mutation:D13K Y106W Non-standard monomer:Yes (specific site not provided by mmCIF) Flagellar motor switch protein fliM × 1 (P06974) X-RAY DIFFRACTION X-ray crystallization conditions:pH 7.9;277 K;PEG 3350, ammonium sulfate, Tris, VAPOR DIFFUSION, temperature 277K, pH 7.90 Resolution 1.50 Å R-free 0.273
2 Protein heterocomplex Heteromer Protein × 2 PDB declaration: dimeric(2) Consistent with protein copy count Chain B; UniProt 1–128 Mutation:D13K Y106W Non-standard monomer:Yes (specific site not provided by mmCIF) Flagellar motor switch protein fliM × 1 (P06974) X-RAY DIFFRACTION X-ray crystallization conditions:pH 7.9;277 K;PEG 3350, ammonium sulfate, Tris, VAPOR DIFFUSION, temperature 277K, pH 7.90 Resolution 1.50 Å R-free 0.273
3 Protein monomer Monomer Protein × 1 PDB declaration: monomeric(1) Consistent with protein copy count Chain C; UniProt 1–128 Mutation:D13K Y106W Non-standard monomer:Yes (specific site not provided by mmCIF) SO4 SULFATE ION × 3 X-RAY DIFFRACTION X-ray crystallization conditions:pH 7.9;277 K;PEG 3350, ammonium sulfate, Tris, VAPOR DIFFUSION, temperature 277K, pH 7.90 Resolution 1.50 Å R-free 0.273
4 Protein monomer Monomer Protein × 1 PDB declaration: monomeric(1) Consistent with protein copy count Chain D; UniProt 1–128 Mutation:D13K Y106W Non-standard monomer:Yes (specific site not provided by mmCIF) SO4 SULFATE ION × 1 X-RAY DIFFRACTION X-ray crystallization conditions:pH 7.9;277 K;PEG 3350, ammonium sulfate, Tris, VAPOR DIFFUSION, temperature 277K, pH 7.90 Resolution 1.50 Å R-free 0.273
5 Protein homooligomer Homooligomer Protein × 2 PDB declaration: dimeric(2) Consistent with protein copy count Chain C; UniProt 1–128 Chain D; UniProt 1–128 Mutation:D13K Y106W Non-standard monomer:Yes (specific site not provided by mmCIF) SO4 SULFATE ION × 4 X-RAY DIFFRACTION X-ray crystallization conditions:pH 7.9;277 K;PEG 3350, ammonium sulfate, Tris, VAPOR DIFFUSION, temperature 277K, pH 7.90 Resolution 1.50 Å R-free 0.273

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.

27 other PDB entries and 42 assemblies. Open the comparison page and filter oligomeric states

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

Flagellar motor switch protein fliM

OrganismNot specified

UniProt P06974

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 1–16 Not recorded Chemotaxis protein cheY × 1 (P06143) X-RAY DIFFRACTION X-ray crystallization conditions:pH 7.9;277 K;PEG 3350, ammonium sulfate, Tris, VAPOR DIFFUSION, temperature 277K, pH 7.90 Resolution 1.50 Å R-free 0.273
2 Protein heterocomplex Heteromer Protein × 2 PDB declaration: dimeric(2) Consistent with protein copy count Chain F; UniProt 1–16 Not recorded Chemotaxis protein cheY × 1 (P06143) X-RAY DIFFRACTION X-ray crystallization conditions:pH 7.9;277 K;PEG 3350, ammonium sulfate, Tris, VAPOR DIFFUSION, temperature 277K, pH 7.90 Resolution 1.50 Å R-free 0.273

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.

2 other PDB entries and 5 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name FLIM_ECOLI
Isoform
PDB entities 2
Chains and sequence ranges Author chain E; PDBConstruct 1–16; UniProt 1–16 Author chain F; PDBConstruct 1–16; UniProt 1–16

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 1u8t

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 1u8t
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2. Structure Basics 2. Structure Basics

Entry ID entry_id1u8t
Deposition date deposition_date2004-08-06
Structure title titleCrystal structure of CheY D13K Y106W alone and in complex with a FliM peptide
Keywords keywordsCHEY, FLIM, (beta/alpha)5, 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_guinier25.06
Radius of gyration Rg (electron density) rg_electron24.19
Forward intensity I(0) i060280100.00
Molecular weight molecular_weight59931.0 kDa
Excluded volume excluded_volume74556 ų
Envelope volume envelope_volume88596 ų
Hydration-shell volume shell_volume30083 ų
Envelope diameter envelope_diameter78.6
Shell Rg shell_rg31.84
Envelope Rg envelope_rg24.13
Shape Rg shape_rg24.22
Total Rg total_rg24.94
Total atoms total_atoms4116
Residues n_residues512
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 dmax76.5
Rg (real space) rg_real24.90
Rg uncertainty (real space) rg_real_error0.46
I(0) (real space) i0_real6.0280e+07
I(0) uncertainty (real space) i0_real_error8.3940e+05
Rg (reciprocal space) rg_reciprocal24.95
I(0) (reciprocal space) i0_reciprocal60280000.0000
Solution quality estimate total_estimate0.9079
Solution quality rating solution_quality EXCELLENT a EXCELLENT solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary30.4
Skewness Skewness skewness0.077
Kurtosis Kurtosis kurtosis-0.591
Angular range angular_range— – 0.3150 −1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha17070000.0000
Real-space data points n_real_points64
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.938; Stabil: 0.999; Sysdev: 1.000; Positv: 1.000; Valcen: 0.993; Smooth: 0.992

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_idd1u8ta_
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_idd1u8tb_
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_idd1u8tc_
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_idd1u8td_
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_id1u8tA00
Class class3 — Alpha Beta
Architecture architecture40 — 3-Layer(aba) Sandwich
Topology topology50 — Rossmann fold
Homologous superfamily homologous superfamily2300 — Response regulator
Domain ID domain_id1u8tB00
Class class3 — Alpha Beta
Architecture architecture40 — 3-Layer(aba) Sandwich
Topology topology50 — Rossmann fold
Homologous superfamily homologous superfamily2300 — Response regulator
Domain ID domain_id1u8tC00
Class class3 — Alpha Beta
Architecture architecture40 — 3-Layer(aba) Sandwich
Topology topology50 — Rossmann fold
Homologous superfamily homologous superfamily2300 — Response regulator
Domain ID domain_id1u8tD00
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)