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5wbf

Double CACHE (dCACHE) sensing domain of TlpC chemoreceptor from Helicobacter pylori

Method: X-RAY DIFFRACTION Dmax: 112.4 Å Quality: GOOD
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1. Protein Identity and Related Structures Protein Identity & Related Structures

Methyl-accepting chemotaxis transducer (TlpC)

Helicobacter pylori

UniProt O24911

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 monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count Chain A； UniProt 34–297 Fragment：Double CACHE (dCACHE) sensing domain (UNP residues 34-297) LAC LACTIC ACID × 1 X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；291.15 K；0.2 M MgCl2, 0.1 M MES/NaOH (pH 6.5), 22% (w/v) PEG 4000 and 10 mM BaCl2H4O2 Resolution 2.19 Å R-free 0.218
2 Protein monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count Chain B； UniProt 34–297 Fragment：Double CACHE (dCACHE) sensing domain (UNP residues 34-297) LAC LACTIC ACID × 1 X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；291.15 K；0.2 M MgCl2, 0.1 M MES/NaOH (pH 6.5), 22% (w/v) PEG 4000 and 10 mM BaCl2H4O2 Resolution 2.19 Å R-free 0.218
3 Protein monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count Chain C； UniProt 34–297 Fragment：Double CACHE (dCACHE) sensing domain (UNP residues 34-297) LAC LACTIC ACID × 1 GOL GLYCEROL × 1 X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；291.15 K；0.2 M MgCl2, 0.1 M MES/NaOH (pH 6.5), 22% (w/v) PEG 4000 and 10 mM BaCl2H4O2 Resolution 2.19 Å R-free 0.218

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 5WBF Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
9EBW Chimeric fluorescence biosensor formed from a lactate-binding protein and GFP, bound to lactate Deposited 2024-11-13 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Insufficient information Homooligomer；Protein × 2 PDB declaration: dimeric
Chain A 30–292（263 aa）
Chain B 30–292（263 aa）
Non-standard monomer：Yes (specific site not provided by mmCIF) Non-standard monomer：Yes (specific site not provided by mmCIF) GOL GLYCEROL × 2 LAC LACTIC ACID × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；296 K；citric acid, PEG 6000, 1,3-propanediol
Resolution 2.78 Å R-free 0.285
9EBW Chimeric fluorescence biosensor formed from a lactate-binding protein and GFP, bound to lactate Deposited 2024-11-13 Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 2 Insufficient information Homooligomer；Protein × 2 PDB declaration: dimeric
Chain C 30–292（263 aa）
Chain D 30–292（263 aa）
Non-standard monomer：Yes (specific site not provided by mmCIF) Non-standard monomer：Yes (specific site not provided by mmCIF) LAC LACTIC ACID × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；296 K；citric acid, PEG 6000, 1,3-propanediol
Resolution 2.78 Å R-free 0.285
9EBX Chimeric fluorescence biosensor formed from a lactate-binding protein and GFP Deposited 2024-11-13 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Insufficient information Monomer；Protein × 1 PDB declaration: monomeric
Chain A 30–292（263 aa）
Non-standard monomer：Yes (specific site not provided by mmCIF) No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；296 K；magnesium chloride hexahydrate, HEPES, PEG 3350
Resolution 2.42 Å R-free 0.280

2 other PDB entries and 3 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name O24911_HELPY
Isoform —
PDB entities 1
Chains and sequence ranges Author chain A； PDBConstruct 7–270； UniProt 34–297 Author chain B； PDBConstruct 7–270； UniProt 34–297 Author chain C； PDBConstruct 7–270； UniProt 34–297

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 5wbf

P(r) Distance Distribution P(r) Distribution

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

Entry ID entry_id5wbf
Deposition date deposition_date2017-06-28
Structure title titleDouble CACHE (dCACHE) sensing domain of TlpC chemoreceptor from Helicobacter pylori
Keywords keywordsBacterial protein, Chemoreceptor sensing domain, double-CACHE domain, Helicobacter pylori, SIGNALING PROTEIN; SIGNALING PROTEIN
Experimental Method methodX-RAY DIFFRACTION
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3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

Radius of gyration Rg (Guinier) rg_guinier35.37 Å
Radius of gyration Rg (electron density) rg_electron34.85 Å
Forward intensity I(0) i0117071000.00
Molecular weight molecular_weight88396.0 kDa
Excluded volume excluded_volume111470 ų
Envelope volume envelope_volume151690 ų
Hydration-shell volume shell_volume37776 ų
Envelope diameter envelope_diameter112.7 Å
Shell Rg shell_rg39.48 Å
Envelope Rg envelope_rg34.70 Å
Shape Rg shape_rg34.78 Å
Total Rg total_rg35.44 Å
Total atoms total_atoms6223
Residues n_residues773
Spherical-harmonic order n_harmonics20
q range q_range— – 0.5000 Å−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
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4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

Maximum dimension Dmax dmax112.4 Å
Rg (real space) rg_real35.43 Å
Rg uncertainty (real space) rg_real_error0.77 Å
I(0) (real space) i0_real1.1710e+08
I(0) uncertainty (real space) i0_real_error1.7820e+06
Rg (reciprocal space) rg_reciprocal35.40 Å
I(0) (reciprocal space) i0_reciprocal117100000.0000
Solution quality estimate total_estimate0.8861
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks1
Primary peak position r_peak_primary35.0 Å
Skewness Skewness skewness0.266
Kurtosis Kurtosis kurtosis-0.710
Angular range angular_range— – 0.2250 Å−1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha19650000.0000
Real-space data points n_real_points46
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.944; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.943; Smooth: 0.741
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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (4)

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8. Citations (1)

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9. Files and Curves (10)