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2k5t

Solution NMR Structure of Putative N-Acetyl Transferase YhhK from E. coli Bound to Coenzyme A: Northeast Structural Genomics Consortium Target ET106

Method: SOLUTION NMR Dmax: 44.7 Å Quality: GOOD
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1. Protein Identity and Related Structures Protein Identity & Related Structures

Uncharacterized protein yhhK

Escherichia coli K12

UniProt P37613

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 1–127 Mutation：A119T COA COENZYME A × 1 SOLUTION NMR NMR measurement conditions：pH 7；293 K；Ionic strength (raw mmCIF value) 300；Pressure ambient NMR sample composition：0.6 mM [U-100% 13C; U-100% 15N] YhhK, 5 mM Coenzyme A, 7 % D2O, 300 mM sodium chloride, 25 mM TRIS, 5 mM DTT, 93% H2O/7% D2O | 93% H2O/7% D2O NMR sample composition：0.6 mM [U-100% 13C; U-100% 15N] YhhK, 5 mM Coenzyme A, 100 % D2O, 300 mM sodium chloride, 25 mM TRIS, 5 mM DTT, 100% D2O | 100% D2O Resolution not provided

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 2K5T Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
4CRY Direct visualisation of strain-induced protein post-translational modification Deposited 2014-03-02 Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 12 PDB declaration: dodecameric
Chain B 1–127（127 aa）
Not recorded ACO ACETYL COENZYME *A × 4 MG MAGNESIUM ION × 4 CL CHLORIDE ION × 4 X-RAY DIFFRACTION
X-ray crystallization conditions pH 7.4；20% (W/V) POLYETHYLENE GLYCOL (PEG) 3350, 0.1 M BIS-TRIS PROPANE PH 7.4, 0.2 M POTASSIUM THIOCYANATE
Resolution 1.61 Å R-free 0.150
4CRZ Direct visualisation of strain-induced protein prost-translational modification Deposited 2014-03-02 Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 8 PDB declaration: octameric
Chain B 1–127（127 aa）
Not recorded SCN THIOCYANATE ION × 4 ACO ACETYL COENZYME *A × 4 MG MAGNESIUM ION × 4 X-RAY DIFFRACTION
X-ray crystallization conditions pH 7.4；20% (W/V) POLYETHYLENE GLYCOL (PEG) 3350, 0.1 M BIS-TRIS PROPANE PH 7.4, 0.2 M POTASSIUM THIOCYANATE
Resolution 1.70 Å R-free 0.175
4CS0 Direct visualisation of strain-induced protein post-translational modification Deposited 2014-03-02 Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 8 PDB declaration: octameric
Chain B 1–127（127 aa）
Not recorded SCN THIOCYANATE ION × 4 ACO ACETYL COENZYME *A × 4 MG MAGNESIUM ION × 4 X-RAY DIFFRACTION
X-ray crystallization conditions pH 7.4；20% (W/V) POLYETHYLENE GLYCOL (PEG) 3350, 0.1 M BIS-TRIS PROPANE PH 7.4, 0.2 M POTASSIUM THIOCYANATE
Resolution 2.10 Å R-free 0.237
5LS7 Complex of wild type E. coli alpha aspartate decarboxylase with its processing factor PanZ Deposited 2016-08-22 Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 12 PDB declaration: dodecameric
Chain B 1–127（127 aa）
Not recorded GOL GLYCEROL × 8 PEG DI(HYDROXYETHYL)ETHER × 8 ACO ACETYL COENZYME *A × 4 MG MAGNESIUM ION × 4 CO2 CARBON DIOXIDE × 12 SCN THIOCYANATE ION × 8 74C methyl radical × 4 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；291 K；200 mM KSCN, 100 mM Bis-Tris propane pH 6.5, 20% v/v PEG 3350
Resolution 1.16 Å R-free 0.137

4 other PDB entries and 4 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name YHHK_ECOLI
Isoform —
PDB entities 1
Chains and sequence ranges Author chain A； PDBConstruct 1–127； UniProt 1–127

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 2k5t

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 2k5t
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2. Structure Basics 2. Structure Basics

Entry ID entry_id2k5t
Deposition date deposition_date2008-06-30
Structure title titleSolution NMR Structure of Putative N-Acetyl Transferase YhhK from E. coli Bound to Coenzyme A: Northeast Structural Genomics Consortium Target ET106
Keywords keywords;N-acetyl transferase, CoA, bound ligand, coenzyme A, Structural Genomics, PSI-2, Protein Structure Initiative, Northeast Structural Genomics Consortium, NESG, unknown function, TRANSFERASE ;; TRANSFERASE
Experimental Method methodSOLUTION NMR
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3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

Radius of gyration Rg (Guinier) rg_guinier14.94 Å
Radius of gyration Rg (electron density) rg_electron14.34 Å
Forward intensity I(0) i01477220000.00
Molecular weight molecular_weight306860.0 kDa
Excluded volume excluded_volume376310 ų
Envelope volume envelope_volume34095 ų
Hydration-shell volume shell_volume17299 ų
Envelope diameter envelope_diameter51.3 Å
Shell Rg shell_rg22.64 Å
Envelope Rg envelope_rg16.28 Å
Shape Rg shape_rg14.32 Å
Total Rg total_rg14.52 Å
Total atoms total_atoms42420
Residues n_residues2560
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 dmax44.7 Å
Rg (real space) rg_real14.80 Å
Rg uncertainty (real space) rg_real_error0.20 Å
I(0) (real space) i0_real1.4770e+09
I(0) uncertainty (real space) i0_real_error1.5780e+07
Rg (reciprocal space) rg_reciprocal14.81 Å
I(0) (reciprocal space) i0_reciprocal1477000000.0000
Solution quality estimate total_estimate0.8249
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary18.7 Å
Skewness Skewness skewness-0.017
Kurtosis Kurtosis kurtosis-0.498
Angular range angular_range— – 0.5000 Å−1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha427200.0000
Real-space data points n_real_points80
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.917; Stabil: 0.998; Sysdev: 1.000; Positv: 1.000; Valcen: 0.973; Smooth: 0.000
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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (2)

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7. Fold Classification (SCOP + CATH) 1 domains

CATH v4.4 (1 domains)

Domain ID domain_id2k5tA00
Class class3 — Alpha Beta
Architecture architecture40 — 3-Layer(aba) Sandwich
Topology topology630 — Aminopeptidase
Homologous superfamily homologous superfamily30 — Gcn5-related N-acetyltransferase (GNAT)
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8. Citations (1)

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9. Files and Curves (10)