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2khk

NMR solution structure of the b30-82 domain of subunit b of Escherichia coli F1FO ATP synthase

Method: SOLUTION NMR Dmax: 90.8 Å Quality: REASONABLE
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1. Protein Identity and Related Structures Protein Identity & Related Structures

ATP synthase subunit b

Escherichia coli

UniProt P0ABA0

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 30–82 Fragment：residues in UNP 30-82 No other associated polymer SOLUTION NMR NMR measurement conditions：pH 6.8；288 K；Ionic strength (raw mmCIF value) 0；Pressure AMBIENT NMR sample composition：1mM [U-99% 13C; U-99% 15N] subunit b 30-82-1, 90% H2O/10% D2O | 90% H2O/10% 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 2KHK Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
1B9U MEMBRANE DOMAIN OF THE SUBUNIT B OF THE E.COLI ATP SYNTHASE Deposited 1999-02-15 Different construct Different mutation/modification Different experimental conditions Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 1–34（34 aa） Fragment：MEMBRANE DOMAIN
Non-standard monomer：Yes (specific site not provided by mmCIF) No recorded non-water small molecule SOLUTION NMR
NMR measurement conditions pH 6；300 K；Ionic strength (raw mmCIF value) 50 mM NACL；Pressure 1
NMR sample composition CHLOROFORM/METHANOL/WATER=4/4/1
Resolution not provided
1L2P ATP Synthase b Subunit Dimerization Domain Deposited 2002-02-22 Different construct Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 62–122（61 aa） Fragment：Dimerization Domain (residues 62-122)
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 5；291 K；30% ISOPROPANOL, 45% 2-METHYL-2,4-PENTANEDIOL, pH 5.0, VAPOR DIFFUSION, SITTING DROP, temperature 18.0K
Resolution 1.55 Å R-free 0.313

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

View Construct and Data Evidence
UniProt name ATPF_ECOLI
Isoform —
PDB entities 1
Chains and sequence ranges Author chain A； PDBConstruct 1–53； UniProt 30–82

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 2khk

P(r) Distance Distribution P(r) Distribution

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

Entry ID entry_id2khk
Deposition date deposition_date2009-04-08
Structure title titleNMR solution structure of the b30-82 domain of subunit b of Escherichia coli F1FO ATP synthase
Keywords keywords;b30-82, F1FO ATP synthase, NMR spectroscopy, ATP synthesis, Cell inner membrane, Cell membrane, CF(0), Hydrogen ion transport, Ion transport, Membrane, Transmembrane, Transport, TRANSPORT PROTEIN ;; TRANSPORT PROTEIN
Experimental Method methodSOLUTION NMR
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3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

Radius of gyration Rg (Guinier) rg_guinier21.97 Å
Radius of gyration Rg (electron density) rg_electron22.44 Å
Forward intensity I(0) i053612700.00
Molecular weight molecular_weight57586.0 kDa
Excluded volume excluded_volume71725 ų
Envelope volume envelope_volume45197 ų
Hydration-shell volume shell_volume14954 ų
Envelope diameter envelope_diameter95.4 Å
Shell Rg shell_rg32.06 Å
Envelope Rg envelope_rg27.85 Å
Shape Rg shape_rg22.33 Å
Total Rg total_rg23.41 Å
Total atoms total_atoms8280
Residues n_residues530
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 dmax90.8 Å
Rg (real space) rg_real22.67 Å
Rg uncertainty (real space) rg_real_error1.48 Å
I(0) (real space) i0_real5.3610e+07
I(0) uncertainty (real space) i0_real_error9.3960e+05
Rg (reciprocal space) rg_reciprocal22.54 Å
I(0) (reciprocal space) i0_reciprocal53610000.0000
Solution quality estimate total_estimate0.6341
Solution quality rating solution_quality REASONABLE a REASONABLE solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary17.6 Å
Skewness Skewness skewness0.613
Kurtosis Kurtosis kurtosis-0.314
Angular range angular_range— – 0.3600 Å−1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha37360.0000
Real-space data points n_real_points68
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.080; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.011; Smooth: 0.988
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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (1)

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7. Fold Classification (SCOP + CATH) 1 domains

CATH v4.4 (1 domains)

Domain ID domain_id2khkA00
Class class6 — Special
Architecture architecture10 — Helix non-globular
Topology topology250 — Single alpha-helices involved in coiled-coils or other helix-helix interfaces
Homologous superfamily homologous superfamily1580 —
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8. Citations (1)

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9. Files and Curves (10)