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3bdo

SOLUTION STRUCTURE OF APO-BIOTINYL DOMAIN FROM ACETYL COENZYME A CARBOXYLASE OF ESCHERICHIA COLI DETERMINED BY TRIPLE-RESONANCE NMR SPECTROSCOPY

Method: SOLUTION NMR Dmax: 47.9 Å Quality: REASONABLE
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1. Protein Identity and Related Structures Protein Identity & Related Structures

PROTEIN (ACETYL-COA CARBOXYLASE)

Escherichia coli

UniProt P0ABD8

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 75–156 Fragment：BIOTINYL DOMAIN, RESIDUES 77 - 156 No other associated polymer SOLUTION NMR NMR measurement conditions：pH 6.8；303 K；Ionic strength (raw mmCIF value) 20mM SODIUM PHOSPHATE；Pressure 1 NMR sample composition：90% WATER/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 3BDO Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
1A6X STRUCTURE OF THE APO-BIOTIN CARBOXYL CARRIER PROTEIN (APO-BCCP87) OF ESCHERICHIA COLI ACETYL-COA CARBOXYLASE, NMR, 49 STRUCTURES Deposited 1998-03-04 Different construct Different experimental conditions Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 70–156（87 aa） Fragment：CARBOXYL-TERMINAL FRAGMENT, RESIDUES 70 - 156
Not recorded No recorded non-water small molecule SOLUTION NMR
NMR measurement conditions pH 7.5；298 K
NMR sample composition PHOSPHATE BUFFER
Resolution not provided
1BDO STRUCTURE OF THE BIOTINYL DOMAIN OF ACETYL-COENZYME A CARBOXYLASE DETERMINED BY MAD PHASING Deposited 1995-11-21 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain A 77–156（80 aa） Fragment：BIOTINYL DOMAIN, RESIDUES 77 - 156
Not recorded BTN BIOTIN × 2 X-RAY DIFFRACTION mmCIF provides none of the parsed conditions Resolution 1.80 Å
2BDO SOLUTION STRUCTURE OF HOLO-BIOTINYL DOMAIN FROM ACETYL COENZYME A CARBOXYLASE OF ESCHERICHIA COLI DETERMINED BY TRIPLE-RESONANCE NMR SPECTROSCOPY Deposited 1999-03-03 Different construct Different ligand/ion Different experimental conditions Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 77–156（80 aa） Fragment：BIOTINYL DOMAIN, RESIDUES 77 - 156
Not recorded BTN BIOTIN × 1 SOLUTION NMR
NMR measurement conditions pH 6.8；303 K；Ionic strength (raw mmCIF value) 20mM SODIUM PHOSPHATE；Pressure 1
Resolution not provided
4HR7 Crystal Structure of Biotin Carboxyl Carrier Protein-Biotin Carboxylase Complex from E.coli Deposited 2012-10-26 Different construct 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 1–156（156 aa）
Chain D 1–156（156 aa）
Chain G 1–156（156 aa）
Chain I 1–156（156 aa）
Not recorded SO4 SULFATE ION × 12 EDO 1,2-ETHANEDIOL × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.5；295.15 K；0.2 M ammonium sulfate, 0.1 M Bis-Tris, pH 6.5, 25% PEG3350, VAPOR DIFFUSION, SITTING DROP, temperature 295.15K
Resolution 2.50 Å R-free 0.229
8UXZ E. coli acetyl-CoA carboxylase, wide stacked local reconstruction, 3.20 Angstrom Deposited 2023-11-11 Different construct 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 × 9 PDB declaration: nonameric
Chain B 80–156（77 aa）
Chain F 80–156（77 aa）
Not recorded BTN BIOTIN × 2 ADP ADENOSINE-5'-DIPHOSPHATE × 2 MG MAGNESIUM ION × 2 ZN ZINC ION × 2 ACO ACETYL COENZYME *A × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5；2.5 mg/ml ACC complex in 50 mM HEPES pH 7.5, 100 mM bicarbonate, 7.5 mM ATP, 20 mM MgCl2 and 1 mM acetyl-CoA
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.20 Å
8UZ2 E. coli acetyl-CoA carboxylase, narrow helical local reconstruction, 3.18 Angstrom Deposited 2023-11-14 Different construct 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 × 9 PDB declaration: nonameric
Chain B 80–156（77 aa）
Chain F 80–156（77 aa）
Not recorded BTN BIOTIN × 2 ADP ADENOSINE-5'-DIPHOSPHATE × 2 MG MAGNESIUM ION × 2 ZN ZINC ION × 2 ACO ACETYL COENZYME *A × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5；2.5 mg/ml ACC complex in 50 mM HEPES pH 7.5, 100 mM bicarbonate, 7.5 mM ATP, 20 mM MgCl2 and 1 mM acetyl-CoA
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.18 Å
9E4N E. coli acetyl-CoA carboxylase, narrow helical tube, 4.04 Angstrom Deposited 2024-10-25 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 152 PDB declaration: 152-meric
Chain B 80–156（77 aa）
Not recorded BTN BIOTIN × 38 ADP ADENOSINE-5'-DIPHOSPHATE × 38 MG MAGNESIUM ION × 38 ZN ZINC ION × 38 ACO ACETYL COENZYME *A × 38 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5；2.5 mg/ml ACC complex in 50 mM HEPES pH 7.5, 100 mM bicarbonate, 7.5 mM ATP, 20 mM MgCl2 and 1 mM acetyl-CoA
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.04 Å
9E4O E. coli acetyl-CoA carboxylase, wide stacked tube, 3.98 Angstrom Deposited 2024-10-25 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 160 PDB declaration: 160-meric
Chain B 80–156（77 aa）
Not recorded BTN BIOTIN × 40 ADP ADENOSINE-5'-DIPHOSPHATE × 40 MG MAGNESIUM ION × 40 ZN ZINC ION × 40 ACO ACETYL COENZYME *A × 40 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5；2.5 mg/ml ACC complex in 50 mM HEPES pH 7.5, 100 mM bicarbonate, 7.5 mM ATP, 20 mM MgCl2 and 1 mM acetyl-CoA
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.98 Å

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

View Construct and Data Evidence
UniProt name BCCP_ECOLI
Isoform —
PDB entities 1
Chains and sequence ranges Author chain A； PDBConstruct 1–82； UniProt 75–156

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 3bdo

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 3bdo
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2. Structure Basics 2. Structure Basics

Entry ID entry_id3bdo
Deposition date deposition_date1999-03-08
Structure title titleSOLUTION STRUCTURE OF APO-BIOTINYL DOMAIN FROM ACETYL COENZYME A CARBOXYLASE OF ESCHERICHIA COLI DETERMINED BY TRIPLE-RESONANCE NMR SPECTROSCOPY
Keywords keywordsBIOTIN, BIOTINYL DOMAIN, ACETYL COA CARBOXYLASE, SWINGING ARM, NMR SPECTROSCOPY, PROTEIN STRUCTURE; BIOTIN
Experimental Method methodSOLUTION NMR
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3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

Radius of gyration Rg (Guinier) rg_guinier12.39 Å
Radius of gyration Rg (electron density) rg_electron12.21 Å
Forward intensity I(0) i0422730000.00
Molecular weight molecular_weight176580.0 kDa
Excluded volume excluded_volume222230 ų
Envelope volume envelope_volume20574 ų
Hydration-shell volume shell_volume12206 ų
Envelope diameter envelope_diameter52.0 Å
Shell Rg shell_rg20.26 Å
Envelope Rg envelope_rg15.30 Å
Shape Rg shape_rg12.15 Å
Total Rg total_rg12.57 Å
Total atoms total_atoms24800
Residues n_residues1640
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 dmax47.9 Å
Rg (real space) rg_real12.35 Å
Rg uncertainty (real space) rg_real_error0.40 Å
I(0) (real space) i0_real4.2270e+08
I(0) uncertainty (real space) i0_real_error5.0330e+06
Rg (reciprocal space) rg_reciprocal12.35 Å
I(0) (reciprocal space) i0_reciprocal422700000.0000
Solution quality estimate total_estimate0.7216
Solution quality rating solution_quality REASONABLE a REASONABLE solution
P(r) peaks n_peaks3
Primary peak position r_peak_primary15.8 Å
Skewness Skewness skewness0.243
Kurtosis Kurtosis kurtosis0.031
Angular range angular_range— – 0.5000 Å−1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha113500.0000
Real-space data points n_real_points80
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.495; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.892; Smooth: 0.000
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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) 2 domains

SCOP 2.08 (1 domains)

Domain ID domain_idd3bdoa_
Class classb — All beta proteins
Fold Fold foldb.84 — Barrel-sandwich hybrid
Superfamily Superfamily superfamilyb.84.1 — Single hybrid motif
Family Family familyb.84.1.1 — Biotinyl/lipoyl-carrier proteins and domains

CATH v4.4 (1 domains)

Domain ID domain_id3bdoA00
Class class2 — Mainly Beta
Architecture architecture40 — Beta Barrel
Topology topology50 — OB fold (Dihydrolipoamide Acetyltransferase, E2P)
Homologous superfamily homologous superfamily100 — RNA polymerase II/Efflux pump adaptor protein, barrel-sandwich hybrid domain
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8. Citations (1)

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9. Files and Curves (10)