SAXSdb — 1bdo

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

ACETYL-COA CARBOXYLASE

Escherichia coli

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 homooligomer Homooligomer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count	Chain A； UniProt 77–156	Fragment：BIOTINYL DOMAIN, RESIDUES 77 - 156	BTN BIOTIN × 2	X-RAY DIFFRACTION mmCIF provides none of the parsed experimental conditions	Resolution 1.80 Å

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 1BDO	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 oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	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
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 oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	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
3BDO SOLUTION STRUCTURE OF APO-BIOTINYL DOMAIN FROM ACETYL COENZYME A CARBOXYLASE OF ESCHERICHIA COLI DETERMINED BY TRIPLE-RESONANCE NMR SPECTROSCOPY Deposited 1999-03-08	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 75–156（82 aa） Fragment：BIOTINYL DOMAIN, RESIDUES 77 - 156	Not recorded	No recorded non-water small molecule	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
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 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 1–80； UniProt 77–156

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.

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2. Structure Basics 2. Structure Basics

Entry ID entry_id	1bdo
Deposition date deposition_date	1995-11-21
Structure title title	STRUCTURE OF THE BIOTINYL DOMAIN OF ACETYL-COENZYME A CARBOXYLASE DETERMINED BY MAD PHASING
Keywords keywords	BCCPSC, CARBOXYL TRANSFERASE, FATTY ACID BIOSYNTHESIS, HAMMERHEAD STRUCTURE, SELENOMETHIONINE, LIGASE, TRANSFERASE; TRANSFERASE
Experimental Method method	X-RAY DIFFRACTION

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3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

Radius of gyration Rg (Guinier) rg_guinier	13.43 Å
Radius of gyration Rg (electron density) rg_electron	12.11 Å
Forward intensity I(0) i0	1697220.00
Molecular weight molecular_weight	8914.0 kDa
Excluded volume excluded_volume	11221 Å³
Envelope volume envelope_volume	12439 Å³
Hydration-shell volume shell_volume	9074 Å³
Envelope diameter envelope_diameter	41.8 Å
Shell Rg shell_rg	17.37 Å
Envelope Rg envelope_rg	12.43 Å
Shape Rg shape_rg	12.05 Å
Total Rg total_rg	13.58 Å
Total atoms total_atoms	622
Residues n_residues	80
Spherical-harmonic order n_harmonics	20
q range q_range	— – 0.5000 Å⁻¹
Data points n_points	101
Shell type shell_type	directional
Solvent electron density solvent_density	0.3340 e/Å³
Shell contrast contrast_shell	0.0300 e/Å³
CRYSOL version crysol_version	4.1.3

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4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

Maximum dimension Dmax dmax	43.2 Å
Rg (real space) rg_real	13.36 Å
Rg uncertainty (real space) rg_real_error	0.26 Å
I(0) (real space) i0_real	1.6970e+06
I(0) uncertainty (real space) i0_real_error	1.7840e+04
Rg (reciprocal space) rg_reciprocal	13.37 Å
I(0) (reciprocal space) i0_reciprocal	1697000.0000
Solution quality estimate total_estimate	0.8892
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	17.0 Å
Skewness Skewness skewness	0.176
Kurtosis Kurtosis kurtosis	-0.297
Angular range angular_range	— – 0.5000 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	326900.0000
Real-space data points n_real_points	80
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.853; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.999; Smooth: 0.996

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (3)

Entity 1 Entity 1 polymer

Description description	ACETYL-COA CARBOXYLASE
Molecular weight formula_weight	8700.0 kDa
EC 编号 ec_number	6.4.1.2
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A
Atom count atom_count	704

EISGHIVRSPMVGTFYRTPSPDAKAFIEVGQKVNVGDTLCIVEAMKMMNQIEADKSGTVKAILVESGQPVEFDEPLVVIE

来源 Source

来源生物 organism	Escherichia coli
NCBI Class编号 ncbi_taxonomy_id	562
宿主生物 host_organism	Escherichia coli

Entity 2 Entity 2 non-polymer

Description description	BIOTIN
Molecular weight formula_weight	244.3 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 3 Entity 3 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	74

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7. Fold Classification (SCOP + CATH) 2 domains

SCOP 2.08 (1 domains)

Domain ID domain_id	d1bdoa_
Class class	b — All beta proteins
Fold Fold fold	b.84 — Barrel-sandwich hybrid
Superfamily Superfamily superfamily	b.84.1 — Single hybrid motif
Family Family family	b.84.1.1 — Biotinyl/lipoyl-carrier proteins and domains

CATH v4.4 (1 domains)

Domain ID domain_id	1bdoA00
Class class	2 — Mainly Beta
Architecture architecture	40 — Beta Barrel
Topology topology	50 — OB fold (Dihydrolipoamide Acetyltransferase, E2P)
Homologous superfamily homologous superfamily	100 — RNA polymerase II/Efflux pump adaptor protein, barrel-sandwich hybrid domain

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8. Citations (1)

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Unit-cell length a length_a	65.460 Å
Unit-cell length b length_b	37.260 Å
Unit-cell length c length_c	35.450 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	90.00 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	4

Space group space_group	P 21 21 2
Space-group number int_tables_number	18
Crystal system crystal_system	—

Resolution resolution	1.800 Å
Low-resolution limit resolution_low	10.000 Å
R factor r_factor	0.1890
R_work r_work	0.1890
R_free r_free	—

fit	/app/data/saxs_computation/bd/1bdo/1bdo.fit
pddf	/app/data/pr_computation/bd/1bdo/1bdo.pr.out
profile	/app/data/saxs_computation/bd/1bdo/1bdo.dat

STRUCTURE OF THE BIOTINYL DOMAIN OF ACETYL-COENZYME A CARBOXYLASE DETERMINED BY MAD PHASING

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

ACETYL-COA CARBOXYLASE

State in the Current Structure

Other States of the Same Protein in the Database

SAXS scattering curve SAXS Profile

P(r) Distance Distribution P(r) Distribution