2yl2

Crystal structure of human acetyl-CoA carboxylase 1, biotin carboxylase (BC) domain

Method: X-RAY DIFFRACTION Dmax: 105.7 Å Quality: GOOD

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

ACETYL-COA CARBOXYLASE 1

HOMO SAPIENS

UniProt Q13085

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 78–617 Fragment:BIOTIN CARBOXYLASE (BC) DOMAIN, RESIDUES 78-617 No other associated polymer X-RAY DIFFRACTION X-ray crystallization conditions:20% PEG 3350, 200 MM NA(MALONATE) PH 7.0 Resolution 2.30 Å R-free 0.241
2 Protein monomer Monomer Protein × 1 PDB declaration: monomeric(1) Consistent with protein copy count Chain B; UniProt 78–617 Fragment:BIOTIN CARBOXYLASE (BC) DOMAIN, RESIDUES 78-617 No other associated polymer X-RAY DIFFRACTION X-ray crystallization conditions:20% PEG 3350, 200 MM NA(MALONATE) PH 7.0 Resolution 2.30 Å R-free 0.241

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.

9 other PDB entries and 18 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name ACACA_HUMAN
Isoform
PDB entities 1
Chains and sequence ranges Author chain A; PDBConstruct 1–540; UniProt 78–617 Author chain B; PDBConstruct 1–540; UniProt 78–617

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 2yl2

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 2yl2
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2. Structure Basics 2. Structure Basics

Entry ID entry_id2yl2
Deposition date deposition_date2011-05-31
Structure title titleCrystal structure of human acetyl-CoA carboxylase 1, biotin carboxylase (BC) domain
Keywords keywordsLIGASE; LIGASE
Experimental Method methodX-RAY DIFFRACTION

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

Radius of gyration Rg (Guinier) rg_guinier33.11
Radius of gyration Rg (electron density) rg_electron32.40
Forward intensity I(0) i0169922000.00
Molecular weight molecular_weight104830.0 kDa
Excluded volume excluded_volume131410 ų
Envelope volume envelope_volume168080 ų
Hydration-shell volume shell_volume43199 ų
Envelope diameter envelope_diameter106.7
Shell Rg shell_rg39.49
Envelope Rg envelope_rg31.59
Shape Rg shape_rg32.40
Total Rg total_rg33.00
Total atoms total_atoms7384
Residues n_residues968
Spherical-harmonic order n_harmonics20
q range q_range— – 0.5000 −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

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

Maximum dimension Dmax dmax105.7
Rg (real space) rg_real33.08
Rg uncertainty (real space) rg_real_error0.73
I(0) (real space) i0_real1.6990e+08
I(0) uncertainty (real space) i0_real_error2.6800e+06
Rg (reciprocal space) rg_reciprocal33.10
I(0) (reciprocal space) i0_reciprocal169900000.0000
Solution quality estimate total_estimate0.8959
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks1
Primary peak position r_peak_primary37.4
Skewness Skewness skewness0.295
Kurtosis Kurtosis kurtosis-0.543
Angular range angular_range— – 0.2400 −1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha35430000.0000
Real-space data points n_real_points49
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.920; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.994; Smooth: 0.888

5. Crystallography and Experiment 5. Crystallography & Experiment

6. Entities and Polymers Entities & Polymers (2)

7. Fold Classification (SCOP + CATH) 8 domains

CATH v4.4 (8 domains)

Domain ID domain_id2yl2A01
Class class3 — Alpha Beta
Architecture architecture40 — 3-Layer(aba) Sandwich
Topology topology50 — Rossmann fold
Homologous superfamily homologous superfamily20
Domain ID domain_id2yl2A02
Class class3 — Alpha Beta
Architecture architecture90 — Alpha-Beta Complex
Topology topology1770 — PreATP-grasp fold
Homologous superfamily homologous superfamily10 — PreATP-grasp domain
Domain ID domain_id2yl2A03
Class class3 — Alpha Beta
Architecture architecture30 — 2-Layer Sandwich
Topology topology1490 — Dna Ligase; domain 1
Homologous superfamily homologous superfamily20 — ATP-grasp fold, A domain
Domain ID domain_id2yl2A04
Class class3 — Alpha Beta
Architecture architecture30 — 2-Layer Sandwich
Topology topology470 — D-amino Acid Aminotransferase; Chain A, domain 1
Homologous superfamily homologous superfamily20 — ATP-grasp fold, B domain
Domain ID domain_id2yl2B01
Class class3 — Alpha Beta
Architecture architecture40 — 3-Layer(aba) Sandwich
Topology topology50 — Rossmann fold
Homologous superfamily homologous superfamily20
Domain ID domain_id2yl2B02
Class class3 — Alpha Beta
Architecture architecture90 — Alpha-Beta Complex
Topology topology1770 — PreATP-grasp fold
Homologous superfamily homologous superfamily10 — PreATP-grasp domain
Domain ID domain_id2yl2B03
Class class3 — Alpha Beta
Architecture architecture30 — 2-Layer Sandwich
Topology topology1490 — Dna Ligase; domain 1
Homologous superfamily homologous superfamily20 — ATP-grasp fold, A domain
Domain ID domain_id2yl2B04
Class class3 — Alpha Beta
Architecture architecture30 — 2-Layer Sandwich
Topology topology470 — D-amino Acid Aminotransferase; Chain A, domain 1
Homologous superfamily homologous superfamily20 — ATP-grasp fold, B domain

8. Citations (1)

9. Files and Curves (10)