9zvm

Dimer structure of Thlaspi arvense plastid biotin carboxylase

Method: ELECTRON MICROSCOPY Dmax: 123.2 Å Quality: GOOD

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

Maltodextrin-binding protein,Biotin carboxylase

Thlaspi arvense

UniProt A0AAU9SW86

State in the Current Structure

Assembly Oligomeric State Construct Mutations and Modifications Ligands, Ions and Associated Components Method and Experimental Conditions Structure Quality
1 Insufficient information Homooligomer Protein × 2 PDB declaration: dimeric(2) Consistent with protein copy count Chain C; UniProt 71–535 Chain D; UniProt 71–535 Not recorded No other associated polymer ELECTRON MICROSCOPY cryo-EM buffer:pH 8;50mM HEPES pH 8.0, 4mM MgCl2, 5% glycerol, 0.5mM TCEP cryo-EM vitrification conditions:Cryogen ETHANE Resolution 2.85 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.

No other PDB entry for the same UniProt protein was found.

View Construct and Data Evidence
UniProt name A0AAU9SW86_THLAR
Isoform
PDB entities 1
Chains and sequence ranges Author chain C; PDBConstruct 396–860; UniProt 71–535 Author chain D; PDBConstruct 396–860; UniProt 71–535

Maltodextrin-binding protein,Biotin carboxylase

Thlaspi arvense

UniProt C3SHQ8

State in the Current Structure

Assembly Oligomeric State Construct Mutations and Modifications Ligands, Ions and Associated Components Method and Experimental Conditions Structure Quality
1 Insufficient information Homooligomer Protein × 2 PDB declaration: dimeric(2) Consistent with protein copy count Chain C; UniProt 27–392 Chain D; UniProt 27–392 Not recorded No other associated polymer ELECTRON MICROSCOPY cryo-EM buffer:pH 8;50mM HEPES pH 8.0, 4mM MgCl2, 5% glycerol, 0.5mM TCEP cryo-EM vitrification conditions:Cryogen ETHANE Resolution 2.85 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.

15 other PDB entries and 21 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name C3SHQ8_ECOLX
Isoform
PDB entities 1
Chains and sequence ranges Author chain C; PDBConstruct 2–367; UniProt 27–392 Author chain D; PDBConstruct 2–367; UniProt 27–392

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 9zvm

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 9zvm
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2. Structure Basics 2. Structure Basics

Entry ID entry_id9zvm
Deposition date deposition_date2025-12-30
Structure title titleDimer structure of Thlaspi arvense plastid biotin carboxylase
Keywords keywordsligase, homodimer, carboxylase; LIGASE
Experimental Method methodELECTRON MICROSCOPY

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

Radius of gyration Rg (Guinier) rg_guinier33.42
Radius of gyration Rg (electron density) rg_electron32.97
Forward intensity I(0) i0156894000.00
Molecular weight molecular_weight99086.0 kDa
Excluded volume excluded_volume124020 ų
Envelope volume envelope_volume168790 ų
Hydration-shell volume shell_volume43809 ų
Envelope diameter envelope_diameter130.1
Shell Rg shell_rg38.31
Envelope Rg envelope_rg33.54
Shape Rg shape_rg32.97
Total Rg total_rg33.41
Total atoms total_atoms13924
Residues n_residues898
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 dmax123.2
Rg (real space) rg_real33.59
Rg uncertainty (real space) rg_real_error1.03
I(0) (real space) i0_real1.5690e+08
I(0) uncertainty (real space) i0_real_error2.6620e+06
Rg (reciprocal space) rg_reciprocal33.49
I(0) (reciprocal space) i0_reciprocal156900000.0000
Solution quality estimate total_estimate0.8116
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks3
Primary peak position r_peak_primary36.7
Skewness Skewness skewness0.627
Kurtosis Kurtosis kurtosis0.316
Angular range angular_range— – 0.2350 −1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha36980000.0000
Real-space data points n_real_points48
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.591; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.839; Smooth: 0.934

5. Crystallography and Experiment 5. Crystallography & Experiment

6. Entities and Polymers Entities & Polymers (1)

8. Citations (2)

9. Files and Curves (10)