10bm

Crystal structure of Phosphoribosylaminoimidazole carboxylase from Burkholderia xenovorans (AMP, ADP and sulfate complex)

Method: X-RAY DIFFRACTION Dmax: 121.0 Å Quality: GOOD

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

N5-carboxyaminoimidazole ribonucleotide synthase

Paraburkholderia xenovorans LB400

UniProt Q13UJ9

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 9–397 Fragment:residues 9-397 AMP ADENOSINE MONOPHOSPHATE × 1 PEG DI(HYDROXYETHYL)ETHER × 1 MG MAGNESIUM ION × 1 SO4 SULFATE ION × 6 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, SITTING DROP;pH 7;291 K;Berkeley H5: 100 mM MgCl2, 100 mM Li2SO4, 25% PEG 400. BuxeA.00036.a.B2.PW39468 at 23.8 mg/mL. Cocrystallization with 3mM ATP but hydrolyzed AMP and ADP were observed. plate 20560 A12 drop 1, Puck: PSL-1103, Cryo: 20% PEG 200 + 80% crystallant Resolution 2.49 Å R-free 0.249
2 Protein monomer Monomer Protein × 1 PDB declaration: monomeric(1) Consistent with protein copy count Chain B; UniProt 9–397 Fragment:residues 9-397 AMP ADENOSINE MONOPHOSPHATE × 1 MG MAGNESIUM ION × 1 SO4 SULFATE ION × 6 PG4 TETRAETHYLENE GLYCOL × 1 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, SITTING DROP;pH 7;291 K;Berkeley H5: 100 mM MgCl2, 100 mM Li2SO4, 25% PEG 400. BuxeA.00036.a.B2.PW39468 at 23.8 mg/mL. Cocrystallization with 3mM ATP but hydrolyzed AMP and ADP were observed. plate 20560 A12 drop 1, Puck: PSL-1103, Cryo: 20% PEG 200 + 80% crystallant Resolution 2.49 Å R-free 0.249
3 Protein monomer Monomer Protein × 1 PDB declaration: monomeric(1) Consistent with protein copy count Chain C; UniProt 9–397 Fragment:residues 9-397 MG MAGNESIUM ION × 1 SO4 SULFATE ION × 7 ADP ADENOSINE-5'-DIPHOSPHATE × 1 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, SITTING DROP;pH 7;291 K;Berkeley H5: 100 mM MgCl2, 100 mM Li2SO4, 25% PEG 400. BuxeA.00036.a.B2.PW39468 at 23.8 mg/mL. Cocrystallization with 3mM ATP but hydrolyzed AMP and ADP were observed. plate 20560 A12 drop 1, Puck: PSL-1103, Cryo: 20% PEG 200 + 80% crystallant Resolution 2.49 Å R-free 0.249
4 Protein monomer Monomer Protein × 1 PDB declaration: monomeric(1) Consistent with protein copy count Chain D; UniProt 9–397 Fragment:residues 9-397 AMP ADENOSINE MONOPHOSPHATE × 1 SO4 SULFATE ION × 3 PG4 TETRAETHYLENE GLYCOL × 1 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, SITTING DROP;pH 7;291 K;Berkeley H5: 100 mM MgCl2, 100 mM Li2SO4, 25% PEG 400. BuxeA.00036.a.B2.PW39468 at 23.8 mg/mL. Cocrystallization with 3mM ATP but hydrolyzed AMP and ADP were observed. plate 20560 A12 drop 1, Puck: PSL-1103, Cryo: 20% PEG 200 + 80% crystallant Resolution 2.49 Å R-free 0.249

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.

4 other PDB entries and 14 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name Q13UJ9_PARXL
Isoform
PDB entities 1
Chains and sequence ranges Author chain A; PDBConstruct 9–397; UniProt 9–397 Author chain B; PDBConstruct 9–397; UniProt 9–397 Author chain C; PDBConstruct 9–397; UniProt 9–397 Author chain D; PDBConstruct 9–397; UniProt 9–397

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 10bm

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 10bm
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2. Structure Basics 2. Structure Basics

Entry ID entry_id10bm
Deposition date deposition_date2026-01-09
最后修订 last_revision2026-01-21
Structure title titleCrystal structure of Phosphoribosylaminoimidazole carboxylase from Burkholderia xenovorans (AMP, ADP and sulfate complex)
Keywords keywords;SSGCID, STRUCTURAL GENOMICS, SEATTLE STRUCTURAL GENOMICS CENTER FOR INFECTIOUS DISEASE, TRANSFERASE, Phosphoribosylaminoimidazole carboxylase, LYASE ;; LYASE
Experimental Method methodX-RAY DIFFRACTION

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

Radius of gyration Rg (Guinier) rg_guinier37.49
Radius of gyration Rg (electron density) rg_electron36.89
Forward intensity I(0) i0456473000.00
Molecular weight molecular_weight166270.0 kDa
Excluded volume excluded_volume205090 ų
Envelope volume envelope_volume258750 ų
Hydration-shell volume shell_volume57356 ų
Envelope diameter envelope_diameter127.8
Shell Rg shell_rg43.64
Envelope Rg envelope_rg36.93
Shape Rg shape_rg36.89
Total Rg total_rg37.27
Total atoms total_atoms11629
Residues n_residues1544
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 dmax121.0
Rg (real space) rg_real37.37
Rg uncertainty (real space) rg_real_error1.21
I(0) (real space) i0_real4.5650e+08
I(0) uncertainty (real space) i0_real_error8.8430e+06
Rg (reciprocal space) rg_reciprocal37.45
I(0) (reciprocal space) i0_reciprocal456500000.0000
Solution quality estimate total_estimate0.8974
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks1
Primary peak position r_peak_primary40.3
Skewness Skewness skewness0.222
Kurtosis Kurtosis kurtosis-0.522
Angular range angular_range— – 0.2100 −1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha86430000.0000
Real-space data points n_real_points43
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.915; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.997; Smooth: 0.922

5. Crystallography and Experiment 5. Crystallography & Experiment

6. Entities and Polymers Entities & Polymers (8)

8. Citations (1)

9. Files and Curves (10)