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9y8h

Crystal structure of Ornithine carbamoyltransferase from Burkholderia xenovorans in complex with phosphono carbamate

Method: X-RAY DIFFRACTION Dmax: 63.9 Å Quality: EXCELLENT
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1. Protein Identity and Related Structures Protein Identity & Related Structures

Ornithine carbamoyltransferase

Paraburkholderia xenovorans LB400

UniProt Q13H08

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 × 12 PDB declaration: dodecameric（12） Consistent with protein copy count Chain A； UniProt 2–332 Not recorded CP PHOSPHORIC ACID MONO(FORMAMIDE)ESTER × 12 PO4 PHOSPHATE ION × 48 CL CHLORIDE ION × 12 X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, SITTING DROP；pH 6.9；291 K；Index G6 : 1.4 M Sodium phosphate monobasic / Potassium phosphate dibasic pH 6.9. BuxeA.00088.a.B2.PW39423 at 24.5 mg/mL. plate 20257 B6 drop 3 , Puck: PSL-0315, Cryo: 4.0 M Sodium phosphate monobasic / Potassium phosphate dibasic pH 6.9 Resolution 2.67 Å R-free 0.252

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 9Y8H Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
9Y83 Crystal structure of Ornithine carbamoyltransferase from Burkholderia xenovorans Deposited 2025-09-11 Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 12 PDB declaration: dodecameric
Chain A 2–332（331 aa）
Chain B 2–332（331 aa）
Chain C 2–332（331 aa）
Chain D 2–332（331 aa）
Not recorded CL CHLORIDE ION × 15 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.5；291 K；Index F12: 100 mM HEPES, pH 7.5, 25% PEG 3350, 200 mM NaCl. BuxeA.00088.a.B2.PW39423 at 24.5 mg/mL. plate 20257 F12 drop 1, Puck: PSL-0410, Cryo: 20% glycerol + 80% crystallant
Resolution 2.55 Å R-free 0.227

1 other PDB entries and 1 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name Q13H08_PARXL
Isoform —
PDB entities 1
Chains and sequence ranges Author chain A； PDBConstruct 9–339； UniProt 2–332

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 9y8h

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 9y8h
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2. Structure Basics 2. Structure Basics

Entry ID entry_id9y8h
Deposition date deposition_date2025-09-11
最后修订 last_revision2025-09-24
Structure title titleCrystal structure of Ornithine carbamoyltransferase from Burkholderia xenovorans in complex with phosphono carbamate
Keywords keywordsSSGCID, STRUCTURAL GENOMICS, SEATTLE STRUCTURAL GENOMICS CENTER FOR INFECTIOUS DISEASE, TRANSFERASE; TRANSFERASE
Experimental Method methodX-RAY DIFFRACTION
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3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

Radius of gyration Rg (Guinier) rg_guinier20.79 Å
Radius of gyration Rg (electron density) rg_electron19.60 Å
Forward intensity I(0) i025340800.00
Molecular weight molecular_weight37270.0 kDa
Excluded volume excluded_volume46059 ų
Envelope volume envelope_volume53345 ų
Hydration-shell volume shell_volume22257 ų
Envelope diameter envelope_diameter64.9 Å
Shell Rg shell_rg26.52 Å
Envelope Rg envelope_rg19.89 Å
Shape Rg shape_rg19.59 Å
Total Rg total_rg20.48 Å
Total atoms total_atoms2614
Residues n_residues327
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 dmax63.9 Å
Rg (real space) rg_real20.66 Å
Rg uncertainty (real space) rg_real_error0.28 Å
I(0) (real space) i0_real2.5340e+07
I(0) uncertainty (real space) i0_real_error2.9570e+05
Rg (reciprocal space) rg_reciprocal20.69 Å
I(0) (reciprocal space) i0_reciprocal25340000.0000
Solution quality estimate total_estimate0.9020
Solution quality rating solution_quality EXCELLENT a EXCELLENT solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary25.0 Å
Skewness Skewness skewness0.158
Kurtosis Kurtosis kurtosis-0.502
Angular range angular_range— – 0.3800 Å−1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha5477000.0000
Real-space data points n_real_points70
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.922; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.988; Smooth: 0.969
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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (5)

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8. Citations (1)

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9. Files and Curves (10)