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1djo

Crystal structure of Pseudomonas 7A Glutaminase-asparaginase with the inhibitor donv covalently bound in the active site

Method: X-RAY DIFFRACTION Dmax: 87.5 Å Quality: GOOD
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1. Protein Identity and Related Structures Protein Identity & Related Structures

GLUTAMINASE-ASPARAGINASE

OrganismNot specified

UniProt P10182

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 × 4 PDB declaration: tetrameric（4） Consistent with protein copy count Chain A； UniProt 8–337 Chain B； UniProt 8–337 Not recorded CAB 4,4-dihydroxy-5-oxo-L-norvaline × 4 X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 6.4；291 K；2.0 M Ammonium Sulfate, pH 6.4, VAPOR DIFFUSION, HANGING DROP, temperature 291K Resolution 2.00 Å R-free 0.238

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 1DJO Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
1DJP CRYSTAL STRUCTURE OF PSEUDOMONAS 7A GLUTAMINASE-ASPARAGINASE WITH THE INHIBITOR DON COVALENTLY BOUND IN THE ACTIVE SITE Deposited 1999-12-03 Different ligand/ion Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 4 PDB declaration: tetrameric
Chain A 8–337（330 aa）
Chain B 8–337（330 aa）
Not recorded DO2 5,5-dihydroxy-6-oxo-L-norleucine × 4 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.4；291 K；2.0 M Ammonium Sulfate, pH 6.4, VAPOR DIFFUSION, HANGING DROP, temperature 291K
Resolution 1.90 Å R-free 0.228
3PGA STRUCTURAL CHARACTERIZATION OF PSEUDOMONAS 7A GLUTAMINASE-ASPARAGINASE Deposited 1994-07-19 Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 4 PDB declaration: tetrameric
Chain 1 8–337（330 aa）
Chain 2 8–337（330 aa）
Chain 3 8–337（330 aa）
Chain 4 8–337（330 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION mmCIF provides none of the parsed conditions Resolution 2.00 Å
4PGA GLUTAMINASE-ASPARAGINASE FROM PSEUDOMONAS 7A Deposited 1997-01-14 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 4 PDB declaration: tetrameric
Chain A 1–337（337 aa）
Chain B 1–337（337 aa）
Not recorded SO4 SULFATE ION × 4 NH4 AMMONIUM ION × 4 X-RAY DIFFRACTION
X-ray crystallization conditions pH 4.6；pH 4.6
Resolution 1.70 Å R-free 0.254

3 other PDB entries and 3 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name ASPQ_PSES7
Isoform —
PDB entities 1
Chains and sequence ranges Author chain A； PDBConstruct 1–330； UniProt 8–337 Author chain B； PDBConstruct 1–330； UniProt 8–337

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 1djo

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 1djo
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2. Structure Basics 2. Structure Basics

Entry ID entry_id1djo
Deposition date deposition_date1999-12-03
Structure title titleCrystal structure of Pseudomonas 7A Glutaminase-asparaginase with the inhibitor donv covalently bound in the active site
Keywords keywords;PGA, Glutaminase, Asparaginase, DONV, 5-diazo-4-oxo-L-norvaline, Glutaminase-Asparaginase, suicide inhibitor, covalently bound inhibitor, HYDROLASE-HYDROLASE INHIBITOR complex ;; HYDROLASE/HYDROLASE INHIBITOR
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_guinier26.04 Å
Radius of gyration Rg (electron density) rg_electron25.21 Å
Forward intensity I(0) i083986800.00
Molecular weight molecular_weight70971.0 kDa
Excluded volume excluded_volume88572 ų
Envelope volume envelope_volume102990 ų
Hydration-shell volume shell_volume33273 ų
Envelope diameter envelope_diameter89.3 Å
Shell Rg shell_rg33.31 Å
Envelope Rg envelope_rg25.47 Å
Shape Rg shape_rg25.18 Å
Total Rg total_rg26.12 Å
Total atoms total_atoms4988
Residues n_residues660
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 dmax87.5 Å
Rg (real space) rg_real25.98 Å
Rg uncertainty (real space) rg_real_error0.60 Å
I(0) (real space) i0_real8.3990e+07
I(0) uncertainty (real space) i0_real_error1.1460e+06
Rg (reciprocal space) rg_reciprocal26.00 Å
I(0) (reciprocal space) i0_reciprocal83990000.0000
Solution quality estimate total_estimate0.8038
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary30.1 Å
Skewness Skewness skewness0.313
Kurtosis Kurtosis kurtosis-0.308
Angular range angular_range— – 0.3050 Å−1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha27390000.0000
Real-space data points n_real_points62
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.816; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.998; Smooth: 0.000
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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (2)

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7. Fold Classification (SCOP + CATH) 6 domains

SCOP 2.08 (2 domains)

Domain ID domain_idd1djoa_
Class classc — Alpha and beta proteins (a/b)
Fold Fold foldc.88 — Glutaminase/Asparaginase
Superfamily Superfamily superfamilyc.88.1 — Glutaminase/Asparaginase
Family Family familyc.88.1.1 — Glutaminase/Asparaginase
Domain ID domain_idd1djob_
Class classc — Alpha and beta proteins (a/b)
Fold Fold foldc.88 — Glutaminase/Asparaginase
Superfamily Superfamily superfamilyc.88.1 — Glutaminase/Asparaginase
Family Family familyc.88.1.1 — Glutaminase/Asparaginase

CATH v4.4 (4 domains)

Domain ID domain_id1djoA01
Class class3 — Alpha Beta
Architecture architecture40 — 3-Layer(aba) Sandwich
Topology topology50 — Rossmann fold
Homologous superfamily homologous superfamily1170 — L-asparaginase, N-terminal domain
Domain ID domain_id1djoA02
Class class3 — Alpha Beta
Architecture architecture40 — 3-Layer(aba) Sandwich
Topology topology50 — Rossmann fold
Homologous superfamily homologous superfamily40 —
Domain ID domain_id1djoB01
Class class3 — Alpha Beta
Architecture architecture40 — 3-Layer(aba) Sandwich
Topology topology50 — Rossmann fold
Homologous superfamily homologous superfamily1170 — L-asparaginase, N-terminal domain
Domain ID domain_id1djoB02
Class class3 — Alpha Beta
Architecture architecture40 — 3-Layer(aba) Sandwich
Topology topology50 — Rossmann fold
Homologous superfamily homologous superfamily40 —
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8. Citations (1)

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9. Files and Curves (10)