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1dku

CRYSTAL STRUCTURES OF BACILLUS SUBTILIS PHOSPHORIBOSYLPYROPHOSPHATE SYNTHETASE: MOLECULAR BASIS OF ALLOSTERIC INHIBITION AND ACTIVATION.

Method: X-RAY DIFFRACTION Dmax: 82.6 Å Quality: EXCELLENT
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1. Protein Identity and Related Structures Protein Identity & Related Structures

PROTEIN (PHOSPHORIBOSYL PYROPHOSPHATE SYNTHETASE)

Bacillus subtilis

UniProt P14193

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 × 2 PDB declaration: dimeric（2） Consistent with protein copy count Chain A； UniProt 1–317 Chain B； UniProt 1–317 Not recorded AP2 PHOSPHOMETHYLPHOSPHONIC ACID ADENOSYL ESTER × 2 ABM METHYL PHOSPHONIC ACID ADENOSINE ESTER × 2 X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, SITTING DROP；pH 8；293 K；Sodium citrate, Hepes, alpha,beta-methylene ADP, Magnesium chloride, beta- octylglucoside , pH 8.0, VAPOR DIFFUSION, SITTING DROP, temperature 293K Resolution 2.20 Å R-free 0.241
2 Protein homooligomer Homooligomer Protein × 6 PDB declaration: hexameric（6） Consistent with protein copy count Chain A； UniProt 1–317 Chain B； UniProt 1–317 Not recorded AP2 PHOSPHOMETHYLPHOSPHONIC ACID ADENOSYL ESTER × 6 ABM METHYL PHOSPHONIC ACID ADENOSINE ESTER × 6 X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, SITTING DROP；pH 8；293 K；Sodium citrate, Hepes, alpha,beta-methylene ADP, Magnesium chloride, beta- octylglucoside , pH 8.0, VAPOR DIFFUSION, SITTING DROP, temperature 293K Resolution 2.20 Å R-free 0.241
3 Protein homooligomer Homooligomer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count Chain A； UniProt 1–317 Chain B； UniProt 1–317 Not recorded AP2 PHOSPHOMETHYLPHOSPHONIC ACID ADENOSYL ESTER × 2 ABM METHYL PHOSPHONIC ACID ADENOSINE ESTER × 2 X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, SITTING DROP；pH 8；293 K；Sodium citrate, Hepes, alpha,beta-methylene ADP, Magnesium chloride, beta- octylglucoside , pH 8.0, VAPOR DIFFUSION, SITTING DROP, temperature 293K Resolution 2.20 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.

Other PDB Difference from Current Entry 1DKU Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
1DKR CRYSTAL STRUCTURES OF BACILLUS SUBTILIS PHOSPHORIBOSYLPYROPHOSPHATE SYNTHETASE: MOLECULAR BASIS OF ALLOSTERIC INHIBITION AND ACTIVATION. Deposited 1999-12-08 Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 6 PDB declaration: hexameric
Chain A 1–317（317 aa）
Chain B 1–317（317 aa）
Not recorded SO4 SULFATE ION × 12 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.5；298 K；AMMONIUM SULFATE; TRISHCL; PEG 400; SODIUM PHOSPHATE; BETA-OCTYLGLUCOSIDE; ALPHA, BETA-METHYLENE ATP; RIBOSE-5-PHOSPHATE; MAGNESIUM SULFATE; ADP, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 298K
Resolution 2.30 Å R-free 0.240
1IBS PHOSPHORIBOSYLDIPHOSPHATE SYNTHETASE IN COMPLEX WITH CADMIUM IONS Deposited 2001-03-29 Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 6 PDB declaration: hexameric
Chain A 1–317（317 aa）
Chain B 1–317（317 aa）
Not recorded SO4 SULFATE ION × 12 CD CADMIUM ION × 12 ABM METHYL PHOSPHONIC ACID ADENOSINE ESTER × 6 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.5；298 K；sodium phosphate, alpha, beta methylene ATP, ADP, magnesium chloride, ribose-5-phosphate, ammonium sulfate, TrisHCl, PEG 400. Crystal was soaked in cadmium chloride in phosphate free conditions, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 298.0K
Resolution 2.80 Å R-free 0.273

2 other PDB entries and 2 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name KPRS_BACSU
Isoform —
PDB entities 1
Chains and sequence ranges Author chain A； PDBConstruct 1–317； UniProt 1–317 Author chain B； PDBConstruct 1–317； UniProt 1–317

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 1dku

P(r) Distance Distribution P(r) Distribution

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

Entry ID entry_id1dku
Deposition date deposition_date1999-12-08
Structure title titleCRYSTAL STRUCTURES OF BACILLUS SUBTILIS PHOSPHORIBOSYLPYROPHOSPHATE SYNTHETASE: MOLECULAR BASIS OF ALLOSTERIC INHIBITION AND ACTIVATION.
Keywords keywordsOPEN ALPHA-BETA STRUCTURE, DOMAIN DUPLICATION, PHOSPHORIBOSYLTRANSFERASE TYPE I FOLD, 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_guinier27.06 Å
Radius of gyration Rg (electron density) rg_electron26.02 Å
Forward intensity I(0) i071128300.00
Molecular weight molecular_weight66208.0 kDa
Excluded volume excluded_volume83281 ų
Envelope volume envelope_volume100480 ų
Hydration-shell volume shell_volume31996 ų
Envelope diameter envelope_diameter83.4 Å
Shell Rg shell_rg33.41 Å
Envelope Rg envelope_rg26.06 Å
Shape Rg shape_rg26.00 Å
Total Rg total_rg26.87 Å
Total atoms total_atoms4644
Residues n_residues590
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 dmax82.6 Å
Rg (real space) rg_real26.95 Å
Rg uncertainty (real space) rg_real_error0.49 Å
I(0) (real space) i0_real7.1130e+07
I(0) uncertainty (real space) i0_real_error1.0510e+06
Rg (reciprocal space) rg_reciprocal26.99 Å
I(0) (reciprocal space) i0_reciprocal71130000.0000
Solution quality estimate total_estimate0.9099
Solution quality rating solution_quality EXCELLENT a EXCELLENT solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary30.8 Å
Skewness Skewness skewness0.206
Kurtosis Kurtosis kurtosis-0.534
Angular range angular_range— – 0.2950 Å−1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha18920000.0000
Real-space data points n_real_points60
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.960; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 1.000; Smooth: 0.945
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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (4)

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7. Fold Classification (SCOP + CATH) 8 domains

SCOP 2.08 (4 domains)

Domain ID domain_idd1dkua1
Class classc — Alpha and beta proteins (a/b)
Fold Fold foldc.61 — PRTase-like
Superfamily Superfamily superfamilyc.61.1 — PRTase-like
Family Family familyc.61.1.2 — Phosphoribosylpyrophosphate synthetase-like
Domain ID domain_idd1dkua2
Class classc — Alpha and beta proteins (a/b)
Fold Fold foldc.61 — PRTase-like
Superfamily Superfamily superfamilyc.61.1 — PRTase-like
Family Family familyc.61.1.2 — Phosphoribosylpyrophosphate synthetase-like
Domain ID domain_idd1dkub1
Class classc — Alpha and beta proteins (a/b)
Fold Fold foldc.61 — PRTase-like
Superfamily Superfamily superfamilyc.61.1 — PRTase-like
Family Family familyc.61.1.2 — Phosphoribosylpyrophosphate synthetase-like
Domain ID domain_idd1dkub2
Class classc — Alpha and beta proteins (a/b)
Fold Fold foldc.61 — PRTase-like
Superfamily Superfamily superfamilyc.61.1 — PRTase-like
Family Family familyc.61.1.2 — Phosphoribosylpyrophosphate synthetase-like

CATH v4.4 (4 domains)

Domain ID domain_id1dkuA01
Class class3 — Alpha Beta
Architecture architecture40 — 3-Layer(aba) Sandwich
Topology topology50 — Rossmann fold
Homologous superfamily homologous superfamily2020 —
Domain ID domain_id1dkuA02
Class class3 — Alpha Beta
Architecture architecture40 — 3-Layer(aba) Sandwich
Topology topology50 — Rossmann fold
Homologous superfamily homologous superfamily2020 —
Domain ID domain_id1dkuB01
Class class3 — Alpha Beta
Architecture architecture40 — 3-Layer(aba) Sandwich
Topology topology50 — Rossmann fold
Homologous superfamily homologous superfamily2020 —
Domain ID domain_id1dkuB02
Class class3 — Alpha Beta
Architecture architecture40 — 3-Layer(aba) Sandwich
Topology topology50 — Rossmann fold
Homologous superfamily homologous superfamily2020 —
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8. Citations (2)

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9. Files and Curves (10)