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1dj0

THE CRYSTAL STRUCTURE OF E. COLI PSEUDOURIDINE SYNTHASE I AT 1.5 ANGSTROM RESOLUTION

Method: X-RAY DIFFRACTION Dmax: 84.3 Å Quality: EXCELLENT
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1. Protein Identity and Related Structures Protein Identity & Related Structures

PSEUDOURIDINE SYNTHASE I

Escherichia coli

UniProt P07649

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 7–270 Chain B； UniProt 7–270 Not recorded CL CHLORIDE ION × 2 X-RAY DIFFRACTION X-ray crystallization conditions：MICRODIALYSIS；pH 6.5；298 K；MES BUFFER, pH 6.5, MICRODIALYSIS, temperature 298K Resolution 1.50 Å R-free 0.221

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 1DJ0 Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
2NQP Crystal structure of pseudoudirinde synthase TruA in complex with leucyl tRNA Deposited 2006-10-31 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Homooligomer；Protein × 2 PDB declaration: trimeric
Chain C 7–270（264 aa）
Chain D 7–270（264 aa）
Not recorded K POTASSIUM ION × 6 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；298 K；20% PEG 3350, 0.2 M K3 Citrate, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Resolution 3.50 Å R-free 0.279
2NQP Crystal structure of pseudoudirinde synthase TruA in complex with leucyl tRNA Deposited 2006-10-31 Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain A 7–270（264 aa）
Chain B 7–270（264 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；298 K；20% PEG 3350, 0.2 M K3 Citrate, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Resolution 3.50 Å R-free 0.279
2NR0 Crystal structure of pseudoudirinde synthase TruA in complex with leucyl tRNA Deposited 2006-11-01 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Homooligomer；Protein × 2 PDB declaration: tetrameric
Chain A 7–270（264 aa）
Chain B 7–270（264 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；298 K；20% PEG 3350, 0.2 M K3 Citrate, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Resolution 3.90 Å R-free 0.350
2NR0 Crystal structure of pseudoudirinde synthase TruA in complex with leucyl tRNA Deposited 2006-11-01 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein–RNA Homooligomer；Protein × 2 PDB declaration: tetrameric
Chain C 7–270（264 aa）
Chain D 7–270（264 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；298 K；20% PEG 3350, 0.2 M K3 Citrate, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Resolution 3.90 Å R-free 0.350
2NRE Crystal structure of pseudoudirinde synthase TruA in complex with leucyl tRNA Deposited 2006-11-01 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Homooligomer；Protein × 2 PDB declaration: tetrameric
Chain A 7–270（264 aa）
Not recorded K POTASSIUM ION × 4 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；298 K；20% PEG 3350, 0.2 M K3 Citrate, 5 mM spermine, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Resolution 4.00 Å R-free 0.357

3 other PDB entries and 5 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name TRUA_ECOLI
Isoform —
PDB entities 1
Chains and sequence ranges Author chain A； PDBConstruct 1–264； UniProt 7–270 Author chain B； PDBConstruct 1–264； UniProt 7–270

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 1dj0

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 1dj0
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2. Structure Basics 2. Structure Basics

Entry ID entry_id1dj0
Deposition date deposition_date1999-11-30
Structure title titleTHE CRYSTAL STRUCTURE OF E. COLI PSEUDOURIDINE SYNTHASE I AT 1.5 ANGSTROM RESOLUTION
Keywords keywordsALPHA/BETA FOLD, RNA-BINDING MOTIF, RNA-MODIFYING ENZYME, LYASE; LYASE
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_guinier26.36 Å
Radius of gyration Rg (electron density) rg_electron25.43 Å
Forward intensity I(0) i059024800.00
Molecular weight molecular_weight59443.0 kDa
Excluded volume excluded_volume74293 ų
Envelope volume envelope_volume87883 ų
Hydration-shell volume shell_volume28994 ų
Envelope diameter envelope_diameter91.0 Å
Shell Rg shell_rg32.38 Å
Envelope Rg envelope_rg25.50 Å
Shape Rg shape_rg25.42 Å
Total Rg total_rg26.22 Å
Total atoms total_atoms4196
Residues n_residues528
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 dmax84.3 Å
Rg (real space) rg_real26.28 Å
Rg uncertainty (real space) rg_real_error0.53 Å
I(0) (real space) i0_real5.9020e+07
I(0) uncertainty (real space) i0_real_error8.1100e+05
Rg (reciprocal space) rg_reciprocal26.31 Å
I(0) (reciprocal space) i0_reciprocal59030000.0000
Solution quality estimate total_estimate0.9027
Solution quality rating solution_quality EXCELLENT a EXCELLENT solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary29.5 Å
Skewness Skewness skewness0.216
Kurtosis Kurtosis kurtosis-0.534
Angular range angular_range— – 0.3000 Å−1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha15870000.0000
Real-space data points n_real_points61
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.924; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.997; Smooth: 0.963
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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (3)

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7. Fold Classification (SCOP + CATH) 6 domains

SCOP 2.08 (2 domains)

Domain ID domain_idd1dj0a_
Class classd — Alpha and beta proteins (a+b)
Fold Fold foldd.265 — Pseudouridine synthase
Superfamily Superfamily superfamilyd.265.1 — Pseudouridine synthase
Family Family familyd.265.1.1 — Pseudouridine synthase I TruA
Domain ID domain_idd1dj0b_
Class classd — Alpha and beta proteins (a+b)
Fold Fold foldd.265 — Pseudouridine synthase
Superfamily Superfamily superfamilyd.265.1 — Pseudouridine synthase
Family Family familyd.265.1.1 — Pseudouridine synthase I TruA

CATH v4.4 (4 domains)

Domain ID domain_id1dj0A01
Class class3 — Alpha Beta
Architecture architecture30 — 2-Layer Sandwich
Topology topology70 — Alpha-Beta Plaits
Homologous superfamily homologous superfamily660 — Pseudouridine synthase I, catalytic domain, C-terminal subdomain
Domain ID domain_id1dj0A02
Class class3 — Alpha Beta
Architecture architecture30 — 2-Layer Sandwich
Topology topology70 — Alpha-Beta Plaits
Homologous superfamily homologous superfamily580 — Pseudouridine synthase I, catalytic domain, N-terminal subdomain
Domain ID domain_id1dj0B01
Class class3 — Alpha Beta
Architecture architecture30 — 2-Layer Sandwich
Topology topology70 — Alpha-Beta Plaits
Homologous superfamily homologous superfamily660 — Pseudouridine synthase I, catalytic domain, C-terminal subdomain
Domain ID domain_id1dj0B02
Class class3 — Alpha Beta
Architecture architecture30 — 2-Layer Sandwich
Topology topology70 — Alpha-Beta Plaits
Homologous superfamily homologous superfamily580 — Pseudouridine synthase I, catalytic domain, N-terminal subdomain
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8. Citations (1)

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9. Files and Curves (10)