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1tpt

THREE-DIMENSIONAL STRUCTURE OF THYMIDINE PHOSPHORYLASE FROM ESCHERICHIA COLI AT 2.8 ANGSTROMS RESOLUTION

Method: X-RAY DIFFRACTION Dmax: 70.2 Å Quality: REASONABLE
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1. Protein Identity and Related Structures Protein Identity & Related Structures

THYMIDINE PHOSPHORYLASE

Escherichia coli

UniProt P07650

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 1–441 Not recorded SO4 SULFATE ION × 2 TDR THYMINE × 2 X-RAY DIFFRACTION mmCIF provides none of the parsed experimental conditions Resolution 2.80 Å

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 1TPT Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
1AZY STRUCTURAL AND THEORETICAL STUDIES SUGGEST DOMAIN MOVEMENT PRODUCES AN ACTIVE CONFORMATION OF THYMIDINE PHOSPHORYLASE Deposited 1997-11-24 Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain A 2–440（439 aa）
Chain B 2–440（439 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions pH 4.6；pH 4.6
Resolution 3.00 Å R-free 0.276
1OTP STRUCTURAL AND THEORETICAL STUDIES SUGGEST DOMAIN MOVEMENT PRODUCES AN ACTIVE CONFORMATION OF THYMIDINE PHOSPHORYLASE Deposited 1997-11-09 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain A 2–440（439 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions pH 6.4；PROTEIN WAS CRYSTALLIZED FROM 0.9 - 1.2 M SODIUM CITRATE (PH 6.4 - 6.8) AND 2MM DTT AT ROOM TEMPERATURE USING HANGING DROP METHOD
Resolution 2.80 Å R-free 0.248
2TPT STRUCTURAL AND THEORETICAL STUDIES SUGGEST DOMAIN MOVEMENT PRODUCES AN ACTIVE CONFORMATION OF THYMIDINE PHOSPHORYLASE Deposited 1997-11-24 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain A 2–440（439 aa）
Not recorded SO4 SULFATE ION × 2 X-RAY DIFFRACTION
X-ray crystallization conditions pH 5.5；pH 5.5
Resolution 2.60 Å R-free 0.244
4EAD Thymidine phosphorylase from E.coli with 3'-azido-2'-fluoro-dideoxyuridine Deposited 2012-03-22 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain A 2–440（439 aa）
Not recorded 0NP 2',3'-dideoxy-2'-fluoro-3'-triaza-1,2-dien-2-ium-1-yluridine × 2 SO4 SULFATE ION × 12 GOL GLYCEROL × 8 X-RAY DIFFRACTION
X-ray crystallization conditions 273 K；COUNTER DIFFUSION, LIQUID DIFFUSION, temperature 273K
Resolution 1.50 Å R-free 0.192
4EAF Thymidine phosphorylase from E.coli Deposited 2012-03-22 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain A 2–440（439 aa）
Not recorded SO4 SULFATE ION × 14 GOL GLYCEROL × 4 X-RAY DIFFRACTION
X-ray crystallization conditions LIQUID DIFFUSION；273 K；COUNTER DIFFUSION, temperature 273K, LIQUID DIFFUSION
Resolution 1.55 Å R-free 0.207
4LHM Thymidine phosphorylase from E.coli with 3'-azido-3'-deoxythymidine Deposited 2013-07-01 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain A 2–440（439 aa）
Not recorded SO4 SULFATE ION × 14 GOL GLYCEROL × 4 AZZ 3'-azido-3'-deoxythymidine × 2 X-RAY DIFFRACTION
X-ray crystallization conditions COUNTER-DIFFUSION；298 K；COUNTER DIFFUSION, temperature 298.0K
Resolution 1.52 Å R-free 0.196

6 other PDB entries and 6 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name TYPH_ECOLI
Isoform —
PDB entities 1
Chains and sequence ranges Author chain A； PDBConstruct 1–440； UniProt 1–441

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 1tpt

P(r) Distance Distribution P(r) Distribution

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

Entry ID entry_id1tpt
Deposition date deposition_date1990-06-14
Structure title titleTHREE-DIMENSIONAL STRUCTURE OF THYMIDINE PHOSPHORYLASE FROM ESCHERICHIA COLI AT 2.8 ANGSTROMS RESOLUTION
Keywords keywordsTHYMIDINE PHOSPHORYLASE; THYMIDINE PHOSPHORYLASE
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_guinier22.63 Å
Radius of gyration Rg (electron density) rg_electron22.02 Å
Forward intensity I(0) i037212200.00
Molecular weight molecular_weight47395.0 kDa
Excluded volume excluded_volume58221 ų
Envelope volume envelope_volume43946 ų
Hydration-shell volume shell_volume18649 ų
Envelope diameter envelope_diameter73.1 Å
Shell Rg shell_rg25.84 Å
Envelope Rg envelope_rg20.51 Å
Shape Rg shape_rg21.59 Å
Total Rg total_rg22.38 Å
Total atoms total_atoms14
Residues n_residues—
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 dmax70.2 Å
Rg (real space) rg_real22.54 Å
Rg uncertainty (real space) rg_real_error0.25 Å
I(0) (real space) i0_real3.7210e+07
I(0) uncertainty (real space) i0_real_error4.5600e+05
Rg (reciprocal space) rg_reciprocal22.57 Å
I(0) (reciprocal space) i0_reciprocal37210000.0000
Solution quality estimate total_estimate0.7324
Solution quality rating solution_quality REASONABLE a REASONABLE solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary27.6 Å
Skewness Skewness skewness0.235
Kurtosis Kurtosis kurtosis-0.424
Angular range angular_range— – 0.3500 Å−1
Current regularization parameter α current_alpha0.0001
Highest regularization parameter α highest_alpha9834000.0000
Real-space data points n_real_points67
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.933; Stabil: 1.000; Sysdev: 0.242; Positv: 1.000; Valcen: 0.997; Smooth: 0.994
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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) 3 domains

SCOP 2.08 (3 domains)

Domain ID domain_idd1tpta1
Class classa — All alpha proteins
Fold Fold folda.46 — Methionine synthase domain-like
Superfamily Superfamily superfamilya.46.2 — Nucleoside phosphorylase/phosphoribosyltransferase N-terminal domain
Family Family familya.46.2.1 — Nucleoside phosphorylase/phosphoribosyltransferase N-terminal domain
Domain ID domain_idd1tpta2
Class classc — Alpha and beta proteins (a/b)
Fold Fold foldc.27 — Nucleoside phosphorylase/phosphoribosyltransferase catalytic domain
Superfamily Superfamily superfamilyc.27.1 — Nucleoside phosphorylase/phosphoribosyltransferase catalytic domain
Family Family familyc.27.1.1 — Nucleoside phosphorylase/phosphoribosyltransferase catalytic domain
Domain ID domain_idd1tpta3
Class classd — Alpha and beta proteins (a+b)
Fold Fold foldd.41 — alpha/beta-Hammerhead
Superfamily Superfamily superfamilyd.41.3 — Pyrimidine nucleoside phosphorylase C-terminal domain
Family Family familyd.41.3.1 — Pyrimidine nucleoside phosphorylase C-terminal domain
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8. Citations (1)

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9. Files and Curves (10)