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4lhm

Thymidine phosphorylase from E.coli with 3'-azido-3'-deoxythymidine

Method: X-RAY DIFFRACTION Dmax: 76.7 Å Quality: GOOD
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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 2–440 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

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 4LHM 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 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
1TPT THREE-DIMENSIONAL STRUCTURE OF THYMIDINE PHOSPHORYLASE FROM ESCHERICHIA COLI AT 2.8 ANGSTROMS RESOLUTION Deposited 1990-06-14 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain A 1–441（441 aa）
Not recorded SO4 SULFATE ION × 2 TDR THYMINE × 2 X-RAY DIFFRACTION mmCIF provides none of the parsed conditions Resolution 2.80 Å
2TPT STRUCTURAL AND THEORETICAL STUDIES SUGGEST DOMAIN MOVEMENT PRODUCES AN ACTIVE CONFORMATION OF THYMIDINE PHOSPHORYLASE Deposited 1997-11-24 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 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 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

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 2–440； UniProt 2–440

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 4lhm

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 4lhm
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2. Structure Basics 2. Structure Basics

Entry ID entry_id4lhm
Deposition date deposition_date2013-07-01
Structure title titleThymidine phosphorylase from E.coli with 3'-azido-3'-deoxythymidine
Keywords keywordstransferase; 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_guinier23.10 Å
Radius of gyration Rg (electron density) rg_electron22.11 Å
Forward intensity I(0) i041212300.00
Molecular weight molecular_weight48302.0 kDa
Excluded volume excluded_volume59922 ų
Envelope volume envelope_volume69358 ų
Hydration-shell volume shell_volume26028 ų
Envelope diameter envelope_diameter80.3 Å
Shell Rg shell_rg29.33 Å
Envelope Rg envelope_rg22.37 Å
Shape Rg shape_rg22.13 Å
Total Rg total_rg22.84 Å
Total atoms total_atoms3372
Residues n_residues440
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 dmax76.7 Å
Rg (real space) rg_real23.01 Å
Rg uncertainty (real space) rg_real_error0.44 Å
I(0) (real space) i0_real4.1210e+07
I(0) uncertainty (real space) i0_real_error5.2930e+05
Rg (reciprocal space) rg_reciprocal23.03 Å
I(0) (reciprocal space) i0_reciprocal41210000.0000
Solution quality estimate total_estimate0.8837
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary28.3 Å
Skewness Skewness skewness0.261
Kurtosis Kurtosis kurtosis-0.365
Angular range angular_range— – 0.3450 Å−1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha14450000.0000
Real-space data points n_real_points66
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.831; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 1.000; Smooth: 0.989
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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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7. Fold Classification (SCOP + CATH) 7 domains

SCOP 2.08 (4 domains)

Domain ID domain_idd4lhma1
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_idd4lhma2
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_idd4lhma3
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
Domain ID domain_idd4lhma4
Class classl — Artifacts
Fold Fold foldl.1 — Tags
Superfamily Superfamily superfamilyl.1.1 — Tags
Family Family familyl.1.1.1 — Tags

CATH v4.4 (3 domains)

Domain ID domain_id4lhmA01
Class class1 — Mainly Alpha
Architecture architecture20 — Up-down Bundle
Topology topology970 — Transferase, Pyrimidine Nucleoside Phosphorylase; Chain A, domain 3
Homologous superfamily homologous superfamily10 — Transferase, Pyrimidine Nucleoside Phosphorylase; Chain C
Domain ID domain_id4lhmA02
Class class3 — Alpha Beta
Architecture architecture40 — 3-Layer(aba) Sandwich
Topology topology1030 — Pyrimidine Nucleoside Phosphorylase; Chain A, domain 2
Homologous superfamily homologous superfamily10 — Nucleoside phosphorylase/phosphoribosyltransferase catalytic domain
Domain ID domain_id4lhmA03
Class class3 — Alpha Beta
Architecture architecture90 — Alpha-Beta Complex
Topology topology1170 — Aldehyde Oxidoreductase; domain 3
Homologous superfamily homologous superfamily30 — Pyrimidine nucleoside phosphorylase-like, C-terminal domain
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8. Citations (1)

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9. Files and Curves (10)