2g8x

Escherichia coli Y209W apoprotein

Method: X-RAY DIFFRACTION Dmax: 73.1 Å Quality: EXCELLENT

1. Protein Identity and Related Structures Protein Identity & Related Structures

thymidylate synthase

Escherichia coli

UniProt P0A884

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 1–264 Chain B; UniProt 1–264 Mutation:Y209W, N-terminus is carbamylated Non-standard monomer:Yes (specific site not provided by mmCIF) CO3 CARBONATE ION × 3 PO4 PHOSPHATE ION × 2 DTT 2,3-DIHYDROXY-1,4-DITHIOBUTANE × 2 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, HANGING DROP;pH 7.5;295 K;7.8mg/ml protein, 25mM KPO4, pH 7.5, and 5mM DTT equilibrated against a well buffer containing 28% PEG 4K, 100 mM Tris-Cl, pH 8.9, 200mM sodium acetate and 5mM DTT, VAPOR DIFFUSION, HANGING DROP, temperature 295K Resolution 1.83 Å R-free 0.202

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.

56 other PDB entries and 63 assemblies. Open the comparison page and filter oligomeric states

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

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 2g8x

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 2g8x
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2. Structure Basics 2. Structure Basics

Entry ID entry_id2g8x
Deposition date deposition_date2006-03-03
Structure title titleEscherichia coli Y209W apoprotein
Keywords keywordsbeta sheet, alpha/beta protein, DTT, TRANSFERASE; TRANSFERASE
Experimental Method methodX-RAY DIFFRACTION

3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

Radius of gyration Rg (Guinier) rg_guinier24.17
Radius of gyration Rg (electron density) rg_electron22.83
Forward intensity I(0) i062790900.00
Molecular weight molecular_weight61264.0 kDa
Excluded volume excluded_volume76244 ų
Envelope volume envelope_volume86985 ų
Hydration-shell volume shell_volume30482 ų
Envelope diameter envelope_diameter74.3
Shell Rg shell_rg31.02
Envelope Rg envelope_rg23.08
Shape Rg shape_rg22.83
Total Rg total_rg23.70
Total atoms total_atoms4314
Residues n_residues522
Spherical-harmonic order n_harmonics20
q range q_range— – 0.5000 −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

4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

Maximum dimension Dmax dmax73.1
Rg (real space) rg_real24.00
Rg uncertainty (real space) rg_real_error0.28
I(0) (real space) i0_real6.2790e+07
I(0) uncertainty (real space) i0_real_error8.5770e+05
Rg (reciprocal space) rg_reciprocal24.04
I(0) (reciprocal space) i0_reciprocal62790000.0000
Solution quality estimate total_estimate0.9039
Solution quality rating solution_quality EXCELLENT a EXCELLENT solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary30.8
Skewness Skewness skewness0.164
Kurtosis Kurtosis kurtosis-0.405
Angular range angular_range— – 0.3300 −1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha15550000.0000
Real-space data points n_real_points65
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: 0.983; Smooth: 0.990

5. Crystallography and Experiment 5. Crystallography & Experiment

6. Entities and Polymers Entities & Polymers (5)

7. Fold Classification (SCOP + CATH) 4 domains

SCOP 2.08 (2 domains)

Domain ID domain_idd2g8xa_
Class classd — Alpha and beta proteins (a+b)
Fold Fold foldd.117 — Thymidylate synthase/dCMP hydroxymethylase
Superfamily Superfamily superfamilyd.117.1 — Thymidylate synthase/dCMP hydroxymethylase
Family Family familyd.117.1.1 — Thymidylate synthase/dCMP hydroxymethylase
Domain ID domain_idd2g8xb_
Class classd — Alpha and beta proteins (a+b)
Fold Fold foldd.117 — Thymidylate synthase/dCMP hydroxymethylase
Superfamily Superfamily superfamilyd.117.1 — Thymidylate synthase/dCMP hydroxymethylase
Family Family familyd.117.1.1 — Thymidylate synthase/dCMP hydroxymethylase

CATH v4.4 (2 domains)

Domain ID domain_id2g8xA00
Class class3 — Alpha Beta
Architecture architecture30 — 2-Layer Sandwich
Topology topology572 — Thymidylate Synthase; Chain A
Homologous superfamily homologous superfamily10 — Thymidylate synthase/dCMP hydroxymethylase domain
Domain ID domain_id2g8xB00
Class class3 — Alpha Beta
Architecture architecture30 — 2-Layer Sandwich
Topology topology572 — Thymidylate Synthase; Chain A
Homologous superfamily homologous superfamily10 — Thymidylate synthase/dCMP hydroxymethylase domain

8. Citations (1)

9. Files and Curves (10)