2wsq

MonoTIM mutant RMM0-1, dimeric form.

Method: X-RAY DIFFRACTION Dmax: 110.2 Å Quality: GOOD

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

TRIOSE PHOSPHATE ISOMERASE, GLYCOSOMAL

TRYPANOSOMA BRUCEI BRUCEI

UniProt P04789

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 B; UniProt 2–67 Chain B; UniProt 84–250 Chain C; UniProt 2–67 Chain C; UniProt 84–250 Fragment:RESIDUES 2-67,84-250 Mutation:YES SO4 SULFATE ION × 5 X-RAY DIFFRACTION X-ray crystallization conditions:pH 6.2;303 K;100 MM MES BUFFER PH 6.2, 180 MM LI2SO4, 26 PERCENT PEG 6000, 5 MM DITHIOTHREITOL, 1 MM EDTA AND 1 MM NAN3, AT 30 DEGREES CELSIUS. Resolution 2.10 Å R-free 0.244
2 Protein homooligomer Homooligomer Protein × 2 PDB declaration: dimeric(2) Consistent with protein copy count Chain A; UniProt 2–67 Chain A; UniProt 84–250 Chain D; UniProt 2–67 Chain D; UniProt 84–250 Fragment:RESIDUES 2-67,84-250 Mutation:YES SO4 SULFATE ION × 3 X-RAY DIFFRACTION X-ray crystallization conditions:pH 6.2;303 K;100 MM MES BUFFER PH 6.2, 180 MM LI2SO4, 26 PERCENT PEG 6000, 5 MM DITHIOTHREITOL, 1 MM EDTA AND 1 MM NAN3, AT 30 DEGREES CELSIUS. Resolution 2.10 Å R-free 0.244

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.

48 other PDB entries and 79 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name TPIS_TRYBB
Isoform
PDB entities 1
Chains and sequence ranges Author chain A; PDBConstruct 1–66; UniProt 2–67 Author chain A; PDBConstruct 76–242; UniProt 84–250 Author chain B; PDBConstruct 1–66; UniProt 2–67 Author chain B; PDBConstruct 76–242; UniProt 84–250 Author chain C; PDBConstruct 1–66; UniProt 2–67 Author chain C; PDBConstruct 76–242; UniProt 84–250 Author chain D; PDBConstruct 1–66; UniProt 2–67 Author chain D; PDBConstruct 76–242; UniProt 84–250

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 2wsq

P(r) Distance Distribution P(r) Distribution

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

Entry ID entry_id2wsq
Deposition date deposition_date2009-09-08
Structure title titleMonoTIM mutant RMM0-1, dimeric form.
Keywords keywords;TEMPERATURE DEPENDANT EQUILIBRIUM, CATALYSIS, ISOMERASE, GLYCOSOME, GLYCOLYSIS, PENTOSE SHUNT, GLUCONEOGENESIS, LIPID SYNTHESIS, FATTY ACID BIOSYNTHESIS ;; ISOMERASE
Experimental Method methodX-RAY DIFFRACTION

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

Radius of gyration Rg (Guinier) rg_guinier33.81
Radius of gyration Rg (electron density) rg_electron33.21
Forward intensity I(0) i0170004000.00
Molecular weight molecular_weight104470.0 kDa
Excluded volume excluded_volume130960 ų
Envelope volume envelope_volume163160 ų
Hydration-shell volume shell_volume41392 ų
Envelope diameter envelope_diameter117.1
Shell Rg shell_rg39.59
Envelope Rg envelope_rg32.72
Shape Rg shape_rg33.20
Total Rg total_rg33.74
Total atoms total_atoms7351
Residues n_residues968
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 dmax110.2
Rg (real space) rg_real33.85
Rg uncertainty (real space) rg_real_error0.85
I(0) (real space) i0_real1.7000e+08
I(0) uncertainty (real space) i0_real_error2.9840e+06
Rg (reciprocal space) rg_reciprocal33.83
I(0) (reciprocal space) i0_reciprocal170000000.0000
Solution quality estimate total_estimate0.8878
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary35.2
Skewness Skewness skewness0.354
Kurtosis Kurtosis kurtosis-0.419
Angular range angular_range— – 0.2350 −1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha52350000.0000
Real-space data points n_real_points48
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.910; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.960; Smooth: 0.846

5. Crystallography and Experiment 5. Crystallography & Experiment

6. Entities and Polymers Entities & Polymers (3)

7. Fold Classification (SCOP + CATH) 8 domains

SCOP 2.08 (4 domains)

Domain ID domain_idd2wsqa_
Class classc — Alpha and beta proteins (a/b)
Fold Fold foldc.1 — TIM beta/alpha-barrel
Superfamily Superfamily superfamilyc.1.1 — Triosephosphate isomerase (TIM)
Family Family familyc.1.1.1 — Triosephosphate isomerase (TIM)
Domain ID domain_idd2wsqb_
Class classc — Alpha and beta proteins (a/b)
Fold Fold foldc.1 — TIM beta/alpha-barrel
Superfamily Superfamily superfamilyc.1.1 — Triosephosphate isomerase (TIM)
Family Family familyc.1.1.1 — Triosephosphate isomerase (TIM)
Domain ID domain_idd2wsqc_
Class classc — Alpha and beta proteins (a/b)
Fold Fold foldc.1 — TIM beta/alpha-barrel
Superfamily Superfamily superfamilyc.1.1 — Triosephosphate isomerase (TIM)
Family Family familyc.1.1.1 — Triosephosphate isomerase (TIM)
Domain ID domain_idd2wsqd_
Class classc — Alpha and beta proteins (a/b)
Fold Fold foldc.1 — TIM beta/alpha-barrel
Superfamily Superfamily superfamilyc.1.1 — Triosephosphate isomerase (TIM)
Family Family familyc.1.1.1 — Triosephosphate isomerase (TIM)

CATH v4.4 (4 domains)

Domain ID domain_id2wsqA00
Class class3 — Alpha Beta
Architecture architecture20 — Alpha-Beta Barrel
Topology topology20 — TIM Barrel
Homologous superfamily homologous superfamily70 — Aldolase class I
Domain ID domain_id2wsqB00
Class class3 — Alpha Beta
Architecture architecture20 — Alpha-Beta Barrel
Topology topology20 — TIM Barrel
Homologous superfamily homologous superfamily70 — Aldolase class I
Domain ID domain_id2wsqC00
Class class3 — Alpha Beta
Architecture architecture20 — Alpha-Beta Barrel
Topology topology20 — TIM Barrel
Homologous superfamily homologous superfamily70 — Aldolase class I
Domain ID domain_id2wsqD00
Class class3 — Alpha Beta
Architecture architecture20 — Alpha-Beta Barrel
Topology topology20 — TIM Barrel
Homologous superfamily homologous superfamily70 — Aldolase class I

8. Citations (1)

9. Files and Curves (10)