2v2h

The A178L mutation in the C-terminal hinge of the flexible loop-6 of triosephosphate isomerase (TIM) induces a more closed conformation of this hinge region in dimeric and monomeric TIM

Method: X-RAY DIFFRACTION Dmax: 88.3 Å Quality: EXCELLENT

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

TRIOSEPHOSPHATE 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 × 3 PDB declaration: trimeric(3) Consistent with protein copy count Chain A; UniProt 1–13 Chain A; UniProt 15–72 Chain A; UniProt 80–250 Chain B; UniProt 1–13 Chain B; UniProt 15–72 Chain B; UniProt 80–250 Chain C; UniProt 1–13 Chain C; UniProt 15–72 Chain C; UniProt 80–250 Mutation:YES PGA 2-PHOSPHOGLYCOLIC ACID × 3 CL CHLORIDE ION × 3 X-RAY DIFFRACTION X-ray crystallization conditions:pH 5.5;0.1 M CITRIC ACID PH 5.5, 20% PEG 6K, 3% TERT.BUTANOL Resolution 1.18 Å R-free 0.187

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 80 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 1–13; UniProt 1–13 Author chain A; PDBConstruct 14–71; UniProt 15–72 Author chain A; PDBConstruct 72–242; UniProt 80–250 Author chain B; PDBConstruct 1–13; UniProt 1–13 Author chain B; PDBConstruct 14–71; UniProt 15–72 Author chain B; PDBConstruct 72–242; UniProt 80–250 Author chain C; PDBConstruct 1–13; UniProt 1–13 Author chain C; PDBConstruct 14–71; UniProt 15–72 Author chain C; PDBConstruct 72–242; UniProt 80–250

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 2v2h

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 2v2h
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2. Structure Basics 2. Structure Basics

Entry ID entry_id2v2h
Deposition date deposition_date2007-06-06
Structure title titleThe A178L mutation in the C-terminal hinge of the flexible loop-6 of triosephosphate isomerase (TIM) induces a more closed conformation of this hinge region in dimeric and monomeric TIM
Keywords keywords;GLUCONEOGENESIS, LIPID SYNTHESIS, 2-PHOSPHO GLYCOLATE, GLYCOLYSIS, ENGINEERING, PENTOSE SHUNT, POINT MUTATION, TIM, 2PG, A178L, LOOP6, HINGE, LOOP-6, ENZYME, FATTY ACID BIOSYNTHESIS, TRIOSEPHOSPHATE ISOMERASE, ISOMERASE, GLYCOSOME, MONOMERIC, TIM-BARREL ;; ISOMERASE
Experimental Method methodX-RAY DIFFRACTION

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

Radius of gyration Rg (Guinier) rg_guinier28.26
Radius of gyration Rg (electron density) rg_electron27.25
Forward intensity I(0) i097780100.00
Molecular weight molecular_weight78328.0 kDa
Excluded volume excluded_volume98500 ų
Envelope volume envelope_volume120370 ų
Hydration-shell volume shell_volume36286 ų
Envelope diameter envelope_diameter87.4
Shell Rg shell_rg35.18
Envelope Rg envelope_rg26.74
Shape Rg shape_rg27.24
Total Rg total_rg28.08
Total atoms total_atoms5517
Residues n_residues723
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 dmax88.3
Rg (real space) rg_real28.06
Rg uncertainty (real space) rg_real_error0.47
I(0) (real space) i0_real9.7780e+07
I(0) uncertainty (real space) i0_real_error1.3350e+06
Rg (reciprocal space) rg_reciprocal28.13
I(0) (reciprocal space) i0_reciprocal97780000.0000
Solution quality estimate total_estimate0.9076
Solution quality rating solution_quality EXCELLENT a EXCELLENT solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary36.3
Skewness Skewness skewness0.091
Kurtosis Kurtosis kurtosis-0.643
Angular range angular_range— – 0.2800 −1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha31130000.0000
Real-space data points n_real_points57
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.933; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.998; Smooth: 0.999

5. Crystallography and Experiment 5. Crystallography & Experiment

6. Entities and Polymers Entities & Polymers (4)

7. Fold Classification (SCOP + CATH) 6 domains

SCOP 2.08 (3 domains)

Domain ID domain_idd2v2ha_
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_idd2v2hb_
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_idd2v2hc_
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 (3 domains)

Domain ID domain_id2v2hA00
Class class3 — Alpha Beta
Architecture architecture20 — Alpha-Beta Barrel
Topology topology20 — TIM Barrel
Homologous superfamily homologous superfamily70 — Aldolase class I
Domain ID domain_id2v2hB00
Class class3 — Alpha Beta
Architecture architecture20 — Alpha-Beta Barrel
Topology topology20 — TIM Barrel
Homologous superfamily homologous superfamily70 — Aldolase class I
Domain ID domain_id2v2hC00
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)