SAXSdb — 2oma

▼

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

Triosephosphate isomerase

Trypanosoma cruzi

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 2–251 Chain B； UniProt 2–251	Non-standard monomer：Yes (specific site not provided by mmCIF)	SO4 SULFATE ION × 9 PEG DI(HYDROXYETHYL)ETHER × 3 PGE TRIETHYLENE GLYCOL × 1	X-RAY DIFFRACTION X-ray crystallization conditions：pH 7.5；291 K；5 MICROL OF THE PROTEIN SOLUTION WERE MIXED WITH 5 MICROL OF 2 % POLYETHYLENE GLYCOL 400, 0.1 M HEPES, 2.0M AMMONIUM SULFATE, PH 7.5, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 291K, PH 7.50. CRYSTAL SOAKED IN DITHIOBENZYLAMINE	Resolution 2.15 Å R-free 0.250

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 2OMA	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
1CI1 CRYSTAL STRUCTURE OF TRIOSEPHOSPHATE ISOMERASE FROM TRYPANOSOMA CRUZI IN HEXANE Deposited 1999-04-06	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 1–251（251 aa） Chain B 1–251（251 aa）	Not recorded	HEX HEXANE × 3	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION；pH 7.5；PROTEIN WAS CRYSTALLIZED AT ROOM TEMPERATUTE BY VAPER DIFFUSION FROM 0.1 M NA HEPES PH7.5, 2%(V/V) PEG400 AND 2.0 M AMMONIUM SULFATE, THEN SOAKED IN ANHYDROUS N-HEXANE. , VAPOR DIFFUSION	Resolution 2.00 Å R-free 0.239
1SUX CRYSTALLOGRAPHIC ANALYSIS OF THE COMPLEX BETWEEN TRIOSEPHOSPHATE ISOMERASE FROM TRYPANOSOMA CRUZI AND 3-(2-benzothiazolylthio)-1-propanesulfonic acid Deposited 2004-03-26	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 1–251（251 aa） Chain B 1–251（251 aa）	Not recorded	SO4 SULFATE ION × 7 BTS 3-(2-BENZOTHIAZOLYLTHIO)-1-PROPANESULFONIC ACID × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；291 K；PEG 400, HEPES, ammonium sulfate, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 291K	Resolution 2.00 Å R-free 0.196
1TCD TRYPANOSOMA CRUZI TRIOSEPHOSPHATE ISOMERASE Deposited 1998-01-29	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 3–251（249 aa） Chain B 3–251（249 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions pH 7.5；pH 7.5	Resolution 1.83 Å R-free 0.258
2V5B The monomerization of Triosephosphate Isomerase from Trypanosoma cruzi Deposited 2008-10-02	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 1–68（68 aa） Fragment：RESIDUES 1-68,84-251 Chain A 84–251（168 aa） Fragment：RESIDUES 1-68,84-251	Non-standard monomer：Yes (specific site not provided by mmCIF) Non-standard monomer：Yes (specific site not provided by mmCIF)	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION；pH 7.5；282 K；CRYSTALS WERE GROWN AT 9 DEGREES. RESERVOIR SOLUTION OF 100 MM HEPES, PH 7.5, 10% PEG 6000, AND 5% 2-METHYL-2,4-PENTANEDIOL. THE CRYSTALS WERE CRYOPROTECTED BY ADDING PEG 400 30% TO THE RESERVOIR. THEY WERE IMMEDIATELY FROZEN IN LIQUID NITROGEN.	Resolution 2.00 Å R-free 0.257
2V5B The monomerization of Triosephosphate Isomerase from Trypanosoma cruzi Deposited 2008-10-02	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1–68（68 aa） Fragment：RESIDUES 1-68,84-251 Chain A 84–251（168 aa） Fragment：RESIDUES 1-68,84-251	Non-standard monomer：Yes (specific site not provided by mmCIF) Non-standard monomer：Yes (specific site not provided by mmCIF)	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION；pH 7.5；282 K；CRYSTALS WERE GROWN AT 9 DEGREES. RESERVOIR SOLUTION OF 100 MM HEPES, PH 7.5, 10% PEG 6000, AND 5% 2-METHYL-2,4-PENTANEDIOL. THE CRYSTALS WERE CRYOPROTECTED BY ADDING PEG 400 30% TO THE RESERVOIR. THEY WERE IMMEDIATELY FROZEN IN LIQUID NITROGEN.	Resolution 2.00 Å R-free 0.257
3Q37 Identification of Amino Acids that Account for Long-Range Interactions in Proteins Using Two Triosephosphate Isomerases from Pathogenic Trypanosomes. Deposited 2010-12-21	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Insufficient information Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 35–90（56 aa） Fragment：UNP P04789 residues 2-35 and 92-119, UNP P52270 residues 35-92 and 121-251 Chain A 121–251（131 aa） Fragment：UNP P04789 residues 2-35 and 92-119, UNP P52270 residues 35-92 and 121-251 Chain B 35–90（56 aa） Fragment：UNP P04789 residues 2-35 and 92-119, UNP P52270 residues 35-92 and 121-251 Chain B 121–251（131 aa） Fragment：UNP P04789 residues 2-35 and 92-119, UNP P52270 residues 35-92 and 121-251	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7；278 K；0.2 Sodium malonate, 20% PEG 3350, pH 7.0, VAPOR DIFFUSION, SITTING DROP, temperature 278K	Resolution 1.65 Å R-free 0.220
3Q37 Identification of Amino Acids that Account for Long-Range Interactions in Proteins Using Two Triosephosphate Isomerases from Pathogenic Trypanosomes. Deposited 2010-12-21	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Insufficient information Homooligomer；Protein × 2 PDB declaration: dimeric	Chain C 35–90（56 aa） Fragment：UNP P04789 residues 2-35 and 92-119, UNP P52270 residues 35-92 and 121-251 Chain C 121–251（131 aa） Fragment：UNP P04789 residues 2-35 and 92-119, UNP P52270 residues 35-92 and 121-251 Chain D 35–90（56 aa） Fragment：UNP P04789 residues 2-35 and 92-119, UNP P52270 residues 35-92 and 121-251 Chain D 121–251（131 aa） Fragment：UNP P04789 residues 2-35 and 92-119, UNP P52270 residues 35-92 and 121-251	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7；278 K；0.2 Sodium malonate, 20% PEG 3350, pH 7.0, VAPOR DIFFUSION, SITTING DROP, temperature 278K	Resolution 1.65 Å R-free 0.220
4HHP Crystal structure of triosephosphate isomerase from trypanosoma cruzi, mutant e105d Deposited 2012-10-10	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 1–251（251 aa） Chain B 1–251（251 aa）	Mutation：E105D Mutation：E105D	GOL GLYCEROL × 2 SO4 SULFATE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8.6；281.15 K；25% w/v PEG monomethyl ether 2000, 0.1 M Tris pH 8.6, 0.01 M Nickel (II) chloride hexahydrate, 5% w/v n-dodecyl-N,N-dimethylamin-N-oxide, VAPOR DIFFUSION, SITTING DROP, temperature 281.15K	Resolution 1.50 Å R-free 0.196

6 other PDB entries and 8 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	TPIS_TRYCR
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–250； UniProt 2–251 Author chain B； PDBConstruct 1–250； UniProt 2–251

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.

▼

2. Structure Basics 2. Structure Basics

Entry ID entry_id	2oma
Deposition date deposition_date	2007-01-21
Structure title title	Crystallographic analysis of a chemically modified triosephosphate isomerase from Trypanosoma cruzi with dithiobenzylamine (DTBA)
Keywords keywords	Triosephosphate isomerase, Trypanosoma cruzi, protein interfaces, dithiobisbenzylamine, ISOMERASE; ISOMERASE
Experimental Method method	X-RAY DIFFRACTION

▼

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

Radius of gyration Rg (Guinier) rg_guinier	25.97 Å
Radius of gyration Rg (electron density) rg_electron	24.80 Å
Forward intensity I(0) i0	52440700.00
Molecular weight molecular_weight	55925.0 kDa
Excluded volume excluded_volume	69966 Å³
Envelope volume envelope_volume	81762 Å³
Hydration-shell volume shell_volume	27818 Å³
Envelope diameter envelope_diameter	84.7 Å
Shell Rg shell_rg	31.99 Å
Envelope Rg envelope_rg	24.93 Å
Shape Rg shape_rg	24.76 Å
Total Rg total_rg	25.73 Å
Total atoms total_atoms	3922
Residues n_residues	498
Spherical-harmonic order n_harmonics	20
q range q_range	— – 0.5000 Å⁻¹
Data points n_points	101
Shell type shell_type	directional
Solvent electron density solvent_density	0.3340 e/Å³
Shell contrast contrast_shell	0.0300 e/Å³
CRYSOL version crysol_version	4.1.3

▼

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

Maximum dimension Dmax dmax	81.9 Å
Rg (real space) rg_real	26.02 Å
Rg uncertainty (real space) rg_real_error	0.55 Å
I(0) (real space) i0_real	5.2440e+07
I(0) uncertainty (real space) i0_real_error	8.0430e+05
Rg (reciprocal space) rg_reciprocal	26.01 Å
I(0) (reciprocal space) i0_reciprocal	52440000.0000
Solution quality estimate total_estimate	0.6824
Solution quality rating solution_quality	REASONABLE a REASONABLE solution
P(r) peaks n_peaks	1
Primary peak position r_peak_primary	80.6 Å
Skewness Skewness skewness	0.409
Kurtosis Kurtosis kurtosis	-0.428
Angular range angular_range	— – 0.3050 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	15300000.0000
Real-space data points n_real_points	62
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.889; Stabil: 1.000; Sysdev: 0.105; Positv: 1.000; Valcen: 0.985; Smooth: 0.901

▶

5. Crystallography and Experiment 5. Crystallography & Experiment

▶

6. Entities and Polymers Entities & Polymers (5)

Entity 1 Entity 1 polymer

Description description	Triosephosphate isomerase
Molecular weight formula_weight	27352.4 kDa
EC 编号 ec_number	5.3.1.1
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B
Atom count atom_count	4210

ASKPQPIAAANWKCNGSESLLVPLIETLNAATFDHDVQCVVAPTFLHIPMTKARLTNPKFQIAAQNAITRSGAFTGEVSLQILKDYGISWVVLGHSERRLYYGETNEIVAEKVAQACAAGFHVIVCVGETNEEREAGRTAAVVLTQLAAVAQKLSKEAWSRVVIAYEPVWAIGTGKVATPQQAQEVHELLRRWVRSKLGTDIAAQLRILYGGSVTAKNARTLYQMRDINGFLVGGASLKPEFVEIIEATK

来源 Source

来源生物 organism	Trypanosoma cruzi
NCBI Class编号 ncbi_taxonomy_id	5693
宿主生物 host_organism	Escherichia coli

Entity 2 Entity 2 non-polymer

Description description	SULFATE ION
Molecular weight formula_weight	96.1 kDa
Source method src_method	syn
Copy count entity_count	9

Entity 3 Entity 3 non-polymer

Description description	DI(HYDROXYETHYL)ETHER
Molecular weight formula_weight	106.1 kDa
Source method src_method	syn
Copy count entity_count	3

Entity 4 Entity 4 non-polymer

Description description	TRIETHYLENE GLYCOL
Molecular weight formula_weight	150.2 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 5 Entity 5 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	267

▼

7. Fold Classification (SCOP + CATH) 4 domains

SCOP 2.08 (2 domains)

Domain ID domain_id	d2omaa_
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.1 — TIM beta/alpha-barrel
Superfamily Superfamily superfamily	c.1.1 — Triosephosphate isomerase (TIM)
Family Family family	c.1.1.1 — Triosephosphate isomerase (TIM)

Domain ID domain_id	d2omab_
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.1 — TIM beta/alpha-barrel
Superfamily Superfamily superfamily	c.1.1 — Triosephosphate isomerase (TIM)
Family Family family	c.1.1.1 — Triosephosphate isomerase (TIM)

CATH v4.4 (2 domains)

Domain ID domain_id	2omaA00
Class class	3 — Alpha Beta
Architecture architecture	20 — Alpha-Beta Barrel
Topology topology	20 — TIM Barrel
Homologous superfamily homologous superfamily	70 — Aldolase class I

Domain ID domain_id	2omaB00
Class class	3 — Alpha Beta
Architecture architecture	20 — Alpha-Beta Barrel
Topology topology	20 — TIM Barrel
Homologous superfamily homologous superfamily	70 — Aldolase class I

▶

8. Citations (2)

▶

Unit-cell length a length_a	43.206 Å
Unit-cell length b length_b	75.337 Å
Unit-cell length c length_c	146.427 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	90.00 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	8

Space group space_group	P 21 21 21
Space-group number int_tables_number	19
Crystal system crystal_system	—

Resolution resolution	2.150 Å
Low-resolution limit resolution_low	41.450 Å
R factor r_factor	0.1990
R_work r_work	0.1960
R_free r_free	0.2500

fit	/app/data/saxs_computation/om/2oma/2oma.fit
pddf	/app/data/pr_computation/om/2oma/2oma.pr.out
profile	/app/data/saxs_computation/om/2oma/2oma.dat

Crystallographic analysis of a chemically modified triosephosphate isomerase from Trypanosoma cruzi with dithiobenzylamine (DTBA)

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

Triosephosphate isomerase

State in the Current Structure

Other States of the Same Protein in the Database

SAXS scattering curve SAXS Profile

P(r) Distance Distribution P(r) Distribution

2. Structure Basics 2. Structure Basics

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

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

5. Crystallography and Experiment 5. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

Diffraction experiment Diffraction