SAXSdb — 9vps

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

Dihydroorotate dehydrogenase (fumarate)

Trypanosoma brucei brucei TREU927

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein homooligomer	Homooligomer	Protein 2	1-DEOXY-1-(7,8-DIMETHYL-2,4-DIOXO-3,4-DIHYDRO-2H-BENZO[G]PTERIDIN-1-ID-10(5H)-YL)-5-O-PHOSPHONATO-D-RIBITOL × 2 MALONATE ION × 6 SULFITE ION × 2 water × 2	Consistent with protein count
2	Protein homooligomer	Homooligomer	Protein 2	1-DEOXY-1-(7,8-DIMETHYL-2,4-DIOXO-3,4-DIHYDRO-2H-BENZO[G]PTERIDIN-1-ID-10(5H)-YL)-5-O-PHOSPHONATO-D-RIBITOL × 2 MALONATE ION × 7 SULFITE ION × 2 water × 2	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	PYRD_TRYB2
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 5–317； UniProt 1–313 Author chain B； PDBConstruct 5–317； UniProt 1–313 Author chain C； PDBConstruct 5–317； UniProt 1–313 Author chain D； PDBConstruct 5–317； UniProt 1–313

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.

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2. Structure Basics 2. Structure Basics

Entry ID entry_id	9vps
Deposition date deposition_date	2025-07-04
Structure title title	Crystal structure of the C131A mutant of Trypanosoma brucei DHODH in FMN-reduced, ligand-free form
Keywords keywords	Ping-Pong Reaction Mechanism, Substrate/Product-enzyme interactions., FLAVOPROTEIN; FLAVOPROTEIN
Experimental Method method	X-RAY DIFFRACTION

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3. Official assembly/model SAXS Official SAXS Profiles

This page reads only the latest assembly calculations. Every curve maps to an explicit PDB entry, official biological assembly and coordinate model.

9vps__assembly_1__model_1

Assembly 1 · Model 1 · CRYSOL 4.1.3-1-20251215 (887e7ef)

Download this curve (.dat)

9vps__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

9vps__assembly_1__model_1 | P(r) · Pending

P(r) will be calculated and displayed separately for the same assembly/model.

Rg（Guinier）	25.82 Å
Rg (electron density)	24.97 Å
Total Rg	25.83 Å
Atom count	4886
Residues	624
Excluded volume	87540 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`9vps__assembly_1__model_1`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`9vps__assembly_2__model_1`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download

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4. Crystallography and Experiment 4. Crystallography & Experiment

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5. Entities and Polymers Entities & Polymers (5)

Entity 1 Entity 1 polymer

Description description	Dihydroorotate dehydrogenase (fumarate)
Molecular weight formula_weight	34441.6 kDa
EC 编号 ec_number	1.3.98.1
Mutation mutation	A115V,C131A
Source method src_method	man
Copy count entity_count	4

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,C,B,D
Atom count atom_count	10512

GPGSMSLKVNILGHEFSNPFMNAAGVLCTTEEDLRRMTESESGSLIGKSCTLAPRTGNPEPRYFGLPLGSINSMGLPNLGVDFYLSYAAQTHDYSRKPLFLSMSGLSVEESVEMVKKLVPITKEKGTILELNLSAPNVPGKPQVGYDFDTTRTYLQKVSEAYGLPFGVKMPPYFDIAHFDMAAAVLNDFPLVKFITCVNSIGNGLVIDPANETVVIKPKQGFGGLGGKYVLPTALANVNAFFRRCPDKLVFGCGGVYSGEEAFLHILAGASMVQVGTALHDEGPIIFARLNKELQEIMTNKGYKTLDEFRGRVKTMD

Source Source

Source organism organism	Trypanosoma brucei brucei TREU927
NCBI taxonomy ID ncbi_taxonomy_id	185431
Host organism host_organism	;Escherichia coli 'BL21-Gold(DE3)pLysS AG' ;

Entity 2 Entity 2 non-polymer

Description description	1-DEOXY-1-(7,8-DIMETHYL-2,4-DIOXO-3,4-DIHYDRO-2H-BENZO[G]PTERIDIN-1-ID-10(5H)-YL)-5-O-PHOSPHONATO-D-RIBITOL
Molecular weight formula_weight	458.4 kDa
Source method src_method	syn
Copy count entity_count	4

Entity 3 Entity 3 non-polymer

Description description	MALONATE ION
Molecular weight formula_weight	102.0 kDa
Source method src_method	syn
Copy count entity_count	13

Entity 4 Entity 4 non-polymer

Description description	SULFITE ION
Molecular weight formula_weight	80.1 kDa
Source method src_method	syn
Copy count entity_count	4

Entity 5 Entity 5 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	681

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Unit-cell length a length_a	139.755 Å
Unit-cell length b length_b	146.734 Å
Unit-cell length c length_c	65.784 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	16

Space group space_group	P 21 21 2
Space-group number int_tables_number	18
Crystal system crystal_system	—

Resolution resolution	1.800 Å
Low-resolution limit resolution_low	32.100 Å
R factor r_factor	0.1863
R_work r_work	0.1851
R_free r_free	0.2087

Crystal structure of the C131A mutant of Trypanosoma brucei DHODH in FMN-reduced, ligand-free form

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

Dihydroorotate dehydrogenase (fumarate)

State in the Current Structure

Other States of the Same Protein in the Database

2. Structure Basics 2. Structure Basics

3. Official assembly/model SAXS Official SAXS Profiles

9vps__assembly_1__model_1

9vps__assembly_1__model_1 | I(q)

9vps__assembly_1__model_1 | P(r) · Pending

4. Crystallography and Experiment 4. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

Diffraction experiment Diffraction

5. Entities and Polymers Entities & Polymers (5)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 non-polymer

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 non-polymer

Entity 5 Entity 5 water

7. Citations (1)

Crystal structure of the C131A mutant of Trypanosoma brucei DHODH in FMN-reduced, ligand-free form

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

Dihydroorotate dehydrogenase (fumarate)

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

2. Structure Basics 2. Structure Basics

3. Official assembly/model SAXS Official SAXS Profiles

9vps__assembly_1__model_1

9vps__assembly_1__model_1 | I(q)

9vps__assembly_1__model_1 | P(r) · Pending

4. Crystallography and Experiment 4. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

Diffraction experiment Diffraction

5. Entities and Polymers Entities & Polymers (5)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 non-polymer

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 non-polymer

Entity 5 Entity 5 water

7. Citations (1)