6t87

Urocanate reductase in complex with urocanate

Method: X-RAY DIFFRACTION

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

Urocanate reductase

Shewanella oneidensis (strain MR-1)

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein homooligomer	Homooligomer	Protein 2	FLAVIN-ADENINE DINUCLEOTIDE × 2 (2E)-3-(1H-IMIDAZOL-4-YL)ACRYLIC ACID × 2 GLYCEROL × 16 SULFATE ION × 8 CHLORIDE ION × 4 SODIUM ION × 2 water × 2	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	URDA_SHEON
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 2–454； UniProt 130–582

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	6t87
Deposition date deposition_date	2019-10-24
Structure title title	Urocanate reductase in complex with urocanate
Keywords keywords	urocanate reductase, bacterial enzyme, OXIDOREDUCTASE; OXIDOREDUCTASE
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.

6t87__assembly_1__model_1

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

Download this curve (.dat)

6t87__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

6t87__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	31.13 Å
Rg (electron density)	30.65 Å
Total Rg	31.35 Å
Atom count	14250
Residues	908
Excluded volume	127210 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`6t87__assembly_1__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 (8)

Entity 1 Entity 1 polymer

Description description	Urocanate reductase
Molecular weight formula_weight	49984.5 kDa
EC 编号 ec_number	1.3.99.33
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A
Atom count atom_count	7991

MEYTYDVVIIGSGGAGFSAGLEAIAAGRSAVIIEKMPIIGGNSLISGAEMNVAGSWVQKNMGITDSKELFISDTLKGGDFKGDPEMVKTMVDNAVGAAEWLRDYVKVEFYPDQLFQFGGHSVKRALIPKGHTGAEVISKFSIKADEVGLPIHTNTKAEKLIQDQTGRIVGVEAAHNGKTITYHAKRGVVIATGGFSSNMEMRKKYNPELDERYGSTGHAGGTGDGIVMAEKIHAAAKNMGYIQSYPICSPTSGAIALIADSRFFGAVLINQKGERFVEELERRDVISHAILAQPGRYTYVLWNQDIENVAHTVEMHQGELKEFTKDGLMYKVDTLEEAAKVFNIPEDKLLSTIKDVNHYAATGKDEAFNHRSGLVDLSKGPYWILKATPSVHHTMGGLVVDTRTRVLDEQGKVIPGLFAAGEVTGLTHGTNRLGGNAYTDIIVYGRIAGQEAAKHHHHHH

Source Source

Source organism organism	Shewanella oneidensis (strain MR-1)
NCBI taxonomy ID ncbi_taxonomy_id	211586
Host organism host_organism	Escherichia coli

Entity 2 Entity 2 non-polymer

Description description	FLAVIN-ADENINE DINUCLEOTIDE
Molecular weight formula_weight	785.5 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 3 Entity 3 non-polymer

Description description	(2E)-3-(1H-IMIDAZOL-4-YL)ACRYLIC ACID
Molecular weight formula_weight	138.1 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 4 Entity 4 non-polymer

Description description	GLYCEROL
Molecular weight formula_weight	92.1 kDa
Source method src_method	syn
Copy count entity_count	8

Entity 5 Entity 5 non-polymer

Description description	SULFATE ION
Molecular weight formula_weight	96.1 kDa
Source method src_method	syn
Copy count entity_count	4

Entity 6 Entity 6 non-polymer

Description description	CHLORIDE ION
Molecular weight formula_weight	35.5 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 7 Entity 7 non-polymer

Description description	SODIUM ION
Molecular weight formula_weight	23.0 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 8 Entity 8 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	588

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6. Fold Classification (SCOP + CATH) 1 domains

CATH v4.4 (1 domains)

Domain ID domain_id	6t87A01
Class class	3 — Alpha Beta
Architecture architecture	90 — Alpha-Beta Complex
Topology topology	700 — Flavocytochrome C3; Chain A, domain 1
Homologous superfamily homologous superfamily	10 — Succinate dehydrogenase/fumarate reductase flavoprotein, catalytic domain

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Unit-cell length a length_a	123.705 Å
Unit-cell length b length_b	123.705 Å
Unit-cell length c length_c	66.300 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	90.00 °
Unit-cell angle γ angle_gamma	120.00 °
Molecules per unit cell Z z_pdb	6

Space group space_group	P 31 2 1
Space-group number int_tables_number	152
Crystal system crystal_system	trigonal

Resolution resolution	1.560 Å
Low-resolution limit resolution_low	45.227 Å
R factor r_factor	0.1152
R_work r_work	0.1136
R_free r_free	0.1457

Urocanate reductase in complex with urocanate

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

Urocanate reductase

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

6t87__assembly_1__model_1

6t87__assembly_1__model_1 | I(q)

6t87__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 (8)

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 non-polymer

Entity 6 Entity 6 non-polymer

Entity 7 Entity 7 non-polymer

Entity 8 Entity 8 water

6. Fold Classification (SCOP + CATH) 1 domains

CATH v4.4 (1 domains)

7. Citations (1)

Urocanate reductase in complex with urocanate

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

Urocanate reductase

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

6t87__assembly_1__model_1

6t87__assembly_1__model_1 | I(q)

6t87__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 (8)

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 non-polymer

Entity 6 Entity 6 non-polymer

Entity 7 Entity 7 non-polymer

Entity 8 Entity 8 water

6. Fold Classification (SCOP + CATH) 1 domains

CATH v4.4 (1 domains)

7. Citations (1)