SAXSdb — 1wd7

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

Uroporphyrinogen III Synthase

Thermus thermophilus

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein monomer	Monomer	Protein 1	water × 1	Consistent with protein count
2	Protein monomer	Monomer	Protein 1	water × 1	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	Q5SKH2_THET8
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 10–261； UniProt 2–253 Author chain B； PDBConstruct 10–261； UniProt 2–253

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	1wd7
Deposition date deposition_date	2004-05-12
Structure title title	Crystal Structure of Uroporphyrinogen III Synthase from an Extremely Thermophilic Bacterium Thermus thermophilus HB8 (Wild type, Native, Form-2 crystal)
Keywords keywords	;Uroporphyrinogen, Porphyrin, Heme, Congenital erythropoietic porphyria, Structural Genomics, RIKEN Structural Genomics/Proteomics Initiative, RSGI, LYASE ;; LYASE
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.

1wd7__assembly_1__model_1

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

Download this curve (.dat)

1wd7__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

1wd7__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	20.68 Å
Rg (electron density)	19.62 Å
Total Rg	20.52 Å
Atom count	1943
Residues	254
Excluded volume	35149 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`1wd7__assembly_1__model_1`	monomeric （1）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`1wd7__assembly_2__model_1`	monomeric （1）	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 (2)

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6. Fold Classification (SCOP + CATH) 8 domains

SCOP 2.08 (4 domains)

Domain ID domain_id	d1wd7a1
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.113 — HemD-like
Superfamily Superfamily superfamily	c.113.1 — HemD-like
Family Family family	c.113.1.1 — HemD-like

Domain ID domain_id	d1wd7a2
Class class	l — Artifacts
Fold Fold fold	l.1 — Tags
Superfamily Superfamily superfamily	l.1.1 — Tags
Family Family family	l.1.1.1 — Tags

Domain ID domain_id	d1wd7b1
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.113 — HemD-like
Superfamily Superfamily superfamily	c.113.1 — HemD-like
Family Family family	c.113.1.1 — HemD-like

Domain ID domain_id	d1wd7b2
Class class	l — Artifacts
Fold Fold fold	l.1 — Tags
Superfamily Superfamily superfamily	l.1.1 — Tags
Family Family family	l.1.1.1 — Tags

CATH v4.4 (4 domains)

Domain ID domain_id	1wd7A01
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	10090 —

Domain ID domain_id	1wd7A02
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	10090 —

Domain ID domain_id	1wd7B01
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	10090 —

Domain ID domain_id	1wd7B02
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	10090 —

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Unit-cell length a length_a	37.900 Å
Unit-cell length b length_b	84.875 Å
Unit-cell length c length_c	73.948 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	91.25 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	4

Space group space_group	P 1 21 1
Space-group number int_tables_number	4
Crystal system crystal_system	—

Resolution resolution	1.600 Å
Low-resolution limit resolution_low	37.890 Å
R factor r_factor	0.2240
R_work r_work	0.2240
R_free r_free	0.2550

Description description	Uroporphyrinogen III Synthase
Molecular weight formula_weight	28441.2 kDa
EC 编号 ec_number	4.2.1.75
Source method src_method	man
Copy count entity_count	2

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B
Atom count atom_count	4357

Crystal Structure of Uroporphyrinogen III Synthase from an Extremely Thermophilic Bacterium Thermus thermophilus HB8 (Wild type, Native, Form-2 crystal)

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

Uroporphyrinogen III Synthase

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

1wd7__assembly_1__model_1

1wd7__assembly_1__model_1 | I(q)

1wd7__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 (2)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 water

6. Fold Classification (SCOP + CATH) 8 domains

SCOP 2.08 (4 domains)

CATH v4.4 (4 domains)

7. Citations (1)

Source organism organism	Thermus thermophilus
NCBI taxonomy ID ncbi_taxonomy_id	274
Host organism host_organism	Escherichia coli BL21(DE3)

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	463

Crystal Structure of Uroporphyrinogen III Synthase from an Extremely Thermophilic Bacterium Thermus thermophilus HB8 (Wild type, Native, Form-2 crystal)

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

Uroporphyrinogen III Synthase

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

1wd7__assembly_1__model_1

1wd7__assembly_1__model_1 | I(q)

1wd7__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 (2)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 water

6. Fold Classification (SCOP + CATH) 8 domains

SCOP 2.08 (4 domains)

CATH v4.4 (4 domains)

7. Citations (1)