1tlb

Yeast coproporphyrinogen oxidase

Method: X-RAY DIFFRACTION

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

Coproporphyrinogen III oxidase

Saccharomyces cerevisiae

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein homooligomer	Homooligomer	Protein 2	water × 2	Consistent with protein count
2	Protein homooligomer	Homooligomer	Protein 2	SULFATE ION × 1 water × 2	Consistent with protein count
3	Protein homooligomer	Homooligomer	Protein 2	water × 2	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	HEM6_YEAST
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–326； UniProt 3–328 Author chain D； PDBConstruct 1–326； UniProt 3–328 Author chain Q； PDBConstruct 1–326； UniProt 3–328 Author chain S； PDBConstruct 1–326； UniProt 3–328 Author chain U； PDBConstruct 1–326； UniProt 3–328 Author chain W； PDBConstruct 1–326； UniProt 3–328

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	1tlb
Deposition date deposition_date	2004-06-09
Structure title title	Yeast coproporphyrinogen oxidase
Keywords keywords	coproporphyrinogen oxidase, heme biosynthesis, 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.

1tlb__assembly_1__model_1

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

Download this curve (.dat)

1tlb__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

1tlb__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	27.00 Å
Rg (electron density)	26.03 Å
Total Rg	26.96 Å
Atom count	5295
Residues	652
Excluded volume	93334 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`1tlb__assembly_1__model_1`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`1tlb__assembly_2__model_1`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
3	1	`1tlb__assembly_3__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 (3)

Entity 1 Entity 1 polymer

Description description	Coproporphyrinogen III oxidase
Molecular weight formula_weight	37535.2 kDa
EC 编号 ec_number	1.3.3.3
Source method src_method	man
Copy count entity_count	6

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,D,Q,S,U,W
Atom count atom_count	16531

APQDPRNLPIRQQMEALIRRKQAEITQGLESIDTVKFHADTWTRGNDGGGGTSMVIQDGTTFEKGGVNVSVVYGQLSPAAVSAMKADHKNLRLPEDPKTGLPVTDGVKFFACGLSMVIHPVNPHAPTTHLNYRYFETWNQDGTPQTWWFGGGADLTPSYLYEEDGQLFHQLHKDALDKHDTALYPRFKKWCDEYFYITHRKETRGIGGIFFDDYDERDPQEILKMVEDCFDAFLPSYLTIVKRRKDMPYTKEEQQWQAIRRGRYVEFNLIYDRGTQFGLRTPGSRVESILMSLPEHASWLYNHHPAPGSREAKLLEVTTKPREWVK

Source Source

Source organism organism	Saccharomyces cerevisiae
Common name common_name	;baker's yeast ;
NCBI taxonomy ID ncbi_taxonomy_id	4932
Host organism 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	1

Entity 3 Entity 3 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	640

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6. Fold Classification (SCOP + CATH) 12 domains

SCOP 2.08 (6 domains)

Domain ID domain_id	d1tlba_
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.248 — Coproporphyrinogen III oxidase
Superfamily Superfamily superfamily	d.248.1 — Coproporphyrinogen III oxidase
Family Family family	d.248.1.1 — Coproporphyrinogen III oxidase

Domain ID domain_id	d1tlbd_
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.248 — Coproporphyrinogen III oxidase
Superfamily Superfamily superfamily	d.248.1 — Coproporphyrinogen III oxidase
Family Family family	d.248.1.1 — Coproporphyrinogen III oxidase

Domain ID domain_id	d1tlbq_
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.248 — Coproporphyrinogen III oxidase
Superfamily Superfamily superfamily	d.248.1 — Coproporphyrinogen III oxidase
Family Family family	d.248.1.1 — Coproporphyrinogen III oxidase

Domain ID domain_id	d1tlbs_
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.248 — Coproporphyrinogen III oxidase
Superfamily Superfamily superfamily	d.248.1 — Coproporphyrinogen III oxidase
Family Family family	d.248.1.1 — Coproporphyrinogen III oxidase

Domain ID domain_id	d1tlbu_
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.248 — Coproporphyrinogen III oxidase
Superfamily Superfamily superfamily	d.248.1 — Coproporphyrinogen III oxidase
Family Family family	d.248.1.1 — Coproporphyrinogen III oxidase

Domain ID domain_id	d1tlbw_
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.248 — Coproporphyrinogen III oxidase
Superfamily Superfamily superfamily	d.248.1 — Coproporphyrinogen III oxidase
Family Family family	d.248.1.1 — Coproporphyrinogen III oxidase

CATH v4.4 (6 domains)

Domain ID domain_id	1tlbA00
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	1500 — oxygen-dependent coproporphyrinogen oxidase
Homologous superfamily homologous superfamily	10 — Coproporphyrinogen III oxidase, aerobic

Domain ID domain_id	1tlbD00
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	1500 — oxygen-dependent coproporphyrinogen oxidase
Homologous superfamily homologous superfamily	10 — Coproporphyrinogen III oxidase, aerobic

Domain ID domain_id	1tlbQ00
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	1500 — oxygen-dependent coproporphyrinogen oxidase
Homologous superfamily homologous superfamily	10 — Coproporphyrinogen III oxidase, aerobic

Domain ID domain_id	1tlbS00
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	1500 — oxygen-dependent coproporphyrinogen oxidase
Homologous superfamily homologous superfamily	10 — Coproporphyrinogen III oxidase, aerobic

Domain ID domain_id	1tlbU00
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	1500 — oxygen-dependent coproporphyrinogen oxidase
Homologous superfamily homologous superfamily	10 — Coproporphyrinogen III oxidase, aerobic

Domain ID domain_id	1tlbW00
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	1500 — oxygen-dependent coproporphyrinogen oxidase
Homologous superfamily homologous superfamily	10 — Coproporphyrinogen III oxidase, aerobic

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Unit-cell length a length_a	232.773 Å
Unit-cell length b length_b	65.238 Å
Unit-cell length c length_c	166.071 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	107.85 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	24

Space group space_group	C 1 2 1
Space-group number int_tables_number	5
Crystal system crystal_system	—

Resolution resolution	2.400 Å
Low-resolution limit resolution_low	158.110 Å
R factor r_factor	0.2119
R_work r_work	0.2082
R_free r_free	0.2824

Yeast coproporphyrinogen oxidase

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

Coproporphyrinogen III oxidase

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

1tlb__assembly_1__model_1

1tlb__assembly_1__model_1 | I(q)

1tlb__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 (3)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 non-polymer

Entity 3 Entity 3 water

6. Fold Classification (SCOP + CATH) 12 domains

SCOP 2.08 (6 domains)

CATH v4.4 (6 domains)

7. Citations (1)

Yeast coproporphyrinogen oxidase

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

Coproporphyrinogen III oxidase

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

1tlb__assembly_1__model_1

1tlb__assembly_1__model_1 | I(q)

1tlb__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 (3)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 non-polymer

Entity 3 Entity 3 water

6. Fold Classification (SCOP + CATH) 12 domains

SCOP 2.08 (6 domains)

CATH v4.4 (6 domains)

7. Citations (1)