2rgz

Ensemble refinement of the protein crystal structure of human heme oxygenase-2 C127A (HO-2) with bound heme

Method: X-RAY DIFFRACTION

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

Heme oxygenase 2

Homo sapiens

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein homooligomer	Homooligomer	Protein 2	PROTOPORPHYRIN IX CONTAINING FE × 2 water × 2	Consistent with protein count
2	Protein monomer	Monomer	Protein 1	PROTOPORPHYRIN IX CONTAINING FE × 1 water × 1	Consistent with protein count
3	Protein monomer	Monomer	Protein 1	PROTOPORPHYRIN IX CONTAINING FE × 1 water × 1	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	HMOX2_HUMAN
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–264； UniProt 1–264 Author chain B； PDBConstruct 1–264； UniProt 1–264

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	2rgz
Deposition date deposition_date	2007-10-05
Structure title title	Ensemble refinement of the protein crystal structure of human heme oxygenase-2 C127A (HO-2) with bound heme
Keywords keywords	;Ensemble Refinement, Refinement Methodology Development, Structural Genomics Medical Relevance, Structural Genomics Community Request, HO-2, HEME Oxygenase, Endoplasmic reticulum, Iron, Metal-binding, Microsome, Oxidoreductase, Structural Genomics, Protein Structure Initiative, PSI, Center for Eukaryotic Structural Genomics, CESG ;; 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.

2rgz__assembly_1__model_1

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

Download this curve (.dat)

2rgz__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

2rgz__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	24.94 Å
Rg (electron density)	23.97 Å
Total Rg	24.89 Å
Atom count	3638
Residues	433
Excluded volume	64647 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`2rgz__assembly_1__model_1`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
1	2	`2rgz__assembly_1__model_2`	dimeric （2）	Excluded	—	—
	Exclusion reason： The official assembly declares water, but that component is absent from the generated coordinate model, leaving the structure composition incomplete.
1	3	`2rgz__assembly_1__model_3`	dimeric （2）	Excluded	—	—
	Exclusion reason： The official assembly declares water, but that component is absent from the generated coordinate model, leaving the structure composition incomplete.
1	4	`2rgz__assembly_1__model_4`	dimeric （2）	Excluded	—	—
	Exclusion reason： The official assembly declares water, but that component is absent from the generated coordinate model, leaving the structure composition incomplete.
1	5	`2rgz__assembly_1__model_5`	dimeric （2）	Excluded	—	—
	Exclusion reason： The official assembly declares water, but that component is absent from the generated coordinate model, leaving the structure composition incomplete.
1	6	`2rgz__assembly_1__model_6`	dimeric （2）	Excluded	—	—
	Exclusion reason： The official assembly declares water, but that component is absent from the generated coordinate model, leaving the structure composition incomplete.
1	7	`2rgz__assembly_1__model_7`	dimeric （2）	Excluded	—	—
	Exclusion reason： The official assembly declares water, but that component is absent from the generated coordinate model, leaving the structure composition incomplete.
1	8	`2rgz__assembly_1__model_8`	dimeric （2）	Excluded	—	—
	Exclusion reason： The official assembly declares water, but that component is absent from the generated coordinate model, leaving the structure composition incomplete.
1	9	`2rgz__assembly_1__model_9`	dimeric （2）	Excluded	—	—
	Exclusion reason： The official assembly declares water, but that component is absent from the generated coordinate model, leaving the structure composition incomplete.
1	10	`2rgz__assembly_1__model_10`	dimeric （2）	Excluded	—	—
	Exclusion reason： The official assembly declares water, but that component is absent from the generated coordinate model, leaving the structure composition incomplete.
1	11	`2rgz__assembly_1__model_11`	dimeric （2）	Excluded	—	—
	Exclusion reason： The official assembly declares water, but that component is absent from the generated coordinate model, leaving the structure composition incomplete.
1	12	`2rgz__assembly_1__model_12`	dimeric （2）	Excluded	—	—
	Exclusion reason： The official assembly declares water, but that component is absent from the generated coordinate model, leaving the structure composition incomplete.
1	13	`2rgz__assembly_1__model_13`	dimeric （2）	Excluded	—	—
	Exclusion reason： The official assembly declares water, but that component is absent from the generated coordinate model, leaving the structure composition incomplete.
1	14	`2rgz__assembly_1__model_14`	dimeric （2）	Excluded	—	—
	Exclusion reason： The official assembly declares water, but that component is absent from the generated coordinate model, leaving the structure composition incomplete.
1	15	`2rgz__assembly_1__model_15`	dimeric （2）	Excluded	—	—
	Exclusion reason： The official assembly declares water, but that component is absent from the generated coordinate model, leaving the structure composition incomplete.
1	16	`2rgz__assembly_1__model_16`	dimeric （2）	Excluded	—	—
	Exclusion reason： The official assembly declares water, but that component is absent from the generated coordinate model, leaving the structure composition incomplete.
2	1	`2rgz__assembly_2__model_1`	monomeric （1）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	2	`2rgz__assembly_2__model_2`	monomeric （1）	Excluded	—	—
	Exclusion reason： The official assembly declares water, but that component is absent from the generated coordinate model, leaving the structure composition incomplete.
2	3	`2rgz__assembly_2__model_3`	monomeric （1）	Excluded	—	—
	Exclusion reason： The official assembly declares water, but that component is absent from the generated coordinate model, leaving the structure composition incomplete.
2	4	`2rgz__assembly_2__model_4`	monomeric （1）	Excluded	—	—
	Exclusion reason： The official assembly declares water, but that component is absent from the generated coordinate model, leaving the structure composition incomplete.
2	5	`2rgz__assembly_2__model_5`	monomeric （1）	Excluded	—	—
	Exclusion reason： The official assembly declares water, but that component is absent from the generated coordinate model, leaving the structure composition incomplete.
2	6	`2rgz__assembly_2__model_6`	monomeric （1）	Excluded	—	—
	Exclusion reason： The official assembly declares water, but that component is absent from the generated coordinate model, leaving the structure composition incomplete.
2	7	`2rgz__assembly_2__model_7`	monomeric （1）	Excluded	—	—
	Exclusion reason： The official assembly declares water, but that component is absent from the generated coordinate model, leaving the structure composition incomplete.
2	8	`2rgz__assembly_2__model_8`	monomeric （1）	Excluded	—	—
	Exclusion reason： The official assembly declares water, but that component is absent from the generated coordinate model, leaving the structure composition incomplete.
2	9	`2rgz__assembly_2__model_9`	monomeric （1）	Excluded	—	—
	Exclusion reason： The official assembly declares water, but that component is absent from the generated coordinate model, leaving the structure composition incomplete.
2	10	`2rgz__assembly_2__model_10`	monomeric （1）	Excluded	—	—
	Exclusion reason： The official assembly declares water, but that component is absent from the generated coordinate model, leaving the structure composition incomplete.
2	11	`2rgz__assembly_2__model_11`	monomeric （1）	Excluded	—	—
	Exclusion reason： The official assembly declares water, but that component is absent from the generated coordinate model, leaving the structure composition incomplete.
2	12	`2rgz__assembly_2__model_12`	monomeric （1）	Excluded	—	—
	Exclusion reason： The official assembly declares water, but that component is absent from the generated coordinate model, leaving the structure composition incomplete.
2	13	`2rgz__assembly_2__model_13`	monomeric （1）	Excluded	—	—
	Exclusion reason： The official assembly declares water, but that component is absent from the generated coordinate model, leaving the structure composition incomplete.
2	14	`2rgz__assembly_2__model_14`	monomeric （1）	Excluded	—	—
	Exclusion reason： The official assembly declares water, but that component is absent from the generated coordinate model, leaving the structure composition incomplete.
2	15	`2rgz__assembly_2__model_15`	monomeric （1）	Excluded	—	—
	Exclusion reason： The official assembly declares water, but that component is absent from the generated coordinate model, leaving the structure composition incomplete.
2	16	`2rgz__assembly_2__model_16`	monomeric （1）	Excluded	—	—
	Exclusion reason： The official assembly declares water, but that component is absent from the generated coordinate model, leaving the structure composition incomplete.
3	1	`2rgz__assembly_3__model_1`	monomeric （1）	Success	4.1.3-1-20251215 (887e7ef)	View Download
3	2	`2rgz__assembly_3__model_2`	monomeric （1）	Excluded	—	—
	Exclusion reason： The official assembly declares water, but that component is absent from the generated coordinate model, leaving the structure composition incomplete.
3	3	`2rgz__assembly_3__model_3`	monomeric （1）	Excluded	—	—
	Exclusion reason： The official assembly declares water, but that component is absent from the generated coordinate model, leaving the structure composition incomplete.
3	4	`2rgz__assembly_3__model_4`	monomeric （1）	Excluded	—	—
	Exclusion reason： The official assembly declares water, but that component is absent from the generated coordinate model, leaving the structure composition incomplete.
3	5	`2rgz__assembly_3__model_5`	monomeric （1）	Excluded	—	—
	Exclusion reason： The official assembly declares water, but that component is absent from the generated coordinate model, leaving the structure composition incomplete.
3	6	`2rgz__assembly_3__model_6`	monomeric （1）	Excluded	—	—
	Exclusion reason： The official assembly declares water, but that component is absent from the generated coordinate model, leaving the structure composition incomplete.
3	7	`2rgz__assembly_3__model_7`	monomeric （1）	Excluded	—	—
	Exclusion reason： The official assembly declares water, but that component is absent from the generated coordinate model, leaving the structure composition incomplete.
3	8	`2rgz__assembly_3__model_8`	monomeric （1）	Excluded	—	—
	Exclusion reason： The official assembly declares water, but that component is absent from the generated coordinate model, leaving the structure composition incomplete.
3	9	`2rgz__assembly_3__model_9`	monomeric （1）	Excluded	—	—
	Exclusion reason： The official assembly declares water, but that component is absent from the generated coordinate model, leaving the structure composition incomplete.
3	10	`2rgz__assembly_3__model_10`	monomeric （1）	Excluded	—	—
	Exclusion reason： The official assembly declares water, but that component is absent from the generated coordinate model, leaving the structure composition incomplete.
3	11	`2rgz__assembly_3__model_11`	monomeric （1）	Excluded	—	—
	Exclusion reason： The official assembly declares water, but that component is absent from the generated coordinate model, leaving the structure composition incomplete.
3	12	`2rgz__assembly_3__model_12`	monomeric （1）	Excluded	—	—
	Exclusion reason： The official assembly declares water, but that component is absent from the generated coordinate model, leaving the structure composition incomplete.
3	13	`2rgz__assembly_3__model_13`	monomeric （1）	Excluded	—	—
	Exclusion reason： The official assembly declares water, but that component is absent from the generated coordinate model, leaving the structure composition incomplete.
3	14	`2rgz__assembly_3__model_14`	monomeric （1）	Excluded	—	—
	Exclusion reason： The official assembly declares water, but that component is absent from the generated coordinate model, leaving the structure composition incomplete.
3	15	`2rgz__assembly_3__model_15`	monomeric （1）	Excluded	—	—
	Exclusion reason： The official assembly declares water, but that component is absent from the generated coordinate model, leaving the structure composition incomplete.
3	16	`2rgz__assembly_3__model_16`	monomeric （1）	Excluded	—	—
	Exclusion reason： The official assembly declares water, but that component is absent from the generated coordinate model, leaving the structure composition incomplete.

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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	Heme oxygenase 2
Molecular weight formula_weight	30491.3 kDa
EC 编号 ec_number	1.14.99.3
Mutation mutation	C127A
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	58291

MSAEVETSEGVDESEKKNSGALEKENQMRMADLSELLKEGTKEAHDRAENTQFVKDFLKGNIKKELFKLATTALYFTYSALEEEMERNKDHPAFAPLYFPMELHRKEALTKDMEYFFGENWEEQVQAPKAAQKYVERIHYIGQNEPELLVAHAYTRYMGDLSGGQVLKKVAQRALKLPSTGEGTQFYLFENVDNAQQFKQLYRARMNALDLNMKTKERIVEEANKAFEYNMQIFNELDQAGSTLARETLEDGFPVHDGKGDMRK

Source Source

Source organism organism	Homo sapiens
Common name common_name	human
NCBI taxonomy ID ncbi_taxonomy_id	9606
Host organism host_organism	Escherichia coli BL21(DE3)

Entity 2 Entity 2 non-polymer

Description description	PROTOPORPHYRIN IX CONTAINING FE
Molecular weight formula_weight	616.5 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 3 Entity 3 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	83

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6. Fold Classification (SCOP + CATH) 4 domains

SCOP 2.08 (2 domains)

Domain ID domain_id	d2rgza_
Class class	a — All alpha proteins
Fold Fold fold	a.132 — Heme oxygenase-like
Superfamily Superfamily superfamily	a.132.1 — Heme oxygenase-like
Family Family family	a.132.1.0 — automated matches

Domain ID domain_id	d2rgzb_
Class class	a — All alpha proteins
Fold Fold fold	a.132 — Heme oxygenase-like
Superfamily Superfamily superfamily	a.132.1 — Heme oxygenase-like
Family Family family	a.132.1.0 — automated matches

CATH v4.4 (2 domains)

Domain ID domain_id	2rgzA00
Class class	1 — Mainly Alpha
Architecture architecture	20 — Up-down Bundle
Topology topology	910 — Heme Oxygenase; Chain A
Homologous superfamily homologous superfamily	10 — Heme oxygenase-like

Domain ID domain_id	2rgzB00
Class class	1 — Mainly Alpha
Architecture architecture	20 — Up-down Bundle
Topology topology	910 — Heme Oxygenase; Chain A
Homologous superfamily homologous superfamily	10 — Heme oxygenase-like

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Unit-cell length a length_a	74.977 Å
Unit-cell length b length_b	85.094 Å
Unit-cell length c length_c	97.846 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	2.610 Å
Low-resolution limit resolution_low	39.020 Å
R factor r_factor	—
R_work r_work	0.1610
R_free r_free	0.2490

Ensemble refinement of the protein crystal structure of human heme oxygenase-2 C127A (HO-2) with bound heme

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

Heme oxygenase 2

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

2rgz__assembly_1__model_1

2rgz__assembly_1__model_1 | I(q)

2rgz__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) 4 domains

SCOP 2.08 (2 domains)

CATH v4.4 (2 domains)

7. Citations (1)

Ensemble refinement of the protein crystal structure of human heme oxygenase-2 C127A (HO-2) with bound heme

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

Heme oxygenase 2

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

2rgz__assembly_1__model_1

2rgz__assembly_1__model_1 | I(q)

2rgz__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) 4 domains

SCOP 2.08 (2 domains)

CATH v4.4 (2 domains)

7. Citations (1)