SAXSdb — 3zh0

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

PROTOGLOBIN

METHANOSARCINA ACETIVORANS C2A

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 FORMIC ACID × 2 GLYCEROL × 3 water × 2	Consistent with protein count
2	Protein homooligomer	Homooligomer	Protein 2	PROTOPORPHYRIN IX CONTAINING FE × 2 FORMIC ACID × 2 GLYCEROL × 5 water × 2	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	Q8TLY9_METAC
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 2–176； UniProt 21–195 Author chain B； PDBConstruct 2–176； UniProt 21–195 Author chain C； PDBConstruct 2–176； UniProt 21–195 Author chain D； PDBConstruct 2–176； UniProt 21–195

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	3zh0
Deposition date deposition_date	2012-12-19
Structure title title	Functional and structural role of the N-terminal extension in Methanosarcina acetivorans protoglobin
Keywords keywords	OXYGEN TRANSPORT, SPECTROSCOPIC PROPERTIES, LIGAND BINDING PROPERTIES, N-TERMINAL TRIMMING.; OXYGEN TRANSPORT
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.

3zh0__assembly_1__model_1

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

Download this curve (.dat)

3zh0__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

3zh0__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	21.40 Å
Rg (electron density)	19.85 Å
Total Rg	20.91 Å
Atom count	3066
Residues	352
Excluded volume	54680 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`3zh0__assembly_1__model_1`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`3zh0__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	PROTOGLOBIN
Molecular weight formula_weight	20868.5 kDa
Mutation mutation	YES
Source method src_method	man
Copy count entity_count	4

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B,C,D
Atom count atom_count	6708

MNLEDLKLLKEAVMFTAEDEEYIQKAGEVLEDQVEEILDTWYGFVGSHPHLLYYFTSPDGTPNEKYLAAVRKRFSRWILDTSNRSYDQAWLDYQYEIGLRHHRTKKNQTDNVESVPNIGYRYLVAFIYPITATMKPFLARKGHTPEEVEKMYQAWFKATTLQVALWSYPYVKYGDF

Source Source

Source organism organism	METHANOSARCINA ACETIVORANS C2A
NCBI taxonomy ID ncbi_taxonomy_id	188937
Host organism host_organism	ESCHERICHIA COLI

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	4

Entity 3 Entity 3 non-polymer

Description description	FORMIC ACID
Molecular weight formula_weight	46.0 kDa
Source method src_method	syn
Copy count entity_count	4

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 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	484

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6. Fold Classification (SCOP + CATH) 4 domains

CATH v4.4 (4 domains)

Domain ID domain_id	3zh0A00
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	490 — Globin-like
Homologous superfamily homologous superfamily	10 — Globins

Domain ID domain_id	3zh0B00
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	490 — Globin-like
Homologous superfamily homologous superfamily	10 — Globins

Domain ID domain_id	3zh0C00
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	490 — Globin-like
Homologous superfamily homologous superfamily	10 — Globins

Domain ID domain_id	3zh0D00
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	490 — Globin-like
Homologous superfamily homologous superfamily	10 — Globins

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Unit-cell length a length_a	80.670 Å
Unit-cell length b length_b	48.620 Å
Unit-cell length c length_c	92.030 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	92.61 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	8

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

Resolution resolution	2.000 Å
Low-resolution limit resolution_low	91.930 Å
R factor r_factor	0.2023
R_work r_work	0.1992
R_free r_free	0.2601

Functional and structural role of the N-terminal extension in Methanosarcina acetivorans protoglobin

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

PROTOGLOBIN

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

3zh0__assembly_1__model_1

3zh0__assembly_1__model_1 | I(q)

3zh0__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

6. Fold Classification (SCOP + CATH) 4 domains

CATH v4.4 (4 domains)

7. Citations (1)

Functional and structural role of the N-terminal extension in Methanosarcina acetivorans protoglobin

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

PROTOGLOBIN

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

3zh0__assembly_1__model_1

3zh0__assembly_1__model_1 | I(q)

3zh0__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

6. Fold Classification (SCOP + CATH) 4 domains

CATH v4.4 (4 domains)

7. Citations (1)