SAXSdb — 2i89

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

Cytochrome b5 type B

Rattus norvegicus

State in the Current Structure

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

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	CYB5B_RAT
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 3–93； UniProt 12–103 Author chain B； PDBConstruct 3–93； UniProt 12–103 Author chain C； PDBConstruct 2–93； UniProt 12–103 Author chain D； PDBConstruct 2–93； UniProt 12–103

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	2i89
Deposition date deposition_date	2006-09-01
Structure title title	Structure of septuple mutant of Rat Outer Mitochondrial Membrane Cytochrome B5
Keywords keywords	CYTOCHROME B5, HEME, ELECTRON TRANSPORT; ELECTRON 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.

2i89__assembly_4__model_1

Assembly 4 · Model 1 · CRYSOL 4.1.3-1-20251215 (887e7ef)

Download this curve (.dat)

2i89__assembly_4__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

2i89__assembly_4__model_1 | P(r) · Pending

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

Rg（Guinier）	13.96 Å
Rg (electron density)	12.60 Å
Total Rg	13.96 Å
Atom count	727
Residues	85
Excluded volume	12684 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`2i89__assembly_1__model_1`	monomeric （1）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`2i89__assembly_2__model_1`	monomeric （1）	Success	4.1.3-1-20251215 (887e7ef)	View Download
3	1	`2i89__assembly_3__model_1`	monomeric （1）	Success	4.1.3-1-20251215 (887e7ef)	View Download
4	1	`2i89__assembly_4__model_1`	monomeric （1）	Success	4.1.3-1-20251215 (887e7ef)	View Download
5	1	`2i89__assembly_5__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 (4)

Entity 1 Entity 1 polymer

Description description	Cytochrome b5 type B
Molecular weight formula_weight	10494.4 kDa
Mutation mutation	R15H/A18S/E20S/I25L/I32L/L47R/L71S
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	3369

MNGQGSDPAVTYYRLEEVAKHNTSESTWMVLHGRVYDLTRFLSEHPGGEEVLREQAGADATESFEDVGHSPDAREMSKQYYIGDVHPNDLKPK

Source Source

Source organism organism	Rattus norvegicus
Common name common_name	Norway rat
NCBI taxonomy ID ncbi_taxonomy_id	10116
Host organism host_organism	Escherichia coli BL21

Entity 2 Entity 2 non-polymer

Description description	MAGNESIUM ION
Molecular weight formula_weight	24.3 kDa
Source method src_method	syn
Copy count entity_count	3

Entity 3 Entity 3 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 4 Entity 4 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	212

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6. Fold Classification (SCOP + CATH) 8 domains

SCOP 2.08 (4 domains)

Domain ID domain_id	d2i89a_
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.120 — Cytochrome b5-like heme/steroid binding domain
Superfamily Superfamily superfamily	d.120.1 — Cytochrome b5-like heme/steroid binding domain
Family Family family	d.120.1.1 — Cytochrome b5

Domain ID domain_id	d2i89b_
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.120 — Cytochrome b5-like heme/steroid binding domain
Superfamily Superfamily superfamily	d.120.1 — Cytochrome b5-like heme/steroid binding domain
Family Family family	d.120.1.1 — Cytochrome b5

Domain ID domain_id	d2i89c_
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.120 — Cytochrome b5-like heme/steroid binding domain
Superfamily Superfamily superfamily	d.120.1 — Cytochrome b5-like heme/steroid binding domain
Family Family family	d.120.1.1 — Cytochrome b5

Domain ID domain_id	d2i89d_
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.120 — Cytochrome b5-like heme/steroid binding domain
Superfamily Superfamily superfamily	d.120.1 — Cytochrome b5-like heme/steroid binding domain
Family Family family	d.120.1.1 — Cytochrome b5

CATH v4.4 (4 domains)

Domain ID domain_id	2i89A00
Class class	3 — Alpha Beta
Architecture architecture	10 — Roll
Topology topology	120 — Flavocytochrome B2; Chain A, domain 1
Homologous superfamily homologous superfamily	10 — Cytochrome b5-like heme/steroid binding domain

Domain ID domain_id	2i89B00
Class class	3 — Alpha Beta
Architecture architecture	10 — Roll
Topology topology	120 — Flavocytochrome B2; Chain A, domain 1
Homologous superfamily homologous superfamily	10 — Cytochrome b5-like heme/steroid binding domain

Domain ID domain_id	2i89C00
Class class	3 — Alpha Beta
Architecture architecture	10 — Roll
Topology topology	120 — Flavocytochrome B2; Chain A, domain 1
Homologous superfamily homologous superfamily	10 — Cytochrome b5-like heme/steroid binding domain

Domain ID domain_id	2i89D00
Class class	3 — Alpha Beta
Architecture architecture	10 — Roll
Topology topology	120 — Flavocytochrome B2; Chain A, domain 1
Homologous superfamily homologous superfamily	10 — Cytochrome b5-like heme/steroid binding domain

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Unit-cell length a length_a	39.965 Å
Unit-cell length b length_b	51.409 Å
Unit-cell length c length_c	167.435 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	16

Space group space_group	P 21 21 21
Space-group number int_tables_number	19
Crystal system crystal_system	—

Resolution resolution	2.100 Å
Low-resolution limit resolution_low	50.000 Å
R factor r_factor	0.2080
R_work r_work	0.2080
R_free r_free	0.2780

Structure of septuple mutant of Rat Outer Mitochondrial Membrane Cytochrome B5

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

Cytochrome b5 type B

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

2i89__assembly_4__model_1

2i89__assembly_4__model_1 | I(q)

2i89__assembly_4__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 (4)

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 water

6. Fold Classification (SCOP + CATH) 8 domains

SCOP 2.08 (4 domains)

CATH v4.4 (4 domains)

7. Citations (1)

Structure of septuple mutant of Rat Outer Mitochondrial Membrane Cytochrome B5

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

Cytochrome b5 type B

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

2i89__assembly_4__model_1

2i89__assembly_4__model_1 | I(q)

2i89__assembly_4__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 (4)

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 water

6. Fold Classification (SCOP + CATH) 8 domains

SCOP 2.08 (4 domains)

CATH v4.4 (4 domains)

7. Citations (1)