1m1p

P21 crystal structure of the tetraheme cytochrome c3 from Shewanella oneidensis MR1

Method: X-RAY DIFFRACTION

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

Small tetraheme cytochrome c

OrganismNot specified

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein monomer	Monomer	Protein 1	SULFATE ION × 1 HEME C × 4 water × 1	Consistent with protein count
10	Protein homooligomer	Homooligomer	Protein 3	SULFATE ION × 1 HEME C × 12 water × 3	Consistent with protein count
11	Protein homooligomer	Homooligomer	Protein 2	SULFATE ION × 1 HEME C × 8 water × 2	Consistent with protein count
12	Protein homooligomer	Homooligomer	Protein 2	HEME C × 8 water × 2	Consistent with protein count
13	Protein homooligomer	Homooligomer	Protein 2	SULFATE ION × 1 HEME C × 8 water × 2	Consistent with protein count
2	Protein monomer	Monomer	Protein 1	SULFATE ION × 1 HEME C × 4 water × 1	Consistent with protein count
3	Protein monomer	Monomer	Protein 1	SULFATE ION × 1 HEME C × 4 water × 1	Consistent with protein count
4	Protein monomer	Monomer	Protein 1	HEME C × 4 water × 1	Consistent with protein count
5	Protein monomer	Monomer	Protein 1	HEME C × 4 water × 1	Consistent with protein count
6	Protein monomer	Monomer	Protein 1	SULFATE ION × 1 HEME C × 4 water × 1	Consistent with protein count
7	Protein homooligomer	Homooligomer	Protein 5	SULFATE ION × 3 HEME C × 20 water × 5	Consistent with protein count
8	Protein homooligomer	Homooligomer	Protein 5	SULFATE ION × 3 HEME C × 20 water × 5	Consistent with protein count
9	Protein homooligomer	Homooligomer	Protein 4	SULFATE ION × 2 HEME C × 16 water × 4	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	Q8EDL6_SHEON
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–91； UniProt 26–116 Author chain B； PDBConstruct 1–91； UniProt 26–116 Author chain C； PDBConstruct 1–91； UniProt 26–116 Author chain D； PDBConstruct 1–91； UniProt 26–116 Author chain E； PDBConstruct 1–91； UniProt 26–116 Author chain F； PDBConstruct 1–91； UniProt 26–116

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	1m1p
Deposition date deposition_date	2002-06-20
Structure title title	P21 crystal structure of the tetraheme cytochrome c3 from Shewanella oneidensis MR1
Keywords keywords	tetraheme cytochrome c, 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.

1m1p__assembly_4__model_1

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

Download this curve (.dat)

1m1p__assembly_4__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

1m1p__assembly_4__model_1 | P(r) · Pending

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

Rg（Guinier）	14.24 Å
Rg (electron density)	13.11 Å
Total Rg	14.18 Å
Atom count	785
Residues	86
Excluded volume	13721 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`1m1p__assembly_1__model_1`	monomeric （1）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`1m1p__assembly_2__model_1`	monomeric （1）	Success	4.1.3-1-20251215 (887e7ef)	View Download
3	1	`1m1p__assembly_3__model_1`	monomeric （1）	Success	4.1.3-1-20251215 (887e7ef)	View Download
4	1	`1m1p__assembly_4__model_1`	monomeric （1）	Success	4.1.3-1-20251215 (887e7ef)	View Download
5	1	`1m1p__assembly_5__model_1`	monomeric （1）	Success	4.1.3-1-20251215 (887e7ef)	View Download
6	1	`1m1p__assembly_6__model_1`	monomeric （1）	Success	4.1.3-1-20251215 (887e7ef)	View Download
7	1	`1m1p__assembly_7__model_1`	pentameric （5）	Success	4.1.3-1-20251215 (887e7ef)	View Download
8	1	`1m1p__assembly_8__model_1`	pentameric （5）	Success	4.1.3-1-20251215 (887e7ef)	View Download
9	1	`1m1p__assembly_9__model_1`	tetrameric （4）	Success	4.1.3-1-20251215 (887e7ef)	View Download
10	1	`1m1p__assembly_10__model_1`	trimeric （3）	Success	4.1.3-1-20251215 (887e7ef)	View Download
11	1	`1m1p__assembly_11__model_1`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
12	1	`1m1p__assembly_12__model_1`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
13	1	`1m1p__assembly_13__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	Small tetraheme cytochrome c
Molecular weight formula_weight	9673.6 kDa
Source method src_method	nat
Copy count entity_count	6

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B,C,D,E,F
Atom count atom_count	5963

ADQKLSDFHAESGGCESCHKDGTPSADGAFEFAQCQSCHGKLSEMDAVHKPHDGNLVCADCHAVHDMNVGQKPTCESCHDDGRTSASVLKK

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	4

Entity 3 Entity 3 non-polymer

Description description	HEME C
Molecular weight formula_weight	618.5 kDa
Source method src_method	syn
Copy count entity_count	24

Entity 4 Entity 4 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	1161

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6. Fold Classification (SCOP + CATH) 12 domains

SCOP 2.08 (6 domains)

Domain ID domain_id	d1m1pa_
Class class	a — All alpha proteins
Fold Fold fold	a.138 — Multiheme cytochromes
Superfamily Superfamily superfamily	a.138.1 — Multiheme cytochromes
Family Family family	a.138.1.3 — Di-heme elbow motif

Domain ID domain_id	d1m1pb_
Class class	a — All alpha proteins
Fold Fold fold	a.138 — Multiheme cytochromes
Superfamily Superfamily superfamily	a.138.1 — Multiheme cytochromes
Family Family family	a.138.1.3 — Di-heme elbow motif

Domain ID domain_id	d1m1pc_
Class class	a — All alpha proteins
Fold Fold fold	a.138 — Multiheme cytochromes
Superfamily Superfamily superfamily	a.138.1 — Multiheme cytochromes
Family Family family	a.138.1.3 — Di-heme elbow motif

Domain ID domain_id	d1m1pd_
Class class	a — All alpha proteins
Fold Fold fold	a.138 — Multiheme cytochromes
Superfamily Superfamily superfamily	a.138.1 — Multiheme cytochromes
Family Family family	a.138.1.3 — Di-heme elbow motif

Domain ID domain_id	d1m1pe_
Class class	a — All alpha proteins
Fold Fold fold	a.138 — Multiheme cytochromes
Superfamily Superfamily superfamily	a.138.1 — Multiheme cytochromes
Family Family family	a.138.1.3 — Di-heme elbow motif

Domain ID domain_id	d1m1pf_
Class class	a — All alpha proteins
Fold Fold fold	a.138 — Multiheme cytochromes
Superfamily Superfamily superfamily	a.138.1 — Multiheme cytochromes
Family Family family	a.138.1.3 — Di-heme elbow motif

CATH v4.4 (6 domains)

Domain ID domain_id	1m1pA00
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	1130 — Flavocytochrome C3; Chain A, domain 2
Homologous superfamily homologous superfamily	10 — Flavocytochrome C3; Chain A

Domain ID domain_id	1m1pB00
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	1130 — Flavocytochrome C3; Chain A, domain 2
Homologous superfamily homologous superfamily	10 — Flavocytochrome C3; Chain A

Domain ID domain_id	1m1pC00
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	1130 — Flavocytochrome C3; Chain A, domain 2
Homologous superfamily homologous superfamily	10 — Flavocytochrome C3; Chain A

Domain ID domain_id	1m1pD00
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	1130 — Flavocytochrome C3; Chain A, domain 2
Homologous superfamily homologous superfamily	10 — Flavocytochrome C3; Chain A

Domain ID domain_id	1m1pE00
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	1130 — Flavocytochrome C3; Chain A, domain 2
Homologous superfamily homologous superfamily	10 — Flavocytochrome C3; Chain A

Domain ID domain_id	1m1pF00
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	1130 — Flavocytochrome C3; Chain A, domain 2
Homologous superfamily homologous superfamily	10 — Flavocytochrome C3; Chain A

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Unit-cell length a length_a	93.690 Å
Unit-cell length b length_b	34.005 Å
Unit-cell length c length_c	108.313 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	110.49 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	12

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

Resolution resolution	1.550 Å
Low-resolution limit resolution_low	14.920 Å
R factor r_factor	0.1745
R_work r_work	0.1726
R_free r_free	0.2115

P21 crystal structure of the tetraheme cytochrome c3 from Shewanella oneidensis MR1

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

Small tetraheme cytochrome c

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

1m1p__assembly_4__model_1

1m1p__assembly_4__model_1 | I(q)

1m1p__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

Entity 2 Entity 2 non-polymer

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 water

6. Fold Classification (SCOP + CATH) 12 domains

SCOP 2.08 (6 domains)

CATH v4.4 (6 domains)

7. Citations (1)

P21 crystal structure of the tetraheme cytochrome c3 from Shewanella oneidensis MR1

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

Small tetraheme cytochrome c

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

1m1p__assembly_4__model_1

1m1p__assembly_4__model_1 | I(q)

1m1p__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

Entity 2 Entity 2 non-polymer

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 water

6. Fold Classification (SCOP + CATH) 12 domains

SCOP 2.08 (6 domains)

CATH v4.4 (6 domains)

7. Citations (1)