SAXSdb — 3bnf

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

Cytochrome c-552

OrganismNot specified

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein homooligomer	Homooligomer	Protein 2	CALCIUM ION × 2 SULFITE ION × 2 YTTRIUM ION × 6 ACETATE ION × 4 PROTOPORPHYRIN IX CONTAINING FE × 10 water × 2	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	NRFA_WOLSU
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–485； UniProt 23–507

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	3bnf
Deposition date deposition_date	2007-12-14
Structure title title	W. succinogenes NrfA Sulfite Complex
Keywords keywords	;c-type cytochrome, nitrite reductase, sulfite complex, Calcium, Electron transport, Heme, Iron, Metal-binding, Oxidoreductase, Periplasm, Transport ;; 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.

3bnf__assembly_1__model_1

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

Download this curve (.dat)

3bnf__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

3bnf__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	32.94 Å
Rg (electron density)	32.55 Å
Total Rg	33.08 Å
Atom count	8005
Residues	942
Excluded volume	142520 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`3bnf__assembly_1__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 (7)

Entity 1 Entity 1 polymer

Description description	Cytochrome c-552
Molecular weight formula_weight	55343.6 kDa
EC 编号 ec_number	1.7.2.2
Source method src_method	nat
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A
Atom count atom_count	4685

SNINEREKERVALNKTAHSQGIEGKAMSEEWARYYPRQFDSWKKTKESDNITDMLKEKPALVVAWAGYPFSKDYNAPRGHYYALQDNINTLRTGAPVDGKTGPLPSACWTCKSPDVPRIIEQDGELEYFTGKWAKYGDEIVNTIGCYNCHDDKSAELKSKVPYLDRGLSAAGFKTFAESTHQEKRSLVCAQCHVEYYFKKTEWKDDKGVDKTAMVVTLPWSKGISTEQMEAYYDEINFADWTHGISKTPMLKAQHPDWELYKTGIHGQKGVSCADCHMPYTQEGAVKYSDHKVGNPLDNMDKSCMNCHRESEQKLKDIVKQKFERKEFLQDIAFDNIGKAHLETGKAMELGATDAELKEIRTHIRHAQWRADMAIAGHGSFFHAPEEVLRLLASGNEEAQKARIKLVKVLAKYGAIDYVAPDFETKEKAQKLAKVDMEAFIAEKLKFKQTLEQEWKKQAIAKGRLNPESLKGVDEKSSYYDKTKK

Entity 2 Entity 2 non-polymer

Description description	CALCIUM ION
Molecular weight formula_weight	40.1 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 3 Entity 3 non-polymer

Description description	SULFITE ION
Molecular weight formula_weight	80.1 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 4 Entity 4 non-polymer

Description description	YTTRIUM ION
Molecular weight formula_weight	88.9 kDa
Source method src_method	syn
Copy count entity_count	3

Entity 5 Entity 5 non-polymer

Description description	ACETATE ION
Molecular weight formula_weight	59.0 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 6 Entity 6 non-polymer

Description description	PROTOPORPHYRIN IX CONTAINING FE
Molecular weight formula_weight	616.5 kDa
Source method src_method	syn
Copy count entity_count	5

Entity 7 Entity 7 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	639

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6. Fold Classification (SCOP + CATH) 3 domains

SCOP 2.08 (1 domains)

Domain ID domain_id	d3bnfa_
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 (2 domains)

Domain ID domain_id	3bnfA01
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	3bnfA02
Class class	1 — Mainly Alpha
Architecture architecture	20 — Up-down Bundle
Topology topology	140 — Butyryl-CoA Dehydrogenase, subunit A; domain 3
Homologous superfamily homologous superfamily	10 — Butyryl-CoA Dehydrogenase, subunit A, domain 3

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Unit-cell length a length_a	119.500 Å
Unit-cell length b length_b	119.500 Å
Unit-cell length c length_c	186.674 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	I 41 2 2
Space-group number int_tables_number	98
Crystal system crystal_system	—

Resolution resolution	1.700 Å
Low-resolution limit resolution_low	22.310 Å
R factor r_factor	0.2350
R_work r_work	0.2327
R_free r_free	0.2795

W. succinogenes NrfA Sulfite Complex

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

Cytochrome c-552

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

3bnf__assembly_1__model_1

3bnf__assembly_1__model_1 | I(q)

3bnf__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 (7)

Entity 1 Entity 1 polymer

Polymer Polymer

Entity 2 Entity 2 non-polymer

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 non-polymer

Entity 5 Entity 5 non-polymer

Entity 6 Entity 6 non-polymer

Entity 7 Entity 7 water

6. Fold Classification (SCOP + CATH) 3 domains

SCOP 2.08 (1 domains)

CATH v4.4 (2 domains)

7. Citations (1)

W. succinogenes NrfA Sulfite Complex

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

Cytochrome c-552

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

3bnf__assembly_1__model_1

3bnf__assembly_1__model_1 | I(q)

3bnf__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 (7)

Entity 1 Entity 1 polymer

Polymer Polymer

Entity 2 Entity 2 non-polymer

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 non-polymer

Entity 5 Entity 5 non-polymer

Entity 6 Entity 6 non-polymer

Entity 7 Entity 7 water

6. Fold Classification (SCOP + CATH) 3 domains

SCOP 2.08 (1 domains)

CATH v4.4 (2 domains)

7. Citations (1)