SAXSdb — 1kss

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

flavocytochrome c

Shewanella frigidimarina

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein monomer	Monomer	Protein 1	SODIUM ION × 1 PROTOPORPHYRIN IX CONTAINING FE × 4 FLAVIN-ADENINE DINUCLEOTIDE × 1 FUMARIC ACID × 1 water × 1	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	FRDA_SHEFR
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–571； UniProt 26–596

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	1kss
Deposition date deposition_date	2002-01-14
Structure title title	Crystal Structure of His505Ala Mutant Flavocytochrome c3 from Shewanella frigidimarina
Keywords keywords	flavocytochrome, fumarate reductase, H505A, OXIDOREDUCTASE; 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.

1kss__assembly_1__model_1

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

Download this curve (.dat)

1kss__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

1kss__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	25.37 Å
Rg (electron density)	24.53 Å
Total Rg	25.31 Å
Atom count	4426
Residues	568
Excluded volume	78199 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`1kss__assembly_1__model_1`	monomeric （1）	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 (6)

Entity 1 Entity 1 polymer

Description description	flavocytochrome c
Molecular weight formula_weight	60560.2 kDa
EC 编号 ec_number	1.3.99.1
Mutation mutation	H505A
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A
Atom count atom_count	5523

ADNLAEFHVQNQECDSCHTPDGELSNDSLTYENTQCVSCHGTLAEVAETTKHEHYNAHASHFPGEVACTSCHSAHEKSMVYCDSCHSFDFNMPYAKKWLRDEPTIAELAKDKSERQAALASAPHDTVDVVVVGSGGAGFSAAISATDSGAKVILIEKEPVIGGNAKLAAGGMNAAWTDQQKAKKITDSPELMFEDTMKGGQNINDPALVKVLSSHSKDSVDWMTAMGADLTDVGMMGGASVNRAHRPTGGAGVGAHVVQVLYDNAVKRNIDLRMNTRGIEVLKDDKGTVKGILVKGMYKGYYWVKADAVILATGGFAKNNERVAKLDPSLKGFISTNQPGAVGDGLDVAENAGGALKDMQYIQAHPTLSVKGGVMVTEAVRGNGAILVNREGKRFVNEITTRDKASAAILAQTGKSAYLIFDDSVRKSLSKIDKYIGLGVAPTADSLVKLGKMEGIDGKALTETVARYNSLVSSGKDTDFERPNLPRALNEGNYYAIEVTPGVHATMGGVMIDTKAEVMNAKKQVIPGLYGAGEVTGGVHGANRLGGNAISDIITFGRLAGEEAAKYSKKN

Source Source

Source organism organism	Shewanella frigidimarina
NCBI taxonomy ID ncbi_taxonomy_id	56812
Host organism host_organism	Shewanella frigidimarina

Entity 2 Entity 2 non-polymer

Description description	SODIUM ION
Molecular weight formula_weight	23.0 kDa
Source method src_method	syn
Copy count entity_count	1

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 non-polymer

Description description	FLAVIN-ADENINE DINUCLEOTIDE
Molecular weight formula_weight	785.5 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 5 Entity 5 non-polymer

Description description	FUMARIC ACID
Molecular weight formula_weight	116.1 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 6 Entity 6 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	1097

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6. Fold Classification (SCOP + CATH) 6 domains

SCOP 2.08 (3 domains)

Domain ID domain_id	d1kssa1
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	d1kssa2
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.3 — FAD/NAD(P)-binding domain
Superfamily Superfamily superfamily	c.3.1 — FAD/NAD(P)-binding domain
Family Family family	c.3.1.4 — Succinate dehydrogenase/fumarate reductase flavoprotein N-terminal domain

Domain ID domain_id	d1kssa3
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.168 — Succinate dehydrogenase/fumarate reductase flavoprotein, catalytic domain
Superfamily Superfamily superfamily	d.168.1 — Succinate dehydrogenase/fumarate reductase flavoprotein, catalytic domain
Family Family family	d.168.1.1 — Succinate dehydrogenase/fumarate reductase flavoprotein, catalytic domain

CATH v4.4 (3 domains)

Domain ID domain_id	1kssA01
Class class	3 — Alpha Beta
Architecture architecture	90 — Alpha-Beta Complex
Topology topology	700 — Flavocytochrome C3; Chain A, domain 1
Homologous superfamily homologous superfamily	10 — Succinate dehydrogenase/fumarate reductase flavoprotein, catalytic domain

Domain ID domain_id	1kssA02
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	1kssA03
Class class	3 — Alpha Beta
Architecture architecture	50 — 3-Layer(bba) Sandwich
Topology topology	50 — FAD/NAD(P)-binding domain
Homologous superfamily homologous superfamily	60 — FAD/NAD(P)-binding domain

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Unit-cell length a length_a	45.632 Å
Unit-cell length b length_b	92.798 Å
Unit-cell length c length_c	79.056 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	91.02 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	2

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

Resolution resolution	1.800 Å
Low-resolution limit resolution_low	10.000 Å
R factor r_factor	—
R_work r_work	0.1564
R_free r_free	0.2061

Crystal Structure of His505Ala Mutant Flavocytochrome c3 from Shewanella frigidimarina

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

flavocytochrome 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

1kss__assembly_1__model_1

1kss__assembly_1__model_1 | I(q)

1kss__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 (6)

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 non-polymer

Entity 6 Entity 6 water

6. Fold Classification (SCOP + CATH) 6 domains

SCOP 2.08 (3 domains)

CATH v4.4 (3 domains)

7. Citations (1)

Crystal Structure of His505Ala Mutant Flavocytochrome c3 from Shewanella frigidimarina

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

flavocytochrome 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

1kss__assembly_1__model_1

1kss__assembly_1__model_1 | I(q)

1kss__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 (6)

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 non-polymer

Entity 6 Entity 6 water

6. Fold Classification (SCOP + CATH) 6 domains

SCOP 2.08 (3 domains)

CATH v4.4 (3 domains)

7. Citations (1)