SAXSdb — 3f9u

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

Putative exported cytochrome C biogenesis-related protein

Bacteroides fragilis NCTC 9343

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein homooligomer	Homooligomer	Protein 2	NITRATE ION × 5 1,2-ETHANEDIOL × 2 water × 2	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	Q5LAZ4_BACFN
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 4–172； UniProt 501–669 Author chain B； PDBConstruct 4–172； UniProt 501–669

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	3f9u
Deposition date deposition_date	2008-11-14
Structure title title	Crystal structure of C-terminal domain of putative exported cytochrome C biogenesis-related protein from Bacteroides fragilis
Keywords keywords	;exported cytochrome C biogenesis-related protein, Bacteroides fragilis, Structural Genomics, PSI-2, Protein Structure Initiative, Midwest Center for Structural Genomics, MCSG, unknown function ;; structural genomics, unknown function
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.

3f9u__assembly_1__model_1

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

Download this curve (.dat)

3f9u__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

3f9u__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)	20.47 Å
Total Rg	21.37 Å
Atom count	2412
Residues	285
Excluded volume	42772 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`3f9u__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 (4)

Entity 1 Entity 1 polymer

Description description	Putative exported cytochrome C biogenesis-related protein
Molecular weight formula_weight	19984.8 kDa
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B
Atom count atom_count	2657

SNAGAPLKAVSAFAPPMKTQDFNLYTNEVHAKFDDYDLGMEYARQHNKPVMLDFTGYGCVNCRKMELAVWTDPKVSSIINNDYVLITLYVDNKTPLTEPVKIMENGTERTLRTVGDKWSYLQRVKFGANAQPFYVLIDNEGNPLNKSYAYDEDISKYINFLQTGLENYRKEK

Source Source

Source organism organism	Bacteroides fragilis NCTC 9343
NCBI taxonomy ID ncbi_taxonomy_id	272559
Host organism host_organism	Escherichia coli

Entity 2 Entity 2 non-polymer

Description description	NITRATE ION
Molecular weight formula_weight	62.0 kDa
Source method src_method	syn
Copy count entity_count	5

Entity 3 Entity 3 non-polymer

Description description	1,2-ETHANEDIOL
Molecular weight formula_weight	62.1 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 4 Entity 4 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	189

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6. Fold Classification (SCOP + CATH) 2 domains

CATH v4.4 (2 domains)

Domain ID domain_id	3f9uA00
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	30 — Glutaredoxin
Homologous superfamily homologous superfamily	10 — Glutaredoxin

Domain ID domain_id	3f9uB00
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	30 — Glutaredoxin
Homologous superfamily homologous superfamily	10 — Glutaredoxin

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Unit-cell length a length_a	64.160 Å
Unit-cell length b length_b	64.160 Å
Unit-cell length c length_c	181.555 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 43 21 2
Space-group number int_tables_number	96
Crystal system crystal_system	—

Resolution resolution	2.200 Å
Low-resolution limit resolution_low	50.000 Å
R factor r_factor	0.1835
R_work r_work	0.1807
R_free r_free	0.2357

Crystal structure of C-terminal domain of putative exported cytochrome C biogenesis-related protein from Bacteroides fragilis

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

Putative exported cytochrome C biogenesis-related protein

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

3f9u__assembly_1__model_1

3f9u__assembly_1__model_1 | I(q)

3f9u__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 (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) 2 domains

CATH v4.4 (2 domains)

7. Citations (1)

Crystal structure of C-terminal domain of putative exported cytochrome C biogenesis-related protein from Bacteroides fragilis

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

Putative exported cytochrome C biogenesis-related protein

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

3f9u__assembly_1__model_1

3f9u__assembly_1__model_1 | I(q)

3f9u__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 (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) 2 domains

CATH v4.4 (2 domains)

7. Citations (1)