SAXSdb — 6cvd

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

Signal recognition particle receptor FtsY

Escherichia coli (strain K12)

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein homooligomer	Homooligomer	Protein 2	methyl 1H-indole-4-carboxylate × 4 AMMONIUM ION × 2 SODIUM ION × 1 water × 2	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	FTSY_ECOLI
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 2–303； UniProt 196–497 Author chain B； PDBConstruct 2–303； UniProt 196–497

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	6cvd
Deposition date deposition_date	2018-03-27
Structure title title	High resolution crystal structure of FtsY-NG domain of E. coli bound to fragment 1
Keywords keywords	cotranslational delivery SRP, PROTEIN TRANSPORT; PROTEIN 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.

6cvd__assembly_1__model_1

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

Download this curve (.dat)

6cvd__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

6cvd__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	29.33 Å
Rg (electron density)	28.48 Å
Total Rg	29.13 Å
Atom count	9492
Residues	605
Excluded volume	84373 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`6cvd__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 (5)

Entity 1 Entity 1 polymer

Description description	Signal recognition particle receptor FtsY
Molecular weight formula_weight	33101.0 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	9883

GFARLKRSLLKTKENLGSGFISLFRGKKIDDDLFEELEEQLLIADVGVETTRKIITNLTEGASRKQLRDAEALYGLLKEEMGEILAKVDEPLNVEGKAPFVILMVGVNGVGKTTTIGKLARQFEQQGKSVMLAAGDTFRAAAVEQLQVWGQRNNIPVIAQHTGADSASVIFDAIQAAKARNIDVLIADTAGRLQNKSHLMEELKKIVRVMKKLDVEAPHEVMLTIDASTGQNAVSQAKLFHEAVGLTGITLTKLDGTAKGGVIFSVADQFGIPIRYIGVGERIEDLRPFKADDFIEALFARED

Source Source

Source organism organism	Escherichia coli (strain K12)
NCBI taxonomy ID ncbi_taxonomy_id	83333
Host organism host_organism	;Escherichia coli 'BL21-Gold(DE3)pLysS AG' ;

Entity 2 Entity 2 non-polymer

Description description	methyl 1H-indole-4-carboxylate
Molecular weight formula_weight	175.2 kDa
Source method src_method	syn
Copy count entity_count	4

Entity 3 Entity 3 non-polymer

Description description	AMMONIUM ION
Molecular weight formula_weight	18.0 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 4 Entity 4 non-polymer

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

Entity 5 Entity 5 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	358

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6. Fold Classification (SCOP + CATH) 10 domains

SCOP 2.08 (6 domains)

Domain ID domain_id	d6cvda1
Class class	a — All alpha proteins
Fold Fold fold	a.24 — Four-helical up-and-down bundle
Superfamily Superfamily superfamily	a.24.13 — Domain of the SRP/SRP receptor G-proteins
Family Family family	a.24.13.0 — automated matches

Domain ID domain_id	d6cvda2
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.37 — P-loop containing nucleoside triphosphate hydrolases
Superfamily Superfamily superfamily	c.37.1 — P-loop containing nucleoside triphosphate hydrolases
Family Family family	c.37.1.10 — Nitrogenase iron protein-like

Domain ID domain_id	d6cvda3
Class class	l — Artifacts
Fold Fold fold	l.1 — Tags
Superfamily Superfamily superfamily	l.1.1 — Tags
Family Family family	l.1.1.1 — Tags

Domain ID domain_id	d6cvdb1
Class class	a — All alpha proteins
Fold Fold fold	a.24 — Four-helical up-and-down bundle
Superfamily Superfamily superfamily	a.24.13 — Domain of the SRP/SRP receptor G-proteins
Family Family family	a.24.13.0 — automated matches

Domain ID domain_id	d6cvdb2
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.37 — P-loop containing nucleoside triphosphate hydrolases
Superfamily Superfamily superfamily	c.37.1 — P-loop containing nucleoside triphosphate hydrolases
Family Family family	c.37.1.10 — Nitrogenase iron protein-like

Domain ID domain_id	d6cvdb3
Class class	l — Artifacts
Fold Fold fold	l.1 — Tags
Superfamily Superfamily superfamily	l.1.1 — Tags
Family Family family	l.1.1.1 — Tags

CATH v4.4 (4 domains)

Domain ID domain_id	6cvdA01
Class class	1 — Mainly Alpha
Architecture architecture	20 — Up-down Bundle
Topology topology	120 — Four Helix Bundle (Hemerythrin (Met), subunit A)
Homologous superfamily homologous superfamily	140 — SRP54, nucleotide-binding domain

Domain ID domain_id	6cvdA02
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	300 — P-loop containing nucleotide triphosphate hydrolases

Domain ID domain_id	6cvdB01
Class class	1 — Mainly Alpha
Architecture architecture	20 — Up-down Bundle
Topology topology	120 — Four Helix Bundle (Hemerythrin (Met), subunit A)
Homologous superfamily homologous superfamily	140 — SRP54, nucleotide-binding domain

Domain ID domain_id	6cvdB02
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	300 — P-loop containing nucleotide triphosphate hydrolases

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Unit-cell length a length_a	34.341 Å
Unit-cell length b length_b	76.008 Å
Unit-cell length c length_c	108.032 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	90.42 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	4

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

Resolution resolution	1.780 Å
Low-resolution limit resolution_low	36.010 Å
R factor r_factor	0.2045
R_work r_work	0.2022
R_free r_free	0.2515

High resolution crystal structure of FtsY-NG domain of E. coli bound to fragment 1

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

Signal recognition particle receptor FtsY

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

6cvd__assembly_1__model_1

6cvd__assembly_1__model_1 | I(q)

6cvd__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 (5)

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 water

6. Fold Classification (SCOP + CATH) 10 domains

SCOP 2.08 (6 domains)

CATH v4.4 (4 domains)

7. Citations (1)

High resolution crystal structure of FtsY-NG domain of E. coli bound to fragment 1

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

Signal recognition particle receptor FtsY

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

6cvd__assembly_1__model_1

6cvd__assembly_1__model_1 | I(q)

6cvd__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 (5)

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 water

6. Fold Classification (SCOP + CATH) 10 domains

SCOP 2.08 (6 domains)

CATH v4.4 (4 domains)

7. Citations (1)