3fif

Crystal structure of the ygdR protein from E.coli. Northeast Structural Genomics target ER382A.

Method: X-RAY DIFFRACTION

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

Uncharacterized lipoprotein ygdR

Escherichia coli K-12

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein monomer	Monomer	Protein 1	water × 1	Consistent with protein count
2	Protein monomer	Monomer	Protein 1	water × 1	Consistent with protein count
3	Protein monomer	Monomer	Protein 1	water × 1	Consistent with protein count
4	Protein monomer	Monomer	Protein 1	water × 1	Consistent with protein count
5	Protein monomer	Monomer	Protein 1	water × 1	Consistent with protein count
6	Protein monomer	Monomer	Protein 1	water × 1	Consistent with protein count
7	Protein monomer	Monomer	Protein 1	water × 1	Consistent with protein count
8	Protein monomer	Monomer	Protein 1	water × 1	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	YGDR_ECOLI
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 2–53； UniProt 21–72 Author chain B； PDBConstruct 2–53； UniProt 21–72 Author chain C； PDBConstruct 2–53； UniProt 21–72 Author chain D； PDBConstruct 2–53； UniProt 21–72 Author chain E； PDBConstruct 2–53； UniProt 21–72 Author chain F； PDBConstruct 2–53； UniProt 21–72 Author chain G； PDBConstruct 2–53； UniProt 21–72 Author chain H； PDBConstruct 2–53； UniProt 21–72

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	3fif
Deposition date deposition_date	2008-12-11
Structure title title	Crystal structure of the ygdR protein from E.coli. Northeast Structural Genomics target ER382A.
Keywords keywords	;ygdR YGDR_ECOLI NESG X-RAY STRUCTURE, Structural Genomics, PSI-2, Protein Structure Initiative, Northeast Structural Genomics Consortium, Cell membrane, Lipoprotein, Membrane, Palmitate, 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.

3fif__assembly_1__model_1

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

Download this curve (.dat)

3fif__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

3fif__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	12.81 Å
Rg (electron density)	11.52 Å
Total Rg	12.52 Å
Atom count	437
Residues	52
Excluded volume	7586 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`3fif__assembly_1__model_1`	monomeric （1）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`3fif__assembly_2__model_1`	monomeric （1）	Success	4.1.3-1-20251215 (887e7ef)	View Download
3	1	`3fif__assembly_3__model_1`	monomeric （1）	Success	4.1.3-1-20251215 (887e7ef)	View Download
4	1	`3fif__assembly_4__model_1`	monomeric （1）	Success	4.1.3-1-20251215 (887e7ef)	View Download
5	1	`3fif__assembly_5__model_1`	monomeric （1）	Success	4.1.3-1-20251215 (887e7ef)	View Download
6	1	`3fif__assembly_6__model_1`	monomeric （1）	Success	4.1.3-1-20251215 (887e7ef)	View Download
7	1	`3fif__assembly_7__model_1`	monomeric （1）	Success	4.1.3-1-20251215 (887e7ef)	View Download
8	1	`3fif__assembly_8__model_1`	monomeric （1）	Success	4.1.3-1-20251215 (887e7ef)	View Download
9	1	`3fif__assembly_9__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 (3)

Entity 1 Entity 1 polymer

Description description	Uncharacterized lipoprotein ygdR
Molecular weight formula_weight	7239.3 kDa
Source method src_method	man
Copy count entity_count	8

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B,C,D,E,F,G,H
Atom count atom_count	3649

MSSDYVMATKDGRMILTDGKPEIDDDTGLVSYHDQQGNAMQINRDDVSQIIERLEHHHHHH

Source Source

Source organism organism	Escherichia coli K-12
NCBI taxonomy ID ncbi_taxonomy_id	83333
Host organism host_organism	Escherichia coli

Entity 2 Entity 2 polymer

Description description	Uncharacterized ligand
Molecular weight formula_weight	417.4 kDa
Source method src_method	nat
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	Y

GGGGGGG

Entity 3 Entity 3 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	91

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6. Fold Classification (SCOP + CATH) 24 domains

SCOP 2.08 (16 domains)

Domain ID domain_id	d3fifa1
Class class	b — All beta proteins
Fold Fold fold	b.38 — Sm-like fold
Superfamily Superfamily superfamily	b.38.1 — Sm-like ribonucleoproteins
Family Family family	b.38.1.6 — YgdI/YgdR-like

Domain ID domain_id	d3fifa2
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	d3fifb1
Class class	b — All beta proteins
Fold Fold fold	b.38 — Sm-like fold
Superfamily Superfamily superfamily	b.38.1 — Sm-like ribonucleoproteins
Family Family family	b.38.1.6 — YgdI/YgdR-like

Domain ID domain_id	d3fifb2
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	d3fifc1
Class class	b — All beta proteins
Fold Fold fold	b.38 — Sm-like fold
Superfamily Superfamily superfamily	b.38.1 — Sm-like ribonucleoproteins
Family Family family	b.38.1.6 — YgdI/YgdR-like

Domain ID domain_id	d3fifc2
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	d3fifd1
Class class	b — All beta proteins
Fold Fold fold	b.38 — Sm-like fold
Superfamily Superfamily superfamily	b.38.1 — Sm-like ribonucleoproteins
Family Family family	b.38.1.6 — YgdI/YgdR-like

Domain ID domain_id	d3fifd2
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	d3fife1
Class class	b — All beta proteins
Fold Fold fold	b.38 — Sm-like fold
Superfamily Superfamily superfamily	b.38.1 — Sm-like ribonucleoproteins
Family Family family	b.38.1.6 — YgdI/YgdR-like

Domain ID domain_id	d3fife2
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	d3fiff1
Class class	b — All beta proteins
Fold Fold fold	b.38 — Sm-like fold
Superfamily Superfamily superfamily	b.38.1 — Sm-like ribonucleoproteins
Family Family family	b.38.1.6 — YgdI/YgdR-like

Domain ID domain_id	d3fiff2
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	d3fifg1
Class class	b — All beta proteins
Fold Fold fold	b.38 — Sm-like fold
Superfamily Superfamily superfamily	b.38.1 — Sm-like ribonucleoproteins
Family Family family	b.38.1.6 — YgdI/YgdR-like

Domain ID domain_id	d3fifg2
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	d3fifh1
Class class	b — All beta proteins
Fold Fold fold	b.38 — Sm-like fold
Superfamily Superfamily superfamily	b.38.1 — Sm-like ribonucleoproteins
Family Family family	b.38.1.6 — YgdI/YgdR-like

Domain ID domain_id	d3fifh2
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 (8 domains)

Domain ID domain_id	3fifA00
Class class	2 — Mainly Beta
Architecture architecture	30 — Roll
Topology topology	30 — SH3 type barrels.
Homologous superfamily homologous superfamily	100 —

Domain ID domain_id	3fifB00
Class class	2 — Mainly Beta
Architecture architecture	30 — Roll
Topology topology	30 — SH3 type barrels.
Homologous superfamily homologous superfamily	100 —

Domain ID domain_id	3fifC00
Class class	2 — Mainly Beta
Architecture architecture	30 — Roll
Topology topology	30 — SH3 type barrels.
Homologous superfamily homologous superfamily	100 —

Domain ID domain_id	3fifD00
Class class	2 — Mainly Beta
Architecture architecture	30 — Roll
Topology topology	30 — SH3 type barrels.
Homologous superfamily homologous superfamily	100 —

Domain ID domain_id	3fifE00
Class class	2 — Mainly Beta
Architecture architecture	30 — Roll
Topology topology	30 — SH3 type barrels.
Homologous superfamily homologous superfamily	100 —

Domain ID domain_id	3fifF00
Class class	2 — Mainly Beta
Architecture architecture	30 — Roll
Topology topology	30 — SH3 type barrels.
Homologous superfamily homologous superfamily	100 —

Domain ID domain_id	3fifG00
Class class	2 — Mainly Beta
Architecture architecture	30 — Roll
Topology topology	30 — SH3 type barrels.
Homologous superfamily homologous superfamily	100 —

Domain ID domain_id	3fifH00
Class class	2 — Mainly Beta
Architecture architecture	30 — Roll
Topology topology	30 — SH3 type barrels.
Homologous superfamily homologous superfamily	100 —

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Unit-cell length a length_a	41.017 Å
Unit-cell length b length_b	41.056 Å
Unit-cell length c length_c	73.748 Å
Unit-cell angle α angle_alpha	99.95 °
Unit-cell angle β angle_beta	102.33 °
Unit-cell angle γ angle_gamma	104.40 °
Molecules per unit cell Z z_pdb	8

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

Resolution resolution	2.700 Å
Low-resolution limit resolution_low	20.000 Å
R factor r_factor	0.2387
R_work r_work	0.2380
R_free r_free	0.2525

Crystal structure of the ygdR protein from E.coli. Northeast Structural Genomics target ER382A.

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

Uncharacterized lipoprotein ygdR

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

3fif__assembly_1__model_1

3fif__assembly_1__model_1 | I(q)

3fif__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 (3)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 polymer

Polymer Polymer

Entity 3 Entity 3 water

6. Fold Classification (SCOP + CATH) 24 domains

SCOP 2.08 (16 domains)

CATH v4.4 (8 domains)

7. Citations (1)

Crystal structure of the ygdR protein from E.coli. Northeast Structural Genomics target ER382A.

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

Uncharacterized lipoprotein ygdR

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

3fif__assembly_1__model_1

3fif__assembly_1__model_1 | I(q)

3fif__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 (3)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 polymer

Polymer Polymer

Entity 3 Entity 3 water

6. Fold Classification (SCOP + CATH) 24 domains

SCOP 2.08 (16 domains)

CATH v4.4 (8 domains)

7. Citations (1)