3bdu

Crystal structure of protein Q6D8G1 at the resolution 1.9 A. Northeast Structural Genomics Consortium target EwR22A.

Method: X-RAY DIFFRACTION

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

Putative lipoprotein

Pectobacterium atrosepticum SCRI1043

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein homooligomer	Homooligomer	Protein 7	water × 7	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	Q6D8G1_ERWCT
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 2–54； UniProt 21–73 Author chain B； PDBConstruct 2–54； UniProt 21–73 Author chain C； PDBConstruct 2–54； UniProt 21–73 Author chain D； PDBConstruct 2–54； UniProt 21–73 Author chain E； PDBConstruct 2–54； UniProt 21–73 Author chain F； PDBConstruct 2–54； UniProt 21–73 Author chain G； PDBConstruct 2–54； UniProt 21–73

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	3bdu
Deposition date deposition_date	2007-11-15
Structure title title	Crystal structure of protein Q6D8G1 at the resolution 1.9 A. Northeast Structural Genomics Consortium target EwR22A.
Keywords keywords	;x_Ray, NESG, Q6D8G1, Structural Genomics, PSI-2, Protein Structure Initiative, Northeast Structural Genomics Consortium, Lipoprotein ;; LIPOPROTEIN
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.

3bdu__assembly_1__model_1

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

Download this curve (.dat)

3bdu__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

3bdu__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	23.74 Å
Rg (electron density)	23.20 Å
Total Rg	23.75 Å
Atom count	2839
Residues	352
Excluded volume	49452 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`3bdu__assembly_1__model_1`	heptameric （7）	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 (2)

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6. Fold Classification (SCOP + CATH) 14 domains

SCOP 2.08 (7 domains)

Domain ID domain_id	d3bdua1
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	d3bdub_
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	d3bduc_
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	d3bdud_
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	d3bdue_
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	d3bduf_
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	d3bdug_
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

CATH v4.4 (7 domains)

Domain ID domain_id	3bduA00
Class class	2 — Mainly Beta
Architecture architecture	30 — Roll
Topology topology	30 — SH3 type barrels.
Homologous superfamily homologous superfamily	100 —

Domain ID domain_id	3bduB00
Class class	2 — Mainly Beta
Architecture architecture	30 — Roll
Topology topology	30 — SH3 type barrels.
Homologous superfamily homologous superfamily	100 —

Domain ID domain_id	3bduC00
Class class	2 — Mainly Beta
Architecture architecture	30 — Roll
Topology topology	30 — SH3 type barrels.
Homologous superfamily homologous superfamily	100 —

Domain ID domain_id	3bduD00
Class class	2 — Mainly Beta
Architecture architecture	30 — Roll
Topology topology	30 — SH3 type barrels.
Homologous superfamily homologous superfamily	100 —

Domain ID domain_id	3bduE00
Class class	2 — Mainly Beta
Architecture architecture	30 — Roll
Topology topology	30 — SH3 type barrels.
Homologous superfamily homologous superfamily	100 —

Domain ID domain_id	3bduF00
Class class	2 — Mainly Beta
Architecture architecture	30 — Roll
Topology topology	30 — SH3 type barrels.
Homologous superfamily homologous superfamily	100 —

Domain ID domain_id	3bduG00
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	105.974 Å
Unit-cell length b length_b	79.077 Å
Unit-cell length c length_c	48.472 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	96.30 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	28

Space group space_group	C 1 2 1
Space-group number int_tables_number	5
Crystal system crystal_system	—

Resolution resolution	1.900 Å
Low-resolution limit resolution_low	19.800 Å
R factor r_factor	0.2100
R_work r_work	0.2100
R_free r_free	0.2470

Description description	Putative lipoprotein
Molecular weight formula_weight	7253.5 kDa
Source method src_method	man
Copy count entity_count	7

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B,C,D,E,F,G
Atom count atom_count	3009

Crystal structure of protein Q6D8G1 at the resolution 1.9 A. Northeast Structural Genomics Consortium target EwR22A.

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

Putative lipoprotein

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

3bdu__assembly_1__model_1

3bdu__assembly_1__model_1 | I(q)

3bdu__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 (2)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 water

6. Fold Classification (SCOP + CATH) 14 domains

SCOP 2.08 (7 domains)

CATH v4.4 (7 domains)

7. Citations (1)

Source organism organism	Pectobacterium atrosepticum SCRI1043
NCBI taxonomy ID ncbi_taxonomy_id	218491
Host organism host_organism	Escherichia coli

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	170

Crystal structure of protein Q6D8G1 at the resolution 1.9 A. Northeast Structural Genomics Consortium target EwR22A.

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

Putative lipoprotein

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

3bdu__assembly_1__model_1

3bdu__assembly_1__model_1 | I(q)

3bdu__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 (2)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 water

6. Fold Classification (SCOP + CATH) 14 domains

SCOP 2.08 (7 domains)

CATH v4.4 (7 domains)

7. Citations (1)