3tgo

Crystal structure of the E. coli BamCD complex

Method: X-RAY DIFFRACTION

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

UPF0169 lipoprotein yfiO

Escherichia coli

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 2	Lipoprotein 34 × 1 （P0A903） POTASSIUM ION × 1 GLYCEROL × 1 PHOSPHATE ION × 1 water × 2	Consistent with protein count
2	Protein heterocomplex	Heteromer	Protein 2	Lipoprotein 34 × 1 （P0A903） GLYCEROL × 3 CHLORIDE ION × 1 SODIUM ION × 1 water × 2	Consistent with protein count
3	Protein heterocomplex	Heteromer	Protein 4	Lipoprotein 34 × 2 （P0A903） POTASSIUM ION × 1 GLYCEROL × 4 CHLORIDE ION × 1 PHOSPHATE ION × 1 SODIUM ION × 1 water × 4	Consistent with protein count
4	Protein heterocomplex	Heteromer	Protein 8	Lipoprotein 34 × 4 （P0A903） POTASSIUM ION × 2 GLYCEROL × 8 CHLORIDE ION × 2 PHOSPHATE ION × 2 SODIUM ION × 2 water × 8	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	YFIO_ECOLI
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 5–229； UniProt 21–245 Author chain B； PDBConstruct 5–229； UniProt 21–245

Lipoprotein 34

Escherichia coli

UniProt P0A903

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 2	UPF0169 lipoprotein yfiO × 1 （P0AC02） POTASSIUM ION × 1 GLYCEROL × 1 PHOSPHATE ION × 1 water × 2	Consistent with protein count
2	Protein heterocomplex	Heteromer	Protein 2	UPF0169 lipoprotein yfiO × 1 （P0AC02） GLYCEROL × 3 CHLORIDE ION × 1 SODIUM ION × 1 water × 2	Consistent with protein count
3	Protein heterocomplex	Heteromer	Protein 4	UPF0169 lipoprotein yfiO × 2 （P0AC02） POTASSIUM ION × 1 GLYCEROL × 4 CHLORIDE ION × 1 PHOSPHATE ION × 1 SODIUM ION × 1 water × 4	Consistent with protein count
4	Protein heterocomplex	Heteromer	Protein 8	UPF0169 lipoprotein yfiO × 4 （P0AC02） POTASSIUM ION × 2 GLYCEROL × 8 CHLORIDE ION × 2 PHOSPHATE ION × 2 SODIUM ION × 2 water × 8	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	NLPB_ECOLI
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain C； PDBConstruct 5–323； UniProt 26–344 Author chain D； PDBConstruct 5–323； UniProt 26–344

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	3tgo
Deposition date deposition_date	2011-08-17
Structure title title	Crystal structure of the E. coli BamCD complex
Keywords keywords	lipoprotein complex, TPR repeat, helix-grip fold, Outer membrane protein assembly, outer membrane, MEMBRANE PROTEIN; MEMBRANE PROTEIN
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.

3tgo__assembly_1__model_1

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

Download this curve (.dat)

3tgo__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

3tgo__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	27.10 Å
Rg (electron density)	26.89 Å
Total Rg	27.44 Å
Atom count	3142
Residues	398
Excluded volume	55547 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`3tgo__assembly_1__model_1`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`3tgo__assembly_2__model_1`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
3	1	`3tgo__assembly_3__model_1`	tetrameric （4）	Success	4.1.3-1-20251215 (887e7ef)	View Download
4	1	`3tgo__assembly_4__model_1`	octameric （8）	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 (8)

Entity 1 Entity 1 polymer

Description description	UPF0169 lipoprotein yfiO
Molecular weight formula_weight	26127.2 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	6466

GSHMSGSKEEVPDNPPNEIYATAQQKLQDGNWRQAITQLEALDNRYPFGPYSQQVQLDLIYAYYKNADLPLAQAAIDRFIRLNPTHPNIDYVMYMRGLTNMALDDSALQGFFGVDRSDRDPQHARAAFSDFSKLVRGYPNSQYTTDATKRLVFLKDRLAKYEYSVAEYYTERGAWVAVVNRVEGMLRDYPDTQATRDALPLMENAYRQMQMNAQAEKVAKIIAANSSNT

Source Source

Source organism organism	Escherichia coli
NCBI taxonomy ID ncbi_taxonomy_id	83333
Host organism host_organism	Escherichia coli

Entity 2 Entity 2 polymer

Description description	Lipoprotein 34
Molecular weight formula_weight	34711.6 kDa
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	C,D

GSHMSSDSRYKRQVSGDEAYLEAAPLAELHAPAGMILPVTSGDYAIPVTNGSGAVGKALDIRPPAQPLALVSGARTQFTGDTASLLVENGRGNTLWPQVVSVLQAKNYTITQRDDAGQTLTTDWVQWNRLDEDEQYRGRYQISVKPQGYQQAVTVKLLNLEQAGKPVADAASMQRYSTEMMNVISAGLDKSATDAANAAQNRASTTMDVQSAADDTGLPMLVVRGPFNVVWQRLPAALEKVGMKVTDSTRSQGNMAVTYKPLSDSDWQELGASDPGLASGDYKLQVGDLDNRSSLQFIDPKGHTLTQSQNDALVAVFQAAFSK

Source Source

Source organism organism	Escherichia coli
NCBI taxonomy ID ncbi_taxonomy_id	83333
Host organism host_organism	Escherichia coli

Entity 3 Entity 3 non-polymer

Description description	POTASSIUM ION
Molecular weight formula_weight	39.1 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 4 Entity 4 non-polymer

Description description	GLYCEROL
Molecular weight formula_weight	92.1 kDa
Source method src_method	syn
Copy count entity_count	4

Entity 5 Entity 5 non-polymer

Description description	CHLORIDE ION
Molecular weight formula_weight	35.5 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 6 Entity 6 non-polymer

Description description	PHOSPHATE ION
Molecular weight formula_weight	95.0 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 7 Entity 7 non-polymer

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

Entity 8 Entity 8 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	124

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6. Fold Classification (SCOP + CATH) 4 domains

CATH v4.4 (4 domains)

Domain ID domain_id	3tgoA00
Class class	1 — Mainly Alpha
Architecture architecture	25 — Alpha Horseshoe
Topology topology	40 — Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat
Homologous superfamily homologous superfamily	10 — Tetratricopeptide repeat domain

Domain ID domain_id	3tgoB00
Class class	1 — Mainly Alpha
Architecture architecture	25 — Alpha Horseshoe
Topology topology	40 — Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat
Homologous superfamily homologous superfamily	10 — Tetratricopeptide repeat domain

Domain ID domain_id	3tgoC01
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	530 — Alpha-D-Glucose-1,6-Bisphosphate; Chain A, domain 4
Homologous superfamily homologous superfamily	50 —

Domain ID domain_id	3tgoD01
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	530 — Alpha-D-Glucose-1,6-Bisphosphate; Chain A, domain 4
Homologous superfamily homologous superfamily	50 —

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Unit-cell length a length_a	73.780 Å
Unit-cell length b length_b	133.380 Å
Unit-cell length c length_c	144.992 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	100.15 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	8

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

Resolution resolution	2.900 Å
Low-resolution limit resolution_low	97.450 Å
R factor r_factor	0.1810
R_work r_work	0.1770
R_free r_free	0.2430

Crystal structure of the E. coli BamCD complex

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

UPF0169 lipoprotein yfiO

State in the Current Structure

Other States of the Same Protein in the Database

Lipoprotein 34

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

3tgo__assembly_1__model_1

3tgo__assembly_1__model_1 | I(q)

3tgo__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 (8)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 polymer

Polymer Polymer

Source Source

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 non-polymer

Entity 5 Entity 5 non-polymer

Entity 6 Entity 6 non-polymer

Entity 7 Entity 7 non-polymer

Entity 8 Entity 8 water

6. Fold Classification (SCOP + CATH) 4 domains

CATH v4.4 (4 domains)

7. Citations (1)

Crystal structure of the E. coli BamCD complex

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

UPF0169 lipoprotein yfiO

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

Lipoprotein 34

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

3tgo__assembly_1__model_1

3tgo__assembly_1__model_1 | I(q)

3tgo__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 (8)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 polymer

Polymer Polymer

Source Source

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 non-polymer

Entity 5 Entity 5 non-polymer

Entity 6 Entity 6 non-polymer

Entity 7 Entity 7 non-polymer

Entity 8 Entity 8 water

6. Fold Classification (SCOP + CATH) 4 domains

CATH v4.4 (4 domains)

7. Citations (1)