9tpm

Structure of LolB from Porphyromonas gingivalis

Method: X-RAY DIFFRACTION

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

DUF4292 domain-containing protein

Porphyromonas gingivalis A7A1-28

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein monomer	Monomer	Protein 1	SULFATE ION × 1 DI(HYDROXYETHYL)ETHER × 3 ACETATE ION × 5 1-ETHOXY-2-(2-ETHOXYETHOXY)ETHANE × 4 ZINC ION × 2 water × 1	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	Q7MVT4_PORGI
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 28–274； UniProt 71–317

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	9tpm
Deposition date deposition_date	2025-12-18
Structure title title	Structure of LolB from Porphyromonas gingivalis
Keywords keywords	lipoprotein transport, insertase, lipoprotein, LIPID BINDING PROTEIN; LIPID BINDING 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.

9tpm__assembly_1__model_1

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

Download this curve (.dat)

9tpm__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

9tpm__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	19.69 Å
Rg (electron density)	18.37 Å
Total Rg	19.43 Å
Atom count	2082
Residues	236
Excluded volume	35286 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`9tpm__assembly_1__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 (7)

Entity 1 Entity 1 polymer

Description description	DUF4292 domain-containing protein
Molecular weight formula_weight	31115.3 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A
Atom count atom_count	2160

MKHHHHHHPMSDYDIPTTENLYFQGAMGNDMEVSSPAALFANIKEHYPRQDRFSATGKAILRFDQKEVNTRIELTLVRNRGIRLVAMPFPLVVAGRAWITPEGMTVTDAINKRYVTASYSQLSELTGIELSYRAFESLFLAQLFKADGASIVASDLLLSTGAQKGHLLSYQDNRKMEYISEIGSNRRPLSISIYDPSTHYRLATTYSSFRKYGAEHNLPANLLLQVLHLGQVKGSLSLDLPKMRFTDIDETDVTPRVNTSTYRRMTLEDLSELF

Source Source

Source organism organism	Porphyromonas gingivalis A7A1-28
NCBI taxonomy ID ncbi_taxonomy_id	1403338
Host organism host_organism	Escherichia coli BL21(DE3)

Entity 2 Entity 2 non-polymer

Description description	SULFATE ION
Molecular weight formula_weight	96.1 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 3 Entity 3 non-polymer

Description description	DI(HYDROXYETHYL)ETHER
Molecular weight formula_weight	106.1 kDa
Source method src_method	syn
Copy count entity_count	3

Entity 4 Entity 4 non-polymer

Description description	ACETATE ION
Molecular weight formula_weight	59.0 kDa
Source method src_method	syn
Copy count entity_count	5

Entity 5 Entity 5 non-polymer

Description description	1-ETHOXY-2-(2-ETHOXYETHOXY)ETHANE
Molecular weight formula_weight	162.2 kDa
Source method src_method	syn
Copy count entity_count	4

Entity 6 Entity 6 non-polymer

Description description	ZINC ION
Molecular weight formula_weight	65.4 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 7 Entity 7 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	78

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Unit-cell length a length_a	94.679 Å
Unit-cell length b length_b	94.679 Å
Unit-cell length c length_c	104.942 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	90.00 °
Unit-cell angle γ angle_gamma	120.00 °
Molecules per unit cell Z z_pdb	12

Space group space_group	P 65 2 2
Space-group number int_tables_number	179
Crystal system crystal_system	hexagonal

Resolution resolution	2.100 Å
Low-resolution limit resolution_low	47.340 Å
R factor r_factor	0.2295
R_work r_work	0.2270
R_free r_free	0.2778

Structure of LolB from Porphyromonas gingivalis

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

DUF4292 domain-containing 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

9tpm__assembly_1__model_1

9tpm__assembly_1__model_1 | I(q)

9tpm__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 (7)

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 non-polymer

Entity 6 Entity 6 non-polymer

Entity 7 Entity 7 water

7. Citations (1)

Structure of LolB from Porphyromonas gingivalis

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

DUF4292 domain-containing 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

9tpm__assembly_1__model_1

9tpm__assembly_1__model_1 | I(q)

9tpm__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 (7)

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 non-polymer

Entity 6 Entity 6 non-polymer

Entity 7 Entity 7 water

7. Citations (1)