SAXSdb — 2h5n

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

Hypothetical protein PG_1108

Porphyromonas gingivalis

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein homooligomer	Homooligomer	Protein 4	MAGNESIUM ION × 3 water × 4	Consistent with protein count
2	Protein homooligomer	Homooligomer	Protein 8	MAGNESIUM ION × 6 water × 8	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	Q7MVF6_PORGI
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–133； UniProt 1–133 Author chain B； PDBConstruct 1–133； UniProt 1–133 Author chain C； PDBConstruct 1–133； UniProt 1–133 Author chain D； PDBConstruct 1–133； UniProt 1–133

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	2h5n
Deposition date deposition_date	2006-05-26
Structure title title	Crystal Structure of Protein of Unknown Function PG1108 from Porphyromonas gingivalis W83
Keywords keywords	;hypothetical protein, SAD, MCSG, PSI, Structural Genomics, Protein Structure Initiative, Midwest Center for Structural Genomics, 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.

2h5n__assembly_2__model_1

Assembly 2 · Model 1 · CRYSOL 4.1.3-1-20251215 (887e7ef)

Download this curve (.dat)

2h5n__assembly_2__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

2h5n__assembly_2__model_1 | P(r) · Pending

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

Rg（Guinier）	36.71 Å
Rg (electron density)	36.41 Å
Total Rg	36.76 Å
Atom count	7650
Residues	1002
Excluded volume	139010 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`2h5n__assembly_1__model_1`	tetrameric （4）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`2h5n__assembly_2__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 (3)

Entity 1 Entity 1 polymer

Description description	Hypothetical protein PG_1108
Molecular weight formula_weight	14635.2 kDa
Source method src_method	man
Copy count entity_count	4

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B,C,D
Atom count atom_count	4234

MGLGRQSLNIMTFSGQELTAIIKMAKSMVMADGKIKPAEIAVMTREFMRFGILQDQVDLLLKASDSIEASQAVALIARMDEERKKYVASYLGVIMASDGDIDDNELALWTLISTLCGLPTMTVMEAINNMKNL

Source Source

Source organism organism	Porphyromonas gingivalis
NCBI taxonomy ID ncbi_taxonomy_id	837
Host organism host_organism	Escherichia coli BL21(DE3)

Entity 2 Entity 2 non-polymer

Description description	MAGNESIUM ION
Molecular weight formula_weight	24.3 kDa
Source method src_method	syn
Copy count entity_count	3

Entity 3 Entity 3 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	331

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6. Fold Classification (SCOP + CATH) 8 domains

SCOP 2.08 (4 domains)

Domain ID domain_id	d2h5na1
Class class	a — All alpha proteins
Fold Fold fold	a.287 — TerB-like
Superfamily Superfamily superfamily	a.287.1 — TerB-like
Family Family family	a.287.1.2 — PG1108-like

Domain ID domain_id	d2h5nb_
Class class	a — All alpha proteins
Fold Fold fold	a.287 — TerB-like
Superfamily Superfamily superfamily	a.287.1 — TerB-like
Family Family family	a.287.1.2 — PG1108-like

Domain ID domain_id	d2h5nc_
Class class	a — All alpha proteins
Fold Fold fold	a.287 — TerB-like
Superfamily Superfamily superfamily	a.287.1 — TerB-like
Family Family family	a.287.1.2 — PG1108-like

Domain ID domain_id	d2h5nd_
Class class	a — All alpha proteins
Fold Fold fold	a.287 — TerB-like
Superfamily Superfamily superfamily	a.287.1 — TerB-like
Family Family family	a.287.1.2 — PG1108-like

CATH v4.4 (4 domains)

Domain ID domain_id	2h5nA01
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	3680 — TerB-like
Homologous superfamily homologous superfamily	10 — TerB-like

Domain ID domain_id	2h5nB01
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	3680 — TerB-like
Homologous superfamily homologous superfamily	10 — TerB-like

Domain ID domain_id	2h5nC00
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	3680 — TerB-like
Homologous superfamily homologous superfamily	10 — TerB-like

Domain ID domain_id	2h5nD00
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	3680 — TerB-like
Homologous superfamily homologous superfamily	10 — TerB-like

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Unit-cell length a length_a	79.961 Å
Unit-cell length b length_b	84.826 Å
Unit-cell length c length_c	164.535 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	90.00 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	32

Space group space_group	C 2 2 21
Space-group number int_tables_number	20
Crystal system crystal_system	—

Resolution resolution	2.010 Å
Low-resolution limit resolution_low	40.000 Å
R factor r_factor	0.1909
R_work r_work	0.1883
R_free r_free	0.2437

Crystal Structure of Protein of Unknown Function PG1108 from Porphyromonas gingivalis W83

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

Hypothetical protein PG_1108

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

2h5n__assembly_2__model_1

2h5n__assembly_2__model_1 | I(q)

2h5n__assembly_2__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 non-polymer

Entity 3 Entity 3 water

6. Fold Classification (SCOP + CATH) 8 domains

SCOP 2.08 (4 domains)

CATH v4.4 (4 domains)

7. Citations (1)

Crystal Structure of Protein of Unknown Function PG1108 from Porphyromonas gingivalis W83

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

Hypothetical protein PG_1108

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

2h5n__assembly_2__model_1

2h5n__assembly_2__model_1 | I(q)

2h5n__assembly_2__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 non-polymer

Entity 3 Entity 3 water

6. Fold Classification (SCOP + CATH) 8 domains

SCOP 2.08 (4 domains)

CATH v4.4 (4 domains)

7. Citations (1)