SAXSdb — 9r99

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

DHH family

Borreliella burgdorferi

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein homooligomer	Homooligomer	Protein 2	MANGANESE (II) ION × 2 FE (III) ION × 2 ;[(2~{R},3~{R},4~{R},5~{R})-5-(6-aminopurin-9-yl)-4-fluoranyl-2-(phosphonooxymethyl)oxolan-3-yl]oxy-[2-[(2~{R},3~{S},5~{R})-5-(6-aminopurin-9-yl)-3-oxidanyl-oxolan-2-yl]ethenyl]phosphinic acid ; × 1	Consistent with protein count
2	Protein homooligomer	Homooligomer	Protein 2	MANGANESE (II) ION × 2 FE (III) ION × 2 ;[(2~{R},3~{R},4~{R},5~{R})-5-(6-aminopurin-9-yl)-4-fluoranyl-2-(phosphonooxymethyl)oxolan-3-yl]oxy-[2-[(2~{R},3~{S},5~{R})-5-(6-aminopurin-9-yl)-3-oxidanyl-oxolan-2-yl]ethenyl]phosphinic acid ; × 1	Consistent with protein count
3	Protein homooligomer	Homooligomer	Protein 2	MANGANESE (II) ION × 2 FE (III) ION × 2 ;[(2~{R},3~{R},4~{R},5~{R})-5-(6-aminopurin-9-yl)-4-fluoranyl-2-(phosphonooxymethyl)oxolan-3-yl]oxy-[2-[(2~{R},3~{S},5~{R})-5-(6-aminopurin-9-yl)-3-oxidanyl-oxolan-2-yl]ethenyl]phosphinic acid ; × 1	Consistent with protein count
4	Protein homooligomer	Homooligomer	Protein 2	MANGANESE (II) ION × 2 FE (III) ION × 2 ;[(2~{R},3~{R},4~{R},5~{R})-5-(6-aminopurin-9-yl)-4-fluoranyl-2-(phosphonooxymethyl)oxolan-3-yl]oxy-[2-[(2~{R},3~{S},5~{R})-5-(6-aminopurin-9-yl)-3-oxidanyl-oxolan-2-yl]ethenyl]phosphinic acid ; × 1	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	O51564_BORBU
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 6–325； UniProt 1–320 Author chain B； PDBConstruct 6–325； UniProt 1–320 Author chain C； PDBConstruct 6–325； UniProt 1–320 Author chain D； PDBConstruct 6–325； UniProt 1–320 Author chain E； PDBConstruct 6–325； UniProt 1–320 Author chain F； PDBConstruct 6–325； UniProt 1–320 Author chain G； PDBConstruct 6–325； UniProt 1–320 Author chain H； PDBConstruct 6–325； UniProt 1–320

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	9r99
Deposition date deposition_date	2025-05-19
Structure title title	DhhP of Borrelia burgdorferi in complex with MD1252
Keywords keywords	phosphodiesterase, c-di-AMP, cyclic di-AMP, heterobimetallic, inhibitor, HYDROLASE; HYDROLASE
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.

9r99__assembly_3__model_1

Assembly 3 · Model 1 · CRYSOL 4.1.3-1-20251215 (887e7ef)

Download this curve (.dat)

9r99__assembly_3__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

9r99__assembly_3__model_1 | P(r) · Pending

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

Rg（Guinier）	28.77 Å
Rg (electron density)	28.05 Å
Total Rg	28.72 Å
Atom count	5164
Residues	646
Excluded volume	92777 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`9r99__assembly_1__model_1`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`9r99__assembly_2__model_1`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
3	1	`9r99__assembly_3__model_1`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
4	1	`9r99__assembly_4__model_1`	dimeric （2）	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 (4)

Entity 1 Entity 1 polymer

Description description	DHH family
Molecular weight formula_weight	36659.1 kDa
Source method src_method	man
Copy count entity_count	8

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,C,E,G,F,D,B,H
Atom count atom_count	20669

GAMGSMRDVINFIKKYNNFVIIGHKDPDFDCIGSSLALSSFLSRIGKNSILLNEGPFIRKEIVPFKDKFLSEWPNIEISEYSVIILDCSILDRIGDEFIFYVKNMPTLVIDHHMSGEKLECEGYIDPFAPSTTFLIEKLIREFGYDLTKEEAWYILVGFCTDTGFFKFISRSDPEPFEMVARLVSKGISLKEVYSYIETTKSLKSIETLKLMLNSLESYWNGKVLFTFLSSSSSGKDGGVSGVNELFYMILSNVENNEILGILKEMEDGSIIVGLRSKDSFDVGKLAEDFGGGGHKNASGFRIKQGSLEIVKNRMLAYIKDNIYL

Source Source

Source organism organism	Borreliella burgdorferi
Common name common_name	Lyme disease spirochete
NCBI taxonomy ID ncbi_taxonomy_id	139
Host organism host_organism	Escherichia coli BL21(DE3)

Entity 2 Entity 2 non-polymer

Description description	MANGANESE (II) ION
Molecular weight formula_weight	54.9 kDa
Source method src_method	syn
Copy count entity_count	8

Entity 3 Entity 3 non-polymer

Description description	FE (III) ION
Molecular weight formula_weight	55.8 kDa
Source method src_method	syn
Copy count entity_count	8

Entity 4 Entity 4 non-polymer

Description description	;[(2~{R},3~{R},4~{R},5~{R})-5-(6-aminopurin-9-yl)-4-fluoranyl-2-(phosphonooxymethyl)oxolan-3-yl]oxy-[2-[(2~{R},3~{S},5~{R})-5-(6-aminopurin-9-yl)-3-oxidanyl-oxolan-2-yl]ethenyl]phosphinic acid ;
Molecular weight formula_weight	658.4 kDa
Source method src_method	syn
Copy count entity_count	4

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Unit-cell length a length_a	74.550 Å
Unit-cell length b length_b	80.310 Å
Unit-cell length c length_c	132.500 Å
Unit-cell angle α angle_alpha	91.92 °
Unit-cell angle β angle_beta	90.99 °
Unit-cell angle γ angle_gamma	92.41 °
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	triclinic

Resolution resolution	3.000 Å
Low-resolution limit resolution_low	34.890 Å
R factor r_factor	0.2066
R_work r_work	0.2049
R_free r_free	0.2381

DhhP of Borrelia burgdorferi in complex with MD1252

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

DHH family

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

9r99__assembly_3__model_1

9r99__assembly_3__model_1 | I(q)

9r99__assembly_3__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 (4)

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

7. Citations (1)

DhhP of Borrelia burgdorferi in complex with MD1252

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

DHH family

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

9r99__assembly_3__model_1

9r99__assembly_3__model_1 | I(q)

9r99__assembly_3__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 (4)

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

7. Citations (1)