SAXSdb — 3n3t

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

PUTATIVE DIGUANYLATE CYCLASE/PHOSPHODIESTERASE

THIOBACILLUS DENITRIFICANS

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein homooligomer	Homooligomer	Protein 2	;9,9'-[(2R,3R,3aS,5S,7aR,9R,10R,10aS,12S,14aR)-3,5,10,12-tetrahydroxy-5,12-dioxidooctahydro-2H,7H-difuro[3,2-d:3',2'-j][1,3,7,9,2,8]tetraoxadiphosphacyclododecine-2,9-diyl]bis(2-amino-1,9-dihydro-6H-purin-6-one) ; × 2 MAGNESIUM ION × 4 CHLORIDE ION × 1 water × 2	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	Q3SJE6_THIDA
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 23–294； UniProt 487–758 Author chain B； PDBConstruct 23–294； UniProt 487–758

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	3n3t
Deposition date deposition_date	2010-05-20
Structure title title	Crystal structure of putative diguanylate cyclase/phosphodiesterase complex with cyclic di-gmp
Keywords keywords	;GGDEF & EAL DOMAINS, STRUCTURAL GENOMICS, PSI-2, PROTEIN STRUCTURE INITIATIVE, MIDWEST CENTER FOR STRUCTURAL GENOMICS, MCSG, 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.

3n3t__assembly_1__model_1

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

Download this curve (.dat)

3n3t__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

3n3t__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	28.25 Å
Rg (electron density)	27.45 Å
Total Rg	27.90 Å
Atom count	4097
Residues	511
Excluded volume	72358 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`3n3t__assembly_1__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 (5)

Entity 1 Entity 1 polymer

Description description	PUTATIVE DIGUANYLATE CYCLASE/PHOSPHODIESTERASE
Molecular weight formula_weight	32876.1 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	4366

MGSSHHHHHHSSGRENLYFQGHERLTLDTRLRQALERNELVLHYQPIVELASGRIVGGEALVRWEDPERGLVMPSAFIPAAEDTGLIVALSDWVLEACCTQLRAWQQQGRAADDLTLSVNISTRQFEGEHLTRAVDRALARSGLRPDCLELEITENVMLVMTDEVRTCLDALRARGVRLALDDFGTGYSSLSYLSQLPFHGLKIDQSFVRKIPAHPSETQIVTTILALARGLGMEVVAEGIETAQQYAFLRDRGCEFGQGNLMSTPQAADAFASLLDRQKASGQRPVHGHETAP

Source Source

Source organism organism	THIOBACILLUS DENITRIFICANS
NCBI taxonomy ID ncbi_taxonomy_id	292415
Host organism host_organism	Escherichia coli

Entity 2 Entity 2 non-polymer

Description description	;9,9'-[(2R,3R,3aS,5S,7aR,9R,10R,10aS,12S,14aR)-3,5,10,12-tetrahydroxy-5,12-dioxidooctahydro-2H,7H-difuro[3,2-d:3',2'-j][1,3,7,9,2,8]tetraoxadiphosphacyclododecine-2,9-diyl]bis(2-amino-1,9-dihydro-6H-purin-6-one) ;
Molecular weight formula_weight	690.4 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 3 Entity 3 non-polymer

Description description	MAGNESIUM ION
Molecular weight formula_weight	24.3 kDa
Source method src_method	syn
Copy count entity_count	4

Entity 4 Entity 4 non-polymer

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

Entity 5 Entity 5 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	225

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6. Fold Classification (SCOP + CATH) 2 domains

CATH v4.4 (2 domains)

Domain ID domain_id	3n3tA00
Class class	3 — Alpha Beta
Architecture architecture	20 — Alpha-Beta Barrel
Topology topology	20 — TIM Barrel
Homologous superfamily homologous superfamily	450 — EAL domain

Domain ID domain_id	3n3tB00
Class class	3 — Alpha Beta
Architecture architecture	20 — Alpha-Beta Barrel
Topology topology	20 — TIM Barrel
Homologous superfamily homologous superfamily	450 — EAL domain

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Unit-cell length a length_a	51.560 Å
Unit-cell length b length_b	63.201 Å
Unit-cell length c length_c	173.987 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	8

Space group space_group	P 21 21 21
Space-group number int_tables_number	19
Crystal system crystal_system	—

Resolution resolution	2.350 Å
Low-resolution limit resolution_low	39.955 Å
R factor r_factor	0.1876
R_work r_work	0.1840
R_free r_free	0.2536

Crystal structure of putative diguanylate cyclase/phosphodiesterase complex with cyclic di-gmp

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

PUTATIVE DIGUANYLATE CYCLASE/PHOSPHODIESTERASE

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

3n3t__assembly_1__model_1

3n3t__assembly_1__model_1 | I(q)

3n3t__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 (5)

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 water

6. Fold Classification (SCOP + CATH) 2 domains

CATH v4.4 (2 domains)

7. Citations (1)

Crystal structure of putative diguanylate cyclase/phosphodiesterase complex with cyclic di-gmp

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

PUTATIVE DIGUANYLATE CYCLASE/PHOSPHODIESTERASE

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

3n3t__assembly_1__model_1

3n3t__assembly_1__model_1 | I(q)

3n3t__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 (5)

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 water

6. Fold Classification (SCOP + CATH) 2 domains

CATH v4.4 (2 domains)

7. Citations (1)