SAXSdb — 3gyd

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

Cyclic nucleotide-binding domain

Methylobacillus flagellatus KT

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein homooligomer	Homooligomer	Protein 2	ADENOSINE-3',5'-CYCLIC-MONOPHOSPHATE × 2 GLYCEROL × 1 water × 2	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	Q1GZZ4_METFK
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 20–187； UniProt 1–168 Author chain B； PDBConstruct 20–187； UniProt 1–168

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	3gyd
Deposition date deposition_date	2009-04-03
Structure title title	Crystal structure of a cyclic nucleotide-binding domain (mfla_1926) from methylobacillus flagellatus kt at 1.79 A resolution
Keywords keywords	;Nucleotide binding protein, structural genomics, Joint Center for Structural Genomics, JCSG, Protein Structure Initiative, PSI-2, dna binding protein ;; DNA 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.

3gyd__assembly_1__model_1

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

Download this curve (.dat)

3gyd__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

3gyd__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	21.70 Å
Rg (electron density)	20.70 Å
Total Rg	21.30 Å
Atom count	2845
Residues	346
Excluded volume	51294 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`3gyd__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 (4)

Entity 1 Entity 1 polymer

Description description	Cyclic nucleotide-binding domain
Molecular weight formula_weight	21321.6 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	3215

MGSDKIHHHHHHENLYFQGMYPDLVHLGGADKYFEEILEIVNKIKLFGDFSNEEVRYLCSYMQCYAAPRDCQLLTEGDPGDYLLLILTGEVNVIKDIPNKGIQTIAKVGAGAIIGEMSMIDGMPRSASCVASLPTDFAVLSRDALYQLLANMPKLGNKVLIRLLQLLTARFRESYDRILPKTLGELI

Source Source

Source organism organism	Methylobacillus flagellatus KT
NCBI taxonomy ID ncbi_taxonomy_id	265072
Host organism host_organism	Escherichia coli

Entity 2 Entity 2 non-polymer

Description description	ADENOSINE-3',5'-CYCLIC-MONOPHOSPHATE
Molecular weight formula_weight	329.2 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 3 Entity 3 non-polymer

Description description	GLYCEROL
Molecular weight formula_weight	92.1 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 4 Entity 4 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	256

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6. Fold Classification (SCOP + CATH) 2 domains

CATH v4.4 (2 domains)

Domain ID domain_id	3gydA00
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	120 — Jelly Rolls
Homologous superfamily homologous superfamily	10 — Jelly Rolls

Domain ID domain_id	3gydB00
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	120 — Jelly Rolls
Homologous superfamily homologous superfamily	10 — Jelly Rolls

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Unit-cell length a length_a	60.032 Å
Unit-cell length b length_b	39.745 Å
Unit-cell length c length_c	70.977 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	101.85 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	4

Space group space_group	P 1 21 1
Space-group number int_tables_number	4
Crystal system crystal_system	—

Resolution resolution	1.790 Å
Low-resolution limit resolution_low	29.374 Å
R factor r_factor	0.1700
R_work r_work	0.1680
R_free r_free	0.2120

Crystal structure of a cyclic nucleotide-binding domain (mfla_1926) from methylobacillus flagellatus kt at 1.79 A resolution

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

Cyclic nucleotide-binding domain

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

3gyd__assembly_1__model_1

3gyd__assembly_1__model_1 | I(q)

3gyd__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 (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 water

6. Fold Classification (SCOP + CATH) 2 domains

CATH v4.4 (2 domains)

7. Citations (1)

Crystal structure of a cyclic nucleotide-binding domain (mfla_1926) from methylobacillus flagellatus kt at 1.79 A resolution

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

Cyclic nucleotide-binding domain

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

3gyd__assembly_1__model_1

3gyd__assembly_1__model_1 | I(q)

3gyd__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 (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 water

6. Fold Classification (SCOP + CATH) 2 domains

CATH v4.4 (2 domains)

7. Citations (1)