SAXSdb — 2gd9

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

Hypothetical protein yyaP

Bacillus subtilis

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein homooligomer	Homooligomer	Protein 2	CHLORIDE ION × 1 PHOSPHATE ION × 2 1,2-ETHANEDIOL × 4 water × 2	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	YYAP_BACSU
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 2–189； UniProt 1–188 Author chain B； PDBConstruct 2–189； UniProt 1–188

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	2gd9
Deposition date deposition_date	2006-03-15
Structure title title	Crystal structure of a putative dihydrofolate reductase (bsu40760, yyap) from bacillus subtilis at 2.30 A resolution
Keywords keywords	Structural genomics, Joint Center for Structural Genomics, JCSG, Protein Structure Initiative, PSI-2, oxidoreductase; OXIDOREDUCTASE
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.

2gd9__assembly_1__model_1

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

Download this curve (.dat)

2gd9__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

2gd9__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	24.08 Å
Rg (electron density)	23.01 Å
Total Rg	23.97 Å
Atom count	2852
Residues	340
Excluded volume	51455 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`2gd9__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	Hypothetical protein yyaP
Molecular weight formula_weight	22007.6 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	3026

GMTNNLKQRRIILDLAVTLDGFIEGKNGEVDWCIMDPDMGFTDFLNQIDTILYGRKSFDLWGQYIPKNEDPDTEKELWKLVHSKKKYVFSRTQNEIDNQAIFINDNILEEVNKLKKNPGKDIWLYGGASLITTFINLGLVDEFRLSIHPVVLGEGKPLFIDVKQRINLKMVNTRTFSSGVVQIVYHWNG

Source Source

Source organism organism	Bacillus subtilis
NCBI taxonomy ID ncbi_taxonomy_id	1423
Host organism host_organism	Escherichia coli

Entity 2 Entity 2 non-polymer

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

Entity 3 Entity 3 non-polymer

Description description	PHOSPHATE ION
Molecular weight formula_weight	95.0 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 4 Entity 4 non-polymer

Description description	1,2-ETHANEDIOL
Molecular weight formula_weight	62.1 kDa
Source method src_method	syn
Copy count entity_count	4

Entity 5 Entity 5 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	155

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6. Fold Classification (SCOP + CATH) 2 domains

CATH v4.4 (2 domains)

Domain ID domain_id	2gd9A01
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	430 — Dihydrofolate Reductase, subunit A
Homologous superfamily homologous superfamily	10 — Dihydrofolate Reductase, subunit A

Domain ID domain_id	2gd9B01
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	430 — Dihydrofolate Reductase, subunit A
Homologous superfamily homologous superfamily	10 — Dihydrofolate Reductase, subunit A

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Unit-cell length a length_a	64.915 Å
Unit-cell length b length_b	64.915 Å
Unit-cell length c length_c	143.648 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 43
Space-group number int_tables_number	78
Crystal system crystal_system	—

Resolution resolution	2.300 Å
Low-resolution limit resolution_low	59.160 Å
R factor r_factor	0.2097
R_work r_work	0.2070
R_free r_free	0.2540

Crystal structure of a putative dihydrofolate reductase (bsu40760, yyap) from bacillus subtilis at 2.30 A resolution

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

Hypothetical protein yyaP

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

2gd9__assembly_1__model_1

2gd9__assembly_1__model_1 | I(q)

2gd9__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 a putative dihydrofolate reductase (bsu40760, yyap) from bacillus subtilis at 2.30 A resolution

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

Hypothetical protein yyaP

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

2gd9__assembly_1__model_1

2gd9__assembly_1__model_1 | I(q)

2gd9__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)