SAXSdb — 9d7l

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

Bifunctional protein PutA

Sinorhizobium meliloti

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein homooligomer	Homooligomer	Protein 2	;{[(3E)-4-{10-[(2S,3S,4R)-5-{[(R)-{[(R)-{[(2R,3S,4R,5R)-5-(6-amino-9H-purin-9-yl)-3,4-dihydroxyoxolan-2-yl]methoxy}(hydroxy)phosphoryl]oxy}(hydroxy)phosphoryl]oxy}-2,3,4-trihydroxypentyl]-7,8-dimethyl-2,4-dioxo-2,3,4,10-tetrahydrobenzo[g]pteridin-5(1H)-yl}but-3-en-2-ylidene]amino}acetic acid (non-preferred name) ; × 2 FORMIC ACID × 2 water × 2	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	F7X6I3_SINMM
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 2–59； UniProt 26–83 Author chain A； PDBConstruct 64–396； UniProt 190–522 Author chain B； PDBConstruct 2–59； UniProt 26–83 Author chain B； PDBConstruct 64–396； UniProt 190–522

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	9d7l
Deposition date deposition_date	2024-08-16
Structure title title	Minimal PutA proline dehydrogenase domain (design #2) covalently inactivated by (S)-but-3-yn-2-ylglycine
Keywords keywords	BETA/ALPHA BARREL, FLAVOENZYME, PROLINE CATABOLISM, 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.

9d7l__assembly_1__model_1

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

Download this curve (.dat)

9d7l__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

9d7l__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	28.54 Å
Rg (electron density)	27.87 Å
Total Rg	28.70 Å
Atom count	5630
Residues	764
Excluded volume	98827 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`9d7l__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	Bifunctional protein PutA
Molecular weight formula_weight	43774.0 kDa
EC 编号 ec_number	1.5.5.2,1.2.1.88
Mutation mutation	residues 84-189 replaced by SSGS
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	5900

SRPQSTLRRAITAAYRRPETECLPPLVEAATQSKEIRDAAASTARKLIEALRGKHSGSGSSGSMMGEQFVTGETIREALKRSKELEEKGFSYSYDMLGEAATTAADAERYYRDYESAIHAIGKASAGRGIYEGPGISIKLSALHPRYSRAQAARVMGELLPRVKALALLAKNYDIGLNIDAEEADRLELSLDLLEVLCLDGDLSGWNGMGFVVQAYGKRCPFVLDFIIDLARRSGRRIMVRLVKGAYWDAEIKRAQLDGLADFPVFTRKIHTDVSYIACAAKLLAATDVVFPQFATHNAQTLAAIYHMAGKDFHVGKYEFQCLHGMGEPLYEEVVGRGKLDRPCRIYAPVGTHETLLAYLVRRLLENGANSSFVHRINDPKVSIDELIADPVEVVR

Source Source

Source organism organism	Sinorhizobium meliloti
NCBI taxonomy ID ncbi_taxonomy_id	707241
Host organism host_organism	Escherichia coli

Entity 2 Entity 2 non-polymer

Description description	;{[(3E)-4-{10-[(2S,3S,4R)-5-{[(R)-{[(R)-{[(2R,3S,4R,5R)-5-(6-amino-9H-purin-9-yl)-3,4-dihydroxyoxolan-2-yl]methoxy}(hydroxy)phosphoryl]oxy}(hydroxy)phosphoryl]oxy}-2,3,4-trihydroxypentyl]-7,8-dimethyl-2,4-dioxo-2,3,4,10-tetrahydrobenzo[g]pteridin-5(1H)-yl}but-3-en-2-ylidene]amino}acetic acid (non-preferred name) ;
Molecular weight formula_weight	912.7 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 3 Entity 3 non-polymer

Description description	FORMIC ACID
Molecular weight formula_weight	46.0 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 4 Entity 4 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	258

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Unit-cell length a length_a	48.528 Å
Unit-cell length b length_b	54.242 Å
Unit-cell length c length_c	75.600 Å
Unit-cell angle α angle_alpha	103.96 °
Unit-cell angle β angle_beta	100.27 °
Unit-cell angle γ angle_gamma	109.32 °
Molecules per unit cell Z z_pdb	2

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

Resolution resolution	1.680 Å
Low-resolution limit resolution_low	48.440 Å
R factor r_factor	0.2006
R_work r_work	0.1993
R_free r_free	0.2264

Minimal PutA proline dehydrogenase domain (design #2) covalently inactivated by (S)-but-3-yn-2-ylglycine

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

Bifunctional protein PutA

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

9d7l__assembly_1__model_1

9d7l__assembly_1__model_1 | I(q)

9d7l__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

7. Citations (1)

Minimal PutA proline dehydrogenase domain (design #2) covalently inactivated by (S)-but-3-yn-2-ylglycine

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

Bifunctional protein PutA

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

9d7l__assembly_1__model_1

9d7l__assembly_1__model_1 | I(q)

9d7l__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

7. Citations (1)