9dl6

Structure of proline utilization A complexed with piperidine-3-carboxylic acid

Method: X-RAY DIFFRACTION

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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	FLAVIN-ADENINE DINUCLEOTIDE × 2 DI(HYDROXYETHYL)ETHER × 7 TRIETHYLENE GLYCOL × 4 FORMIC ACID × 6 (3S)-piperidine-3-carboxylic acid × 2 (3R)-piperidine-3-carboxylic acid × 2 SULFATE ION × 7 NICOTINAMIDE-ADENINE-DINUCLEOTIDE × 2 MAGNESIUM ION × 2 TETRAETHYLENE GLYCOL × 1 water × 2	Consistent with protein count
2	Protein monomer	Monomer	Protein 1	FLAVIN-ADENINE DINUCLEOTIDE × 1 DI(HYDROXYETHYL)ETHER × 4 TRIETHYLENE GLYCOL × 2 FORMIC ACID × 4 (3S)-piperidine-3-carboxylic acid × 1 (3R)-piperidine-3-carboxylic acid × 1 SULFATE ION × 5 NICOTINAMIDE-ADENINE-DINUCLEOTIDE × 1 MAGNESIUM ION × 1 water × 1	Consistent with protein count
3	Protein monomer	Monomer	Protein 1	FLAVIN-ADENINE DINUCLEOTIDE × 1 DI(HYDROXYETHYL)ETHER × 3 TRIETHYLENE GLYCOL × 2 FORMIC ACID × 2 (3S)-piperidine-3-carboxylic acid × 1 (3R)-piperidine-3-carboxylic acid × 1 SULFATE ION × 2 NICOTINAMIDE-ADENINE-DINUCLEOTIDE × 1 MAGNESIUM ION × 1 TETRAETHYLENE GLYCOL × 1 water × 1	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 3–1235； UniProt 1–1233 Author chain B； PDBConstruct 3–1235； UniProt 1–1233

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	9dl6
Deposition date deposition_date	2024-09-10
Structure title title	Structure of proline utilization A complexed with piperidine-3-carboxylic acid
Keywords keywords	;FLAVOENZYME, ROSSMANN FOLD, PROLINE DEHYDROGENASE, ALDEHYDE DEHYDROGENASE, PROLINE CATABOLISM, SUBSTRATE CHANNELING, BIFUNCTIONAL ENZYME, 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.

9dl6__assembly_2__model_1

Assembly 2 · Model 1 · CRYSOL 4.1.3-1-20251215 (887e7ef)

Download this curve (.dat)

9dl6__assembly_2__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

9dl6__assembly_2__model_1 | P(r) · Pending

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

Rg（Guinier）	33.17 Å
Rg (electron density)	32.43 Å
Total Rg	32.95 Å
Atom count	9211
Residues	1218
Excluded volume	163380 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`9dl6__assembly_1__model_1`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`9dl6__assembly_2__model_1`	monomeric （1）	Success	4.1.3-1-20251215 (887e7ef)	View Download
3	1	`9dl6__assembly_3__model_1`	monomeric （1）	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 (12)

Entity 1 Entity 1 polymer

Description description	Bifunctional protein PutA
Molecular weight formula_weight	131961.7 kDa
EC 编号 ec_number	1.5.5.2,1.2.1.88
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	21184

SMMSPNPLQKPAIDAAPAPFADFAPPVRPQSTLRRAITAAYRRPETECLPPLVEAATQSKEIRDAAASTARKLIEALRGKHSGSGVEGLVQEYSLSSQEGVALMCLAEALLRIPDTATRDALIRDKIADGNWKSHLGGSRSLFVNAATWGLVVTGKLTSTVNDRSLAAALTRLISRCGEPVIRRGVDMAMRMMGEQFVTGETIREALKRSKELEEKGFSYSYDMLGEAATTAADAERYYRDYESAIHAIGKASAGRGIYEGPGISIKLSALHPRYSRAQAARVMGELLPRVKALALLAKNYDIGLNIDAEEADRLELSLDLLEVLCLDGDLSGWNGMGFVVQAYGKRCPFVLDFIIDLARRSGRRIMVRLVKGAYWDAEIKRAQLDGLADFPVFTRKIHTDVSYIACAAKLLAATDVVFPQFATHNAQTLAAIYHMAGKDFHVGKYEFQCLHGMGEPLYEEVVGRGKLDRPCRIYAPVGTHETLLAYLVRRLLENGANSSFVHRINDPKVSIDELIADPVEVVRAMPVVGAKHDRIALPAELFGDARTNSAGLDLSNEETLASLTEALRESAAMKWTALPQLATGPAAGETRTVLNPGDHRDVVGSVTETSEEDARRAVRLAADAAPDWAAVPPSERAACLDRAAELMQARMPTLLGLIIREAGKSALNAIAEVREAIDFLRYYAEQTRRTLGPGHGPLGPIVCISPWNFPLAIFTGQIAAALVAGNPVLAKPAEETPLIAAEGVRILREAGIPASALQLLPGDGRVGAALVAAAETAGVMFTGSTEVARLIQAQLADRLSPAGRPIPLIAETGGQNAMIVDSSALAEQVVGDVITSAFDSAGQRCSALRVLCLQEDVADRILTMLKGALHELHIGRTDRLSVDVGPVITSEAKDNIEKHIERMRGLGRKVEQIGLASETGVGTFVPPTIIELEKLSDLQREVFGPVLHVIRYRRDDLDRLVDDVNATGYGLTFGLHTRLDETIAHVTSRIKAGNLYINRNIIGAVVGVQPFGGRGLSGTGPKAGGPLYLGRLVTTAPVPPQHSSVHTDPVLLDFAKWLDGKGARAEAEAARNAGSSSALGLDLELPGPVGERNLYTLHARGRILLVPATESGLYHQLAAALATGNSVAIDAASGLQASLKNLPQTVGLRVSWSKDWAADGPFAGALVEGDAERIRAVNKAIAALPGPLLLVQAASSGEIARNPDAYCLNWLVEEVSASINTAAAGGNASLMAIG

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	FLAVIN-ADENINE DINUCLEOTIDE
Molecular weight formula_weight	785.5 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 3 Entity 3 non-polymer

Description description	DI(HYDROXYETHYL)ETHER
Molecular weight formula_weight	106.1 kDa
Source method src_method	syn
Copy count entity_count	7

Entity 4 Entity 4 non-polymer

Description description	TRIETHYLENE GLYCOL
Molecular weight formula_weight	150.2 kDa
Source method src_method	syn
Copy count entity_count	4

Entity 5 Entity 5 non-polymer

Description description	FORMIC ACID
Molecular weight formula_weight	46.0 kDa
Source method src_method	syn
Copy count entity_count	6

Entity 6 Entity 6 non-polymer

Description description	(3S)-piperidine-3-carboxylic acid
Molecular weight formula_weight	129.2 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 7 Entity 7 non-polymer

Description description	(3R)-piperidine-3-carboxylic acid
Molecular weight formula_weight	129.2 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 8 Entity 8 non-polymer

Description description	SULFATE ION
Molecular weight formula_weight	96.1 kDa
Source method src_method	syn
Copy count entity_count	7

Entity 9 Entity 9 non-polymer

Description description	NICOTINAMIDE-ADENINE-DINUCLEOTIDE
Molecular weight formula_weight	663.4 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 10 Entity 10 non-polymer

Description description	MAGNESIUM ION
Molecular weight formula_weight	24.3 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 11 Entity 11 non-polymer

Description description	TETRAETHYLENE GLYCOL
Molecular weight formula_weight	194.2 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 12 Entity 12 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	2422

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Unit-cell length a length_a	100.514 Å
Unit-cell length b length_b	101.828 Å
Unit-cell length c length_c	126.545 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	106.43 °
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	1.420 Å
Low-resolution limit resolution_low	45.850 Å
R factor r_factor	0.1685
R_work r_work	0.1674
R_free r_free	0.1889

Structure of proline utilization A complexed with piperidine-3-carboxylic acid

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

9dl6__assembly_2__model_1

9dl6__assembly_2__model_1 | I(q)

9dl6__assembly_2__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 (12)

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 non-polymer

Entity 6 Entity 6 non-polymer

Entity 7 Entity 7 non-polymer

Entity 8 Entity 8 non-polymer

Entity 9 Entity 9 non-polymer

Entity 10 Entity 10 non-polymer

Entity 11 Entity 11 non-polymer

Entity 12 Entity 12 water

7. Citations (1)

Structure of proline utilization A complexed with piperidine-3-carboxylic acid

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

9dl6__assembly_2__model_1

9dl6__assembly_2__model_1 | I(q)

9dl6__assembly_2__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 (12)

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 non-polymer

Entity 6 Entity 6 non-polymer

Entity 7 Entity 7 non-polymer

Entity 8 Entity 8 non-polymer

Entity 9 Entity 9 non-polymer

Entity 10 Entity 10 non-polymer

Entity 11 Entity 11 non-polymer

Entity 12 Entity 12 water

7. Citations (1)