2y27

crystal structure of PaaK1 in complex with ATP from Burkholderia cenocepacia

Method: X-RAY DIFFRACTION

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

PHENYLACETATE-COENZYME A LIGASE

BURKHOLDERIA CENOCEPACIA

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein homooligomer	Homooligomer	Protein 2	THIOCYANATE ION × 9 GLYCEROL × 5 BETA-MERCAPTOETHANOL × 5 TETRAETHYLENE GLYCOL × 1 ADENOSINE-5'-TRIPHOSPHATE × 2 MAGNESIUM ION × 6 water × 2	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	B4E7B5_BURCJ
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 7–437； UniProt 2–432 Author chain B； PDBConstruct 7–437； UniProt 2–432

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	2y27
Deposition date deposition_date	2010-12-13
Structure title title	crystal structure of PaaK1 in complex with ATP from Burkholderia cenocepacia
Keywords keywords	LIGASE, PHENYLACETIC ACID DEGRADATION PATHWAY; LIGASE
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.

2y27__assembly_1__model_1

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

Download this curve (.dat)

2y27__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

2y27__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	30.01 Å
Rg (electron density)	29.41 Å
Total Rg	30.02 Å
Atom count	6784
Residues	832
Excluded volume	120880 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`2y27__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 (8)

Entity 1 Entity 1 polymer

Description description	PHENYLACETATE-COENZYME A LIGASE
Molecular weight formula_weight	48709.6 kDa
EC 编号 ec_number	6.2.1.30
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	7801

GSHMASTTPLPLEPIETASRDELTALQLERLKWSLRHAYDHSPVYRRKFDEAGVHPDDLKTLADLSRFPFTTKGDLRDSYPFGMFAVPQDRISRIHASSGTTGKPTVVGYTAADIDTWANLVARSIRAAGARRGDKVHVSYGYGLFTGGLGAHYGAERAGLTVIPFGGGQTEKQVQLIQDFRPDIIMVTPSYMLSIADEIERQGLDPVQSSLRIGIFGAEPWTNDMRVAIEQRMGIDAVDIYGLSEVMGPGVASECVETKDGPTIWEDHFYPEIIDPETGEVLPDGELGELVFTSLTKEALPIIRYRTRDLTRLLPGTARTMRRMEKITGRSDDMMIVRGVNVFPTQIEEQLLKQRALAPHYQIVLTKEGPLDVLTLNVEPCPETAPDTAAIQVAKQALAYDIKSLIGVTAVINVLPVNGIERSVGKARRVVDKRKG

Source Source

Source organism organism	BURKHOLDERIA CENOCEPACIA
NCBI taxonomy ID ncbi_taxonomy_id	216591
Host organism host_organism	ESCHERICHIA COLI

Entity 2 Entity 2 non-polymer

Description description	THIOCYANATE ION
Molecular weight formula_weight	58.1 kDa
Source method src_method	syn
Copy count entity_count	9

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	5

Entity 4 Entity 4 non-polymer

Description description	BETA-MERCAPTOETHANOL
Molecular weight formula_weight	78.1 kDa
Source method src_method	syn
Copy count entity_count	5

Entity 5 Entity 5 non-polymer

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

Entity 6 Entity 6 non-polymer

Description description	ADENOSINE-5'-TRIPHOSPHATE
Molecular weight formula_weight	507.2 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 7 Entity 7 non-polymer

Description description	MAGNESIUM ION
Molecular weight formula_weight	24.3 kDa
Source method src_method	syn
Copy count entity_count	6

Entity 8 Entity 8 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	948

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6. Fold Classification (SCOP + CATH) 4 domains

CATH v4.4 (4 domains)

Domain ID domain_id	2y27A01
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	12780 — ANL, N-terminal domain

Domain ID domain_id	2y27A02
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	300 — GMP Synthetase; Chain A, domain 3
Homologous superfamily homologous superfamily	30 — ANL, C-terminal domain

Domain ID domain_id	2y27B01
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	12780 — ANL, N-terminal domain

Domain ID domain_id	2y27B02
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	300 — GMP Synthetase; Chain A, domain 3
Homologous superfamily homologous superfamily	30 — ANL, C-terminal domain

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Unit-cell length a length_a	56.710 Å
Unit-cell length b length_b	62.470 Å
Unit-cell length c length_c	78.490 Å
Unit-cell angle α angle_alpha	90.97 °
Unit-cell angle β angle_beta	109.81 °
Unit-cell angle γ angle_gamma	106.51 °
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	1.600 Å
Low-resolution limit resolution_low	29.980 Å
R factor r_factor	0.1658
R_work r_work	0.1643
R_free r_free	0.1941

crystal structure of PaaK1 in complex with ATP from Burkholderia cenocepacia

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

PHENYLACETATE-COENZYME A LIGASE

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

2y27__assembly_1__model_1

2y27__assembly_1__model_1 | I(q)

2y27__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 (8)

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 water

6. Fold Classification (SCOP + CATH) 4 domains

CATH v4.4 (4 domains)

7. Citations (1)

crystal structure of PaaK1 in complex with ATP from Burkholderia cenocepacia

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

PHENYLACETATE-COENZYME A LIGASE

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

2y27__assembly_1__model_1

2y27__assembly_1__model_1 | I(q)

2y27__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 (8)

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 water

6. Fold Classification (SCOP + CATH) 4 domains

CATH v4.4 (4 domains)

7. Citations (1)