9u8s

Crystal structure of thiamine pyrophosphate (TPP)-dependent alpha-imino acid decarboxylase (AzcB and AzcC) from Streptomyces mobaraensis in complex with TPP and 5-azacytosine.

Method: X-RAY DIFFRACTION

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

Thiamine pyrophosphate enzyme N-terminal TPP-binding domain-containing protein

Streptomyces mobaraensis

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 12	Thiamine pyrophosphate enzyme TPP-binding domain-containing protein × 6 （A0A7X1IDK5） 6-amino-1,3,5-triazin-2(1H)-one × 6 ZINC ION × 3 THIAMINE DIPHOSPHATE × 6 MAGNESIUM ION × 6 GLYCEROL × 1 water × 12	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	A0A7X1IDQ3_9ACTN
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–168； UniProt 1–168 Author chain B； PDBConstruct 1–168； UniProt 1–168 Author chain C； PDBConstruct 1–168； UniProt 1–168 Author chain D； PDBConstruct 1–168； UniProt 1–168 Author chain E； PDBConstruct 1–168； UniProt 1–168 Author chain F； PDBConstruct 1–168； UniProt 1–168

Thiamine pyrophosphate enzyme TPP-binding domain-containing protein

Streptomyces mobaraensis

UniProt A0A7X1IDK5

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 12	Thiamine pyrophosphate enzyme N-terminal TPP-binding domain-containing protein × 6 （A0A7X1IDQ3） 6-amino-1,3,5-triazin-2(1H)-one × 6 ZINC ION × 3 THIAMINE DIPHOSPHATE × 6 MAGNESIUM ION × 6 GLYCEROL × 1 water × 12	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	A0A7X1IDK5_9ACTN
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain G； PDBConstruct 1–194； UniProt 1–194 Author chain H； PDBConstruct 1–194； UniProt 1–194 Author chain I； PDBConstruct 1–194； UniProt 1–194 Author chain J； PDBConstruct 1–194； UniProt 1–194 Author chain K； PDBConstruct 1–194； UniProt 1–194 Author chain L； PDBConstruct 1–194； UniProt 1–194

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	9u8s
Deposition date deposition_date	2025-03-26
Last revision last_revision	2026-04-01
Structure title title	Crystal structure of thiamine pyrophosphate (TPP)-dependent alpha-imino acid decarboxylase (AzcB and AzcC) from Streptomyces mobaraensis in complex with TPP and 5-azacytosine.
Keywords keywords	thiamine pyrophosphate (TPP)-dependent decarboxylase, AzcB, AzcC, 5-azacytidine biosynthesis, 5-azacytosine, LYASE; LYASE
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.

9u8s__assembly_1__model_1

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

Download this curve (.dat)

9u8s__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

9u8s__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	37.22 Å
Rg (electron density)	36.84 Å
Total Rg	37.22 Å
Atom count	16246
Residues	2157
Excluded volume	289590 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`9u8s__assembly_1__model_1`	dodecameric （12）	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	Thiamine pyrophosphate enzyme N-terminal TPP-binding domain-containing protein
Molecular weight formula_weight	18049.7 kDa
Source method src_method	man
Copy count entity_count	6

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B,C,D,E,F
Atom count atom_count	17135

MSAVTAYEALVGAGVEIVYAVPDSLLAPLCREASMRHEIRYMQVNDEATAVGLAAGARLAGARPLVVMENSGLRRACETLARLTMSHRLHTALLISRRGAFGEPNWWGIPHEETMHQHTAMLSLVTAEVDSCGELAECLRKAYATLDTGQRSVALVANAGLTAELRSA

Source Source

Source organism organism	Streptomyces mobaraensis
NCBI taxonomy ID ncbi_taxonomy_id	35621
Host organism host_organism	Streptomyces lividans

Entity 2 Entity 2 polymer

Description description	Thiamine pyrophosphate enzyme TPP-binding domain-containing protein
Molecular weight formula_weight	20528.6 kDa
Source method src_method	man
Copy count entity_count	6

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	G,H,I,J,K,L

MDTAEFLEALYDRLPTDSVSVAPLGRTSEVMYALRPADTLFTDTMGDVTAISLGMAMAAAPLSVVGIDTDGSFLMNLSVLMALGDQLPRLPNYTLAIVDNRLYESGGGLPSRKAALDWGSLFGAVGLKSILIETPHRIPDVLPLPGTVLIAAVHNPAPAPDALKTIDGVESSYQVERVLAERTGGTPRRPALKP

Source Source

Source organism organism	Streptomyces mobaraensis
NCBI taxonomy ID ncbi_taxonomy_id	35621
Host organism host_organism	Streptomyces lividans

Entity 3 Entity 3 non-polymer

Description description	6-amino-1,3,5-triazin-2(1H)-one
Molecular weight formula_weight	112.1 kDa
Source method src_method	syn
Copy count entity_count	6

Entity 4 Entity 4 non-polymer

Description description	ZINC ION
Molecular weight formula_weight	65.4 kDa
Source method src_method	syn
Copy count entity_count	3

Entity 5 Entity 5 non-polymer

Description description	THIAMINE DIPHOSPHATE
Molecular weight formula_weight	425.3 kDa
Source method src_method	syn
Copy count entity_count	6

Entity 6 Entity 6 non-polymer

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

Entity 7 Entity 7 non-polymer

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

Entity 8 Entity 8 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	883

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Unit-cell length a length_a	119.465 Å
Unit-cell length b length_b	96.918 Å
Unit-cell length c length_c	130.285 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	113.39 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	12

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

Resolution resolution	2.460 Å
Low-resolution limit resolution_low	48.460 Å
R factor r_factor	0.1909
R_work r_work	0.1900
R_free r_free	0.2328

Crystal structure of thiamine pyrophosphate (TPP)-dependent alpha-imino acid decarboxylase (AzcB and AzcC) from Streptomyces mobaraensis in complex with TPP and 5-azacytosine.

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

Thiamine pyrophosphate enzyme N-terminal TPP-binding domain-containing protein

State in the Current Structure

Other States of the Same Protein in the Database

Thiamine pyrophosphate enzyme TPP-binding domain-containing protein

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

9u8s__assembly_1__model_1

9u8s__assembly_1__model_1 | I(q)

9u8s__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 polymer

Polymer Polymer

Source Source

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

7. Citations (1)

Crystal structure of thiamine pyrophosphate (TPP)-dependent alpha-imino acid decarboxylase (AzcB and AzcC) from Streptomyces mobaraensis in complex with TPP and 5-azacytosine.

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

Thiamine pyrophosphate enzyme N-terminal TPP-binding domain-containing protein

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

Thiamine pyrophosphate enzyme TPP-binding domain-containing protein

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

9u8s__assembly_1__model_1

9u8s__assembly_1__model_1 | I(q)

9u8s__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 polymer

Polymer Polymer

Source Source

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

7. Citations (1)