2iss

Structure of the PLP synthase Holoenzyme from Thermotoga maritima

Method: X-RAY DIFFRACTION

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

Pyridoxal biosynthesis lyase pdxS

Thermotoga maritima

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 24	Glutamine amidotransferase subunit pdxT × 12 （Q9WYU3） RIBULOSE-5-PHOSPHATE × 12 PHOSPHATE ION × 12 water × 24	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	PDXS_THEMA
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 21–313； UniProt 1–293 Author chain B； PDBConstruct 21–313； UniProt 1–293 Author chain C； PDBConstruct 21–313； UniProt 1–293

Glutamine amidotransferase subunit pdxT

Thermotoga maritima

UniProt Q9WYU3

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 24	Pyridoxal biosynthesis lyase pdxS × 12 （Q9WYU4） RIBULOSE-5-PHOSPHATE × 12 PHOSPHATE ION × 12 water × 24	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	PDXT_THEMA
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain D； PDBConstruct 21–208； UniProt 1–188 Author chain E； PDBConstruct 21–208； UniProt 1–188 Author chain F； PDBConstruct 21–208； 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	2iss
Deposition date deposition_date	2006-10-18
Structure title title	Structure of the PLP synthase Holoenzyme from Thermotoga maritima
Keywords keywords	(beta/alpha)8-barrel, alpha/beta three layer sandwich, LYASE, TRANSFERASE; LYASE, TRANSFERASE
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.

2iss__assembly_1__model_1

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

Download this curve (.dat)

2iss__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

2iss__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	59.28 Å
Rg (electron density)	59.18 Å
Total Rg	59.24 Å
Atom count	43288
Residues	5596
Excluded volume	781560 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`2iss__assembly_1__model_1`	24-meric （24）	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	Pyridoxal biosynthesis lyase pdxS
Molecular weight formula_weight	34345.1 kDa
EC 编号 ec_number	4.-.-.-
Source method src_method	man
Copy count entity_count	3

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B,C
Atom count atom_count	10860

MGSSHHHHHHSSGLVPRGSHMEIKKGTWIIKKGFAEMFKGGVIMDVTSAEQAKIAEEAGAVAVMALERVPADIRKEGGVARMASIAKIREIMEAVSIPVMAKVRIGHIAEAKILEELGVDFIDESEVLTPADDRFHINKHEFKVPFVCGARDLGEALRRIAEGAAMIRTKGEAGTGNVVEAVKHMRRVMEQIKQVTKMEDEELVAYGKEIGAPVELLREVKRLGRLPVVNFAAGGVATPADAALMMMLGADGVFVGSGIFKSKDPRKMAKAMVLAVTYWDNPRILLKISEDIGEPMRGLDVEELEVRMQERGW

Source Source

Source organism organism	Thermotoga maritima
NCBI taxonomy ID ncbi_taxonomy_id	2336
Host organism host_organism	Escherichia coli

Entity 2 Entity 2 polymer

Description description	Glutamine amidotransferase subunit pdxT
Molecular weight formula_weight	23376.1 kDa
EC 编号 ec_number	2.6.-.-
Source method src_method	man
Copy count entity_count	3

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	D,E,F

MGSSHHHHHHSSGLVPRGSHMKIGVLGVQGDVREHVEALHKLGVETLIVKLPEQLDMVDGLILPGGESTTMIRILKEMDMDEKLVERINNGLPVFATCAGVILLAKRIKNYSQEKLGVLDITVERNAYGRQVESFETFVEIPAVGKDPFRAIFIRAPRIVETGKNVEILATYDYDPVLVKEGNILACTFHPELTDDLRLHRYFLEMVK

Source Source

Source organism organism	Thermotoga maritima
NCBI taxonomy ID ncbi_taxonomy_id	2336
Host organism host_organism	Escherichia coli

Entity 3 Entity 3 non-polymer

Description description	RIBULOSE-5-PHOSPHATE
Molecular weight formula_weight	230.1 kDa
Source method src_method	syn
Copy count entity_count	3

Entity 4 Entity 4 non-polymer

Description description	PHOSPHATE ION
Molecular weight formula_weight	95.0 kDa
Source method src_method	syn
Copy count entity_count	3

Entity 5 Entity 5 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	38

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6. Fold Classification (SCOP + CATH) 15 domains

SCOP 2.08 (9 domains)

Domain ID domain_id	d2issa1
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.1 — TIM beta/alpha-barrel
Superfamily Superfamily superfamily	c.1.2 — Ribulose-phoshate binding barrel
Family Family family	c.1.2.6 — PdxS-like

Domain ID domain_id	d2issa2
Class class	l — Artifacts
Fold Fold fold	l.1 — Tags
Superfamily Superfamily superfamily	l.1.1 — Tags
Family Family family	l.1.1.1 — Tags

Domain ID domain_id	d2issb1
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.1 — TIM beta/alpha-barrel
Superfamily Superfamily superfamily	c.1.2 — Ribulose-phoshate binding barrel
Family Family family	c.1.2.6 — PdxS-like

Domain ID domain_id	d2issb2
Class class	l — Artifacts
Fold Fold fold	l.1 — Tags
Superfamily Superfamily superfamily	l.1.1 — Tags
Family Family family	l.1.1.1 — Tags

Domain ID domain_id	d2issc_
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.1 — TIM beta/alpha-barrel
Superfamily Superfamily superfamily	c.1.2 — Ribulose-phoshate binding barrel
Family Family family	c.1.2.6 — PdxS-like

Domain ID domain_id	d2issd1
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.23 — Flavodoxin-like
Superfamily Superfamily superfamily	c.23.16 — Class I glutamine amidotransferase-like
Family Family family	c.23.16.1 — Class I glutamine amidotransferases (GAT)

Domain ID domain_id	d2issd2
Class class	l — Artifacts
Fold Fold fold	l.1 — Tags
Superfamily Superfamily superfamily	l.1.1 — Tags
Family Family family	l.1.1.1 — Tags

Domain ID domain_id	d2isse_
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.23 — Flavodoxin-like
Superfamily Superfamily superfamily	c.23.16 — Class I glutamine amidotransferase-like
Family Family family	c.23.16.1 — Class I glutamine amidotransferases (GAT)

Domain ID domain_id	d2issf_
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.23 — Flavodoxin-like
Superfamily Superfamily superfamily	c.23.16 — Class I glutamine amidotransferase-like
Family Family family	c.23.16.1 — Class I glutamine amidotransferases (GAT)

CATH v4.4 (6 domains)

Domain ID domain_id	2issA00
Class class	3 — Alpha Beta
Architecture architecture	20 — Alpha-Beta Barrel
Topology topology	20 — TIM Barrel
Homologous superfamily homologous superfamily	70 — Aldolase class I

Domain ID domain_id	2issB00
Class class	3 — Alpha Beta
Architecture architecture	20 — Alpha-Beta Barrel
Topology topology	20 — TIM Barrel
Homologous superfamily homologous superfamily	70 — Aldolase class I

Domain ID domain_id	2issC00
Class class	3 — Alpha Beta
Architecture architecture	20 — Alpha-Beta Barrel
Topology topology	20 — TIM Barrel
Homologous superfamily homologous superfamily	70 — Aldolase class I

Domain ID domain_id	2issD00
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	880 — Class I glutamine amidotransferase (GATase) domain

Domain ID domain_id	2issE00
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	880 — Class I glutamine amidotransferase (GATase) domain

Domain ID domain_id	2issF00
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	880 — Class I glutamine amidotransferase (GATase) domain

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Unit-cell length a length_a	92.529 Å
Unit-cell length b length_b	204.098 Å
Unit-cell length c length_c	221.336 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	24

Space group space_group	I 2 2 2
Space-group number int_tables_number	23
Crystal system crystal_system	—

Resolution resolution	2.900 Å
Low-resolution limit resolution_low	46.340 Å
R factor r_factor	0.2130
R_work r_work	0.2130
R_free r_free	0.2360

Structure of the PLP synthase Holoenzyme from Thermotoga maritima

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

Pyridoxal biosynthesis lyase pdxS

State in the Current Structure

Other States of the Same Protein in the Database

Glutamine amidotransferase subunit pdxT

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

2iss__assembly_1__model_1

2iss__assembly_1__model_1 | I(q)

2iss__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 polymer

Polymer Polymer

Source Source

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 non-polymer

Entity 5 Entity 5 water

6. Fold Classification (SCOP + CATH) 15 domains

SCOP 2.08 (9 domains)

CATH v4.4 (6 domains)

7. Citations (1)

Structure of the PLP synthase Holoenzyme from Thermotoga maritima

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

Pyridoxal biosynthesis lyase pdxS

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

Glutamine amidotransferase subunit pdxT

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

2iss__assembly_1__model_1

2iss__assembly_1__model_1 | I(q)

2iss__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 polymer

Polymer Polymer

Source Source

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 non-polymer

Entity 5 Entity 5 water

6. Fold Classification (SCOP + CATH) 15 domains

SCOP 2.08 (9 domains)

CATH v4.4 (6 domains)

7. Citations (1)