1vkm

Crystal structure of an indigoidine synthase a (idga)-like protein (tm1464) from thermotoga maritima msb8 at 1.90 A resolution

Method: X-RAY DIFFRACTION

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

conserved hypothetical protein TM1464

Thermotoga maritima

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein homooligomer	Homooligomer	Protein 3	MANGANESE (II) ION × 8 UNKNOWN LIGAND × 3 1,2-ETHANEDIOL × 6 water × 3	Consistent with protein count
2	Protein homooligomer	Homooligomer	Protein 3	MANGANESE (II) ION × 8 UNKNOWN LIGAND × 3 1,2-ETHANEDIOL × 5 water × 3	Consistent with protein count
3	Protein homooligomer	Homooligomer	Protein 6	MANGANESE (II) ION × 16 UNKNOWN LIGAND × 6 1,2-ETHANEDIOL × 11 water × 6	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	Q9X1H5_THEMA
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 13–297； UniProt 1–285 Author chain B； PDBConstruct 13–297； UniProt 1–285 Author chain C； PDBConstruct 13–297； UniProt 1–285 Author chain D； PDBConstruct 13–297； UniProt 1–285 Author chain E； PDBConstruct 13–297； UniProt 1–285 Author chain F； PDBConstruct 13–297； UniProt 1–285

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	1vkm
Deposition date deposition_date	2004-06-09
Structure title title	Crystal structure of an indigoidine synthase a (idga)-like protein (tm1464) from thermotoga maritima msb8 at 1.90 A resolution
Keywords keywords	;Indigoidine synthase a-like fold, structural genomics, Joint Center for Structural Genomics, JCSG, Protein Structure Initiative, PSI, biosynthetic protein ;; BIOSYNTHETIC PROTEIN
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.

1vkm__assembly_1__model_1

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

Download this curve (.dat)

1vkm__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

1vkm__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	28.74 Å
Rg (electron density)	27.73 Å
Total Rg	28.41 Å
Atom count	6905
Residues	846
Excluded volume	124930 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`1vkm__assembly_1__model_1`	trimeric （3）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`1vkm__assembly_2__model_1`	trimeric （3）	Success	4.1.3-1-20251215 (887e7ef)	View Download
3	1	`1vkm__assembly_3__model_1`	hexameric （6）	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	conserved hypothetical protein TM1464
Molecular weight formula_weight	33717.5 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	14927

MGSDKIHHHHHHVIIESRIEKGKPVVGMETTVFVHGLPRKEAIELFRRAKEISREKGFQLAVIGILKGKIVAGMSEEELEAMMREGADKVGTREIPIVVAEGKNAATTVSATIFLSRRIGIEVVVTGGTGGVHPGRVDVSQDLTEMSSSRAVLVSSGIKSILDVEATFEMLETLEIPLVGFRTNEFPLFFSRKSGRRVPRIENVEEVLKIYESMKEMELEKTLMVLNPVPEEYEIPHDEIERLLEKIELEVEGKEVTPFLLKKLVEMTNGRTLKANLALLEENVKLAGEIAVKLKRS

Source Source

Source organism organism	Thermotoga maritima
NCBI taxonomy ID ncbi_taxonomy_id	243274
Host organism host_organism	Escherichia coli

Entity 2 Entity 2 non-polymer

Description description	MANGANESE (II) ION
Molecular weight formula_weight	54.9 kDa
Source method src_method	syn
Copy count entity_count	16

Entity 3 Entity 3 non-polymer

Description description	UNKNOWN LIGAND
Source method src_method	syn
Copy count entity_count	6

Entity 4 Entity 4 non-polymer

Description description	1,2-ETHANEDIOL
Molecular weight formula_weight	62.1 kDa
Source method src_method	syn
Copy count entity_count	11

Entity 5 Entity 5 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	984

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6. Fold Classification (SCOP + CATH) 18 domains

SCOP 2.08 (12 domains)

Domain ID domain_id	d1vkma1
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.138 — Indigoidine synthase A-like
Superfamily Superfamily superfamily	c.138.1 — Indigoidine synthase A-like
Family Family family	c.138.1.1 — Indigoidine synthase A-like

Domain ID domain_id	d1vkma2
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	d1vkmb1
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.138 — Indigoidine synthase A-like
Superfamily Superfamily superfamily	c.138.1 — Indigoidine synthase A-like
Family Family family	c.138.1.1 — Indigoidine synthase A-like

Domain ID domain_id	d1vkmb2
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	d1vkmc1
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.138 — Indigoidine synthase A-like
Superfamily Superfamily superfamily	c.138.1 — Indigoidine synthase A-like
Family Family family	c.138.1.1 — Indigoidine synthase A-like

Domain ID domain_id	d1vkmc2
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	d1vkmd1
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.138 — Indigoidine synthase A-like
Superfamily Superfamily superfamily	c.138.1 — Indigoidine synthase A-like
Family Family family	c.138.1.1 — Indigoidine synthase A-like

Domain ID domain_id	d1vkmd2
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	d1vkme1
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.138 — Indigoidine synthase A-like
Superfamily Superfamily superfamily	c.138.1 — Indigoidine synthase A-like
Family Family family	c.138.1.1 — Indigoidine synthase A-like

Domain ID domain_id	d1vkme2
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	d1vkmf1
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.138 — Indigoidine synthase A-like
Superfamily Superfamily superfamily	c.138.1 — Indigoidine synthase A-like
Family Family family	c.138.1.1 — Indigoidine synthase A-like

Domain ID domain_id	d1vkmf2
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

CATH v4.4 (6 domains)

Domain ID domain_id	1vkmA00
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	1790 — Indigoidine synthase fold
Homologous superfamily homologous superfamily	10 — Indigoidine synthase domain

Domain ID domain_id	1vkmB00
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	1790 — Indigoidine synthase fold
Homologous superfamily homologous superfamily	10 — Indigoidine synthase domain

Domain ID domain_id	1vkmC00
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	1790 — Indigoidine synthase fold
Homologous superfamily homologous superfamily	10 — Indigoidine synthase domain

Domain ID domain_id	1vkmD00
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	1790 — Indigoidine synthase fold
Homologous superfamily homologous superfamily	10 — Indigoidine synthase domain

Domain ID domain_id	1vkmE00
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	1790 — Indigoidine synthase fold
Homologous superfamily homologous superfamily	10 — Indigoidine synthase domain

Domain ID domain_id	1vkmF00
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	1790 — Indigoidine synthase fold
Homologous superfamily homologous superfamily	10 — Indigoidine synthase domain

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Unit-cell length a length_a	91.958 Å
Unit-cell length b length_b	130.799 Å
Unit-cell length c length_c	138.750 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	P 21 21 21
Space-group number int_tables_number	19
Crystal system crystal_system	—

Resolution resolution	1.900 Å
Low-resolution limit resolution_low	75.230 Å
R factor r_factor	0.1562
R_work r_work	0.1538
R_free r_free	0.1996

Crystal structure of an indigoidine synthase a (idga)-like protein (tm1464) from thermotoga maritima msb8 at 1.90 A resolution

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

conserved hypothetical protein TM1464

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

1vkm__assembly_1__model_1

1vkm__assembly_1__model_1 | I(q)

1vkm__assembly_1__model_1 | P(r) · Pending

4. Crystallography and Experiment 4. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

5. Entities and Polymers Entities & Polymers (5)

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 water

6. Fold Classification (SCOP + CATH) 18 domains

SCOP 2.08 (12 domains)

CATH v4.4 (6 domains)

7. Citations (1)

Crystal structure of an indigoidine synthase a (idga)-like protein (tm1464) from thermotoga maritima msb8 at 1.90 A resolution

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

conserved hypothetical protein TM1464

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

1vkm__assembly_1__model_1

1vkm__assembly_1__model_1 | I(q)

1vkm__assembly_1__model_1 | P(r) · Pending

4. Crystallography and Experiment 4. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

5. Entities and Polymers Entities & Polymers (5)

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 water

6. Fold Classification (SCOP + CATH) 18 domains

SCOP 2.08 (12 domains)

CATH v4.4 (6 domains)

7. Citations (1)