1t9k

X-ray crystal structure of aIF-2B alpha subunit-related translation initiation factor [Thermotoga maritima]

Method: X-RAY DIFFRACTION

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

Probable methylthioribose-1-phosphate isomerase

Thermotoga maritima

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein homooligomer	Homooligomer	Protein 2	SULFATE ION × 2 CHLORIDE ION × 2 water × 2	Consistent with protein count
2	Protein homooligomer	Homooligomer	Protein 2	SULFATE ION × 2 water × 2	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	MTNA_THEMA
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 3–345； UniProt 1–343 Author chain B； PDBConstruct 3–345； UniProt 1–343 Author chain C； PDBConstruct 3–345； UniProt 1–343 Author chain D； PDBConstruct 3–345； UniProt 1–343

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	1t9k
Deposition date deposition_date	2004-05-17
Structure title title	X-ray crystal structure of aIF-2B alpha subunit-related translation initiation factor [Thermotoga maritima]
Keywords keywords	;structural genomics, translation initiation factor, aIF-2B subunit, PSI, Protein Structure Initiative, Midwest Center for Structural Genomics, MCSG, ISOMERASE ;; ISOMERASE
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.

1t9k__assembly_1__model_1

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

Download this curve (.dat)

1t9k__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

1t9k__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	28.67 Å
Rg (electron density)	28.31 Å
Total Rg	28.78 Å
Atom count	5312
Residues	664
Excluded volume	95466 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`1t9k__assembly_1__model_1`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`1t9k__assembly_2__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 (4)

Entity 1 Entity 1 polymer

Description description	Probable methylthioribose-1-phosphate isomerase
Molecular weight formula_weight	38859.2 kDa
EC 编号 ec_number	5.3.1.23
Source method src_method	man
Copy count entity_count	4

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B,C,D
Atom count atom_count	10854

GHMKLKTKTMEWSGNSLKLLDQRKLPFIEEYVECKTHEEVAHAIKEMIVRGAPAIGVAAAFGYVLGLRDYKTGSLTDWMKQVKETLARTRPTAVNLFWALNRMEKVFFENADRENLFEILENEALKMAYEDIEVNKAIGKNGAQLIKDGSTILTHCNAGALATVDYGTALGVIRAAVESGKRIRVFADETRPYLQGARLTAWELMKDGIEVYVITDNMAGWLMKRGLIDAVVVGADRIALNGDTANKIGTYSLAVLAKRNNIPFYVAAPVSTIDPTIRSGEEIPIEERRPEEVTHCGGNRIAPEGVKVLNPAFDVTENTLITAIITEKGVIRPPFEENIKKILEVGS

Source Source

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

Entity 2 Entity 2 non-polymer

Description description	SULFATE ION
Molecular weight formula_weight	96.1 kDa
Source method src_method	syn
Copy count entity_count	4

Entity 3 Entity 3 non-polymer

Description description	CHLORIDE ION
Molecular weight formula_weight	35.5 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 4 Entity 4 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	198

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6. Fold Classification (SCOP + CATH) 12 domains

SCOP 2.08 (4 domains)

Domain ID domain_id	d1t9ka_
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.124 — NagB/RpiA/CoA transferase-like
Superfamily Superfamily superfamily	c.124.1 — NagB/RpiA/CoA transferase-like
Family Family family	c.124.1.5 — IF2B-like

Domain ID domain_id	d1t9kb_
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.124 — NagB/RpiA/CoA transferase-like
Superfamily Superfamily superfamily	c.124.1 — NagB/RpiA/CoA transferase-like
Family Family family	c.124.1.5 — IF2B-like

Domain ID domain_id	d1t9kc_
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.124 — NagB/RpiA/CoA transferase-like
Superfamily Superfamily superfamily	c.124.1 — NagB/RpiA/CoA transferase-like
Family Family family	c.124.1.5 — IF2B-like

Domain ID domain_id	d1t9kd_
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.124 — NagB/RpiA/CoA transferase-like
Superfamily Superfamily superfamily	c.124.1 — NagB/RpiA/CoA transferase-like
Family Family family	c.124.1.5 — IF2B-like

CATH v4.4 (8 domains)

Domain ID domain_id	1t9kA01
Class class	1 — Mainly Alpha
Architecture architecture	20 — Up-down Bundle
Topology topology	120 — Four Helix Bundle (Hemerythrin (Met), subunit A)
Homologous superfamily homologous superfamily	420 — translation initiation factor eif-2b, domain 1

Domain ID domain_id	1t9kA02
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	10470 — Translation initiation factor eif-2b; domain 2

Domain ID domain_id	1t9kB01
Class class	1 — Mainly Alpha
Architecture architecture	20 — Up-down Bundle
Topology topology	120 — Four Helix Bundle (Hemerythrin (Met), subunit A)
Homologous superfamily homologous superfamily	420 — translation initiation factor eif-2b, domain 1

Domain ID domain_id	1t9kB02
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	10470 — Translation initiation factor eif-2b; domain 2

Domain ID domain_id	1t9kC01
Class class	1 — Mainly Alpha
Architecture architecture	20 — Up-down Bundle
Topology topology	120 — Four Helix Bundle (Hemerythrin (Met), subunit A)
Homologous superfamily homologous superfamily	420 — translation initiation factor eif-2b, domain 1

Domain ID domain_id	1t9kC02
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	10470 — Translation initiation factor eif-2b; domain 2

Domain ID domain_id	1t9kD01
Class class	1 — Mainly Alpha
Architecture architecture	20 — Up-down Bundle
Topology topology	120 — Four Helix Bundle (Hemerythrin (Met), subunit A)
Homologous superfamily homologous superfamily	420 — translation initiation factor eif-2b, domain 1

Domain ID domain_id	1t9kD02
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	10470 — Translation initiation factor eif-2b; domain 2

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Unit-cell length a length_a	103.885 Å
Unit-cell length b length_b	103.885 Å
Unit-cell length c length_c	259.929 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	90.00 °
Unit-cell angle γ angle_gamma	120.00 °
Molecules per unit cell Z z_pdb	24

Space group space_group	P 31 2 1
Space-group number int_tables_number	152
Crystal system crystal_system	—

Resolution resolution	2.600 Å
Low-resolution limit resolution_low	34.330 Å
R factor r_factor	0.2390
R_work r_work	0.2390
R_free r_free	0.2980

X-ray crystal structure of aIF-2B alpha subunit-related translation initiation factor [Thermotoga maritima]

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

Probable methylthioribose-1-phosphate isomerase

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

1t9k__assembly_1__model_1

1t9k__assembly_1__model_1 | I(q)

1t9k__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 (4)

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 water

6. Fold Classification (SCOP + CATH) 12 domains

SCOP 2.08 (4 domains)

CATH v4.4 (8 domains)

7. Citations (1)

X-ray crystal structure of aIF-2B alpha subunit-related translation initiation factor [Thermotoga maritima]

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

Probable methylthioribose-1-phosphate isomerase

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

1t9k__assembly_1__model_1

1t9k__assembly_1__model_1 | I(q)

1t9k__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 (4)

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 water

6. Fold Classification (SCOP + CATH) 12 domains

SCOP 2.08 (4 domains)

CATH v4.4 (8 domains)

7. Citations (1)