1vkd

Crystal structure of a predicted glycosidase (tm1225) from thermotoga maritima msb8 at 2.10 A resolution

Method: X-RAY DIFFRACTION

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

conserved hypothetical protein TM1225

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	2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL × 1 water × 2	Consistent with protein count
2	Protein homooligomer	Homooligomer	Protein 2	2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL × 1 water × 2	Consistent with protein count
3	Protein homooligomer	Homooligomer	Protein 2	water × 2	Consistent with protein count
4	Protein homooligomer	Homooligomer	Protein 6	2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL × 2 water × 6	Consistent with protein count
5	Protein homooligomer	Homooligomer	Protein 3	2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL × 1 water × 3	Consistent with protein count
6	Protein homooligomer	Homooligomer	Protein 3	2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL × 1 water × 3	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	Q9X0V2_THEMA
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 13–338； UniProt 1–326 Author chain B； PDBConstruct 13–338； UniProt 1–326 Author chain C； PDBConstruct 13–338； UniProt 1–326 Author chain D； PDBConstruct 13–338； UniProt 1–326 Author chain E； PDBConstruct 13–338； UniProt 1–326 Author chain F； PDBConstruct 13–338； UniProt 1–326

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	1vkd
Deposition date deposition_date	2004-05-12
Structure title title	Crystal structure of a predicted glycosidase (tm1225) from thermotoga maritima msb8 at 2.10 A resolution
Keywords keywords	Structural genomics, Joint Center for Structural Genomics, JCSG, Protein Structure Initiative, PSI, hydrolase; HYDROLASE
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.

1vkd__assembly_1__model_1

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

Download this curve (.dat)

1vkd__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

1vkd__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	27.97 Å
Rg (electron density)	27.32 Å
Total Rg	28.06 Å
Atom count	5302
Residues	643
Excluded volume	94226 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`1vkd__assembly_1__model_1`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`1vkd__assembly_2__model_1`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
3	1	`1vkd__assembly_3__model_1`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
4	1	`1vkd__assembly_4__model_1`	hexameric （6）	Success	4.1.3-1-20251215 (887e7ef)	View Download
5	1	`1vkd__assembly_5__model_1`	trimeric （3）	Success	4.1.3-1-20251215 (887e7ef)	View Download
6	1	`1vkd__assembly_6__model_1`	trimeric （3）	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 (3)

Entity 1 Entity 1 polymer

Description description	conserved hypothetical protein TM1225
Molecular weight formula_weight	38994.1 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	16823

MGSDKIHHHHHHMKVFTEKIPNIPWEERPEGYTGPVWRYSKNPIIGRNPVPKGARVFNSAVVPYNGEFVGVFRIDHKNTRPFLHFGRSKDGINWEIEPEEIQWVDVNGEPFQPSYAYDPRVVKIEDTYYITFCTDDHGPTIGVGMTKDFKTFVRLPNAYVPFNRNGVLFPRKINGKYVMLNRPSDNGHTPFGDIFLSESPDMIHWGNHRFVLGRSSYNWWENLKIGAGPYPIETSEGWLLIYHGVTLTCNGYVYSFGAALLDLDDPSKVLYRSRYYLLTPEEEYETVGFVPNVVFPCAALCDADTGRVAIYYGAADTHVALAFGYIDEIVDFVKRNSM

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	2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL
Molecular weight formula_weight	122.1 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 3 Entity 3 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	954

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6. Fold Classification (SCOP + CATH) 13 domains

SCOP 2.08 (7 domains)

Domain ID domain_id	d1vkda1
Class class	b — All beta proteins
Fold Fold fold	b.67 — 5-bladed beta-propeller
Superfamily Superfamily superfamily	b.67.2 — Arabinanase/levansucrase/invertase
Family Family family	b.67.2.4 — TM1225-like predicted glycosylases

Domain ID domain_id	d1vkda2
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	d1vkdb_
Class class	b — All beta proteins
Fold Fold fold	b.67 — 5-bladed beta-propeller
Superfamily Superfamily superfamily	b.67.2 — Arabinanase/levansucrase/invertase
Family Family family	b.67.2.4 — TM1225-like predicted glycosylases

Domain ID domain_id	d1vkdc_
Class class	b — All beta proteins
Fold Fold fold	b.67 — 5-bladed beta-propeller
Superfamily Superfamily superfamily	b.67.2 — Arabinanase/levansucrase/invertase
Family Family family	b.67.2.4 — TM1225-like predicted glycosylases

Domain ID domain_id	d1vkdd_
Class class	b — All beta proteins
Fold Fold fold	b.67 — 5-bladed beta-propeller
Superfamily Superfamily superfamily	b.67.2 — Arabinanase/levansucrase/invertase
Family Family family	b.67.2.4 — TM1225-like predicted glycosylases

Domain ID domain_id	d1vkde_
Class class	b — All beta proteins
Fold Fold fold	b.67 — 5-bladed beta-propeller
Superfamily Superfamily superfamily	b.67.2 — Arabinanase/levansucrase/invertase
Family Family family	b.67.2.4 — TM1225-like predicted glycosylases

Domain ID domain_id	d1vkdf_
Class class	b — All beta proteins
Fold Fold fold	b.67 — 5-bladed beta-propeller
Superfamily Superfamily superfamily	b.67.2 — Arabinanase/levansucrase/invertase
Family Family family	b.67.2.4 — TM1225-like predicted glycosylases

CATH v4.4 (6 domains)

Domain ID domain_id	1vkdA00
Class class	2 — Mainly Beta
Architecture architecture	115 — 5 Propeller
Topology topology	10 — Tachylectin-2; Chain A
Homologous superfamily homologous superfamily	20 — Glycosyl hydrolase domain; family 43

Domain ID domain_id	1vkdB00
Class class	2 — Mainly Beta
Architecture architecture	115 — 5 Propeller
Topology topology	10 — Tachylectin-2; Chain A
Homologous superfamily homologous superfamily	20 — Glycosyl hydrolase domain; family 43

Domain ID domain_id	1vkdC00
Class class	2 — Mainly Beta
Architecture architecture	115 — 5 Propeller
Topology topology	10 — Tachylectin-2; Chain A
Homologous superfamily homologous superfamily	20 — Glycosyl hydrolase domain; family 43

Domain ID domain_id	1vkdD00
Class class	2 — Mainly Beta
Architecture architecture	115 — 5 Propeller
Topology topology	10 — Tachylectin-2; Chain A
Homologous superfamily homologous superfamily	20 — Glycosyl hydrolase domain; family 43

Domain ID domain_id	1vkdE00
Class class	2 — Mainly Beta
Architecture architecture	115 — 5 Propeller
Topology topology	10 — Tachylectin-2; Chain A
Homologous superfamily homologous superfamily	20 — Glycosyl hydrolase domain; family 43

Domain ID domain_id	1vkdF00
Class class	2 — Mainly Beta
Architecture architecture	115 — 5 Propeller
Topology topology	10 — Tachylectin-2; Chain A
Homologous superfamily homologous superfamily	20 — Glycosyl hydrolase domain; family 43

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Unit-cell length a length_a	86.867 Å
Unit-cell length b length_b	100.908 Å
Unit-cell length c length_c	253.433 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	2.100 Å
Low-resolution limit resolution_low	82.170 Å
R factor r_factor	0.1642
R_work r_work	0.1620
R_free r_free	0.2040

Crystal structure of a predicted glycosidase (tm1225) from thermotoga maritima msb8 at 2.10 A resolution

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

conserved hypothetical protein TM1225

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

1vkd__assembly_1__model_1

1vkd__assembly_1__model_1 | I(q)

1vkd__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 (3)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 non-polymer

Entity 3 Entity 3 water

6. Fold Classification (SCOP + CATH) 13 domains

SCOP 2.08 (7 domains)

CATH v4.4 (6 domains)

7. Citations (1)

Crystal structure of a predicted glycosidase (tm1225) from thermotoga maritima msb8 at 2.10 A resolution

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

conserved hypothetical protein TM1225

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

1vkd__assembly_1__model_1

1vkd__assembly_1__model_1 | I(q)

1vkd__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 (3)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 non-polymer

Entity 3 Entity 3 water

6. Fold Classification (SCOP + CATH) 13 domains

SCOP 2.08 (7 domains)

CATH v4.4 (6 domains)

7. Citations (1)