SAXSdb — 1o4t

▼

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

putative oxalate decarboxylase

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	MANGANESE (II) ION × 2 OXALATE ION × 2 water × 2	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	Q9X113_THEMA
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 13–133； UniProt 1–121 Author chain B； PDBConstruct 13–133； UniProt 1–121

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.

▼

2. Structure Basics 2. Structure Basics

Entry ID entry_id	1o4t
Deposition date deposition_date	2003-07-03
Structure title title	Crystal structure of a predicted oxalate decarboxylase (tm1287) from thermotoga maritima at 1.95 A resolution
Keywords keywords	;Double-stranded beta-helix fold, structural genomics, Joint Center for Structural Genomics, JCSG, Protein Structure Initiative, PSI, lyase ;; LYASE
Experimental Method method	X-RAY DIFFRACTION

▼

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.

1o4t__assembly_1__model_1

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

Download this curve (.dat)

1o4t__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

1o4t__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	18.45 Å
Rg (electron density)	17.02 Å
Total Rg	17.94 Å
Atom count	1786
Residues	230
Excluded volume	31685 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`1o4t__assembly_1__model_1`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download

▶

4. Crystallography and Experiment 4. Crystallography & Experiment

▶

5. Entities and Polymers Entities & Polymers (4)

Entity 1 Entity 1 polymer

Description description	putative oxalate decarboxylase
Molecular weight formula_weight	14750.8 kDa
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B
Atom count atom_count	1993

MGSDKIHHHHHHMKEGTGMVVRSSEITPERISNMRGGKGEVEMAHLLSKEAMHNKARLFARMKLPPGSSVGLHKHEGEFEIYYILLGEGVFHDNGKDVPIKAGDVCFTDSGESHSIENTGNTDLEFLAVIILL

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	MANGANESE (II) ION
Molecular weight formula_weight	54.9 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 3 Entity 3 non-polymer

Description description	OXALATE ION
Molecular weight formula_weight	88.0 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

▼

6. Fold Classification (SCOP + CATH) 4 domains

SCOP 2.08 (2 domains)

Domain ID domain_id	d1o4ta_
Class class	b — All beta proteins
Fold Fold fold	b.82 — Double-stranded beta-helix
Superfamily Superfamily superfamily	b.82.1 — RmlC-like cupins
Family Family family	b.82.1.9 — TM1287-like

Domain ID domain_id	d1o4tb_
Class class	b — All beta proteins
Fold Fold fold	b.82 — Double-stranded beta-helix
Superfamily Superfamily superfamily	b.82.1 — RmlC-like cupins
Family Family family	b.82.1.9 — TM1287-like

CATH v4.4 (2 domains)

Domain ID domain_id	1o4tA00
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	120 — Jelly Rolls
Homologous superfamily homologous superfamily	10 — Jelly Rolls

Domain ID domain_id	1o4tB00
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	120 — Jelly Rolls
Homologous superfamily homologous superfamily	10 — Jelly Rolls

▶

Unit-cell length a length_a	89.132 Å
Unit-cell length b length_b	49.738 Å
Unit-cell length c length_c	69.547 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	123.73 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	8

Space group space_group	C 1 2 1
Space-group number int_tables_number	5
Crystal system crystal_system	—

Resolution resolution	1.950 Å
Low-resolution limit resolution_low	25.290 Å
R factor r_factor	0.1630
R_work r_work	0.1600
R_free r_free	0.2170

Crystal structure of a predicted oxalate decarboxylase (tm1287) from thermotoga maritima at 1.95 A resolution

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

putative oxalate decarboxylase

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

1o4t__assembly_1__model_1

1o4t__assembly_1__model_1 | I(q)

1o4t__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) 4 domains

SCOP 2.08 (2 domains)

CATH v4.4 (2 domains)

7. Citations (1)

Crystal structure of a predicted oxalate decarboxylase (tm1287) from thermotoga maritima at 1.95 A resolution

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

putative oxalate decarboxylase

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

1o4t__assembly_1__model_1

1o4t__assembly_1__model_1 | I(q)

1o4t__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) 4 domains

SCOP 2.08 (2 domains)

CATH v4.4 (2 domains)

7. Citations (1)