SAXSdb — 1dvj

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

;OROTIDINE 5'-PHOSPHATE DECARBOXYLASE ;

Methanothermobacter thermautotrophicus

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein homooligomer	Homooligomer	Protein 2	;6-AZA URIDINE 5'-MONOPHOSPHATE ; × 2 water × 2	Consistent with protein count
2	Protein homooligomer	Homooligomer	Protein 2	;6-AZA URIDINE 5'-MONOPHOSPHATE ; × 2 water × 2	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	PYRF_METTH
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–227； UniProt 2–228 Author chain B； PDBConstruct 1–227； UniProt 2–228 Author chain C； PDBConstruct 1–227； UniProt 2–228 Author chain D； PDBConstruct 1–227； UniProt 2–228

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	1dvj
Deposition date deposition_date	2000-03-30
Structure title title	CRYSTAL STRUCTURE OF OROTIDINE MONOPHOSPHATE DECARBOXYLASE COMPLEXED WITH 6-AZAUMP
Keywords keywords	TIM barrel, dimer, LYASE; LYASE
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.

1dvj__assembly_1__model_1

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

Download this curve (.dat)

1dvj__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

1dvj__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	23.07 Å
Rg (electron density)	21.88 Å
Total Rg	22.63 Å
Atom count	3444
Residues	450
Excluded volume	61275 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`1dvj__assembly_1__model_1`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`1dvj__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 (3)

Entity 1 Entity 1 polymer

Description description	;OROTIDINE 5'-PHOSPHATE DECARBOXYLASE ;
Molecular weight formula_weight	26664.6 kDa
EC 编号 ec_number	4.1.1.23
Mutation mutation	R101P, EXTRA C-TERMINAL RESIDUES FROM THE CLONING VECTOR: EDPAANKARKEAELAAATA
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	7675

RSRRVDVMDVMNRLILAMDLMNRDDALRVTGEVREYIDTVKIGYPLVLSEGMDIIAEFRKRFGCRIIADFKVADIPETNEKICRATFKAGADAIIVHGFPGADSVRACLNVAEEMGREVFLLTEMSHPGAEMFIQGAADEIARMGVDLGVKNYVGPSTRPERLSRLREIIGQDSFLISPGVGAQGGDPGETLRFADAIIVGRSIYLADNPAAAAAGIIESIKDLLIPEDPAANKARKEAELAAATA

Source Source

Source organism organism	Methanothermobacter thermautotrophicus
NCBI taxonomy ID ncbi_taxonomy_id	145262
Host organism host_organism	Escherichia coli

Entity 2 Entity 2 non-polymer

Description description	;6-AZA URIDINE 5'-MONOPHOSPHATE ;
Molecular weight formula_weight	325.2 kDa
Source method src_method	syn
Copy count entity_count	4

Entity 3 Entity 3 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	702

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6. Fold Classification (SCOP + CATH) 10 domains

SCOP 2.08 (6 domains)

Domain ID domain_id	d1dvja1
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.1.2.3 — Decarboxylase

Domain ID domain_id	d1dvja2
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	d1dvjb_
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.1.2.3 — Decarboxylase

Domain ID domain_id	d1dvjc1
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.1.2.3 — Decarboxylase

Domain ID domain_id	d1dvjc2
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	d1dvjd_
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.1.2.3 — Decarboxylase

CATH v4.4 (4 domains)

Domain ID domain_id	1dvjA00
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	1dvjB00
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	1dvjC00
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	1dvjD00
Class class	3 — Alpha Beta
Architecture architecture	20 — Alpha-Beta Barrel
Topology topology	20 — TIM Barrel
Homologous superfamily homologous superfamily	70 — Aldolase class I

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Unit-cell length a length_a	72.950 Å
Unit-cell length b length_b	98.620 Å
Unit-cell length c length_c	73.250 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	104.03 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	8

Space group space_group	P 1 21 1
Space-group number int_tables_number	4
Crystal system crystal_system	—

Resolution resolution	1.500 Å
Low-resolution limit resolution_low	30.000 Å
R factor r_factor	0.1740
R_work r_work	0.1740
R_free r_free	0.1880

CRYSTAL STRUCTURE OF OROTIDINE MONOPHOSPHATE DECARBOXYLASE COMPLEXED WITH 6-AZAUMP

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

;OROTIDINE 5'-PHOSPHATE 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

1dvj__assembly_1__model_1

1dvj__assembly_1__model_1 | I(q)

1dvj__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) 10 domains

SCOP 2.08 (6 domains)

CATH v4.4 (4 domains)

7. Citations (1)

CRYSTAL STRUCTURE OF OROTIDINE MONOPHOSPHATE DECARBOXYLASE COMPLEXED WITH 6-AZAUMP

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

;OROTIDINE 5'-PHOSPHATE 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

1dvj__assembly_1__model_1

1dvj__assembly_1__model_1 | I(q)

1dvj__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) 10 domains

SCOP 2.08 (6 domains)

CATH v4.4 (4 domains)

7. Citations (1)