SAXSdb — 1dbt

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

;OROTIDINE 5'-PHOSPHATE DECARBOXYLASE ;

Bacillus subtilis

State in the Current Structure

Assembly	Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Associated Components	Method and Experimental Conditions	Structure Quality
1	Protein homooligomer Homooligomer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count	Chain A； UniProt 1–239 Chain B； UniProt 1–239	Not recorded	U5P URIDINE-5'-MONOPHOSPHATE × 2	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 7.1；295 K；18% (W/V) PEG 4000, 100MM HEPES PH 7.1, 5% 2-PROPANOL, VAPOR DIFFUSION, HANGING DROP, temperature 295K	Resolution 2.40 Å R-free 0.228
2	Protein homooligomer Homooligomer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count	Chain C； UniProt 1–239	Not recorded	U5P URIDINE-5'-MONOPHOSPHATE × 2	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 7.1；295 K；18% (W/V) PEG 4000, 100MM HEPES PH 7.1, 5% 2-PROPANOL, VAPOR DIFFUSION, HANGING DROP, temperature 295K	Resolution 2.40 Å R-free 0.228

Other States of the Same Protein in the Database

Each row is a biological assembly of the same UniProt protein in another PDB entry. The “Difference from current entry” column identifies evidence-level differences; no tag means the currently parsed fields agree.

No other PDB entry for the same UniProt protein was found.

View Construct and Data Evidence

UniProt name	PYRF_BACSU
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–239； UniProt 1–239 Author chain B； PDBConstruct 1–239； UniProt 1–239 Author chain C； PDBConstruct 1–239； UniProt 1–239

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	1dbt
Deposition date deposition_date	1999-11-03
Structure title title	CRYSTAL STRUCTURE OF OROTIDINE 5'-MONOPHOSPHATE DECARBOXYLASE FROM BACILLUS SUBTILIS COMPLEXED WITH UMP
Keywords keywords	DECARBOXYLASE, UMP, TIM BARREL, LYASE; LYASE
Experimental Method method	X-RAY DIFFRACTION

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3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

Radius of gyration Rg (Guinier) rg_guinier	30.02 Å
Radius of gyration Rg (electron density) rg_electron	29.59 Å
Forward intensity I(0) i0	93082500.00
Molecular weight molecular_weight	77493.0 kDa
Excluded volume excluded_volume	97616 Å³
Envelope volume envelope_volume	118520 Å³
Hydration-shell volume shell_volume	34407 Å³
Envelope diameter envelope_diameter	113.3 Å
Shell Rg shell_rg	35.56 Å
Envelope Rg envelope_rg	29.97 Å
Shape Rg shape_rg	29.59 Å
Total Rg total_rg	30.11 Å
Total atoms total_atoms	5434
Residues n_residues	705
Spherical-harmonic order n_harmonics	20
q range q_range	— – 0.5000 Å⁻¹
Data points n_points	101
Shell type shell_type	directional
Solvent electron density solvent_density	0.3340 e/Å³
Shell contrast contrast_shell	0.0300 e/Å³
CRYSOL version crysol_version	4.1.3

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4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

Maximum dimension Dmax dmax	106.7 Å
Rg (real space) rg_real	30.21 Å
Rg uncertainty (real space) rg_real_error	0.97 Å
I(0) (real space) i0_real	9.3080e+07
I(0) uncertainty (real space) i0_real_error	1.5210e+06
Rg (reciprocal space) rg_reciprocal	30.13 Å
I(0) (reciprocal space) i0_reciprocal	93080000.0000
Solution quality estimate total_estimate	0.8333
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	30.2 Å
Skewness Skewness skewness	0.550
Kurtosis Kurtosis kurtosis	-0.157
Angular range angular_range	— – 0.2650 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	23170000.0000
Real-space data points n_real_points	54
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.669; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.860; Smooth: 0.962

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (3)

Entity 1 Entity 1 polymer

Description description	;OROTIDINE 5'-PHOSPHATE DECARBOXYLASE ;
Molecular weight formula_weight	26024.1 kDa
EC 编号 ec_number	4.1.1.23
Source method src_method	man
Copy count entity_count	3

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B,C
Atom count atom_count	5660

MKNNLPIIALDFASAEETLAFLAPFQQEPLFVKVGMELFYQEGPSIVKQLKERNCELFLDLKLHDIPTTVNKAMKRLASLGVDLVNVHAAGGKKMMQAALEGLEEGTPAGKKRPSLIAVTQLTSTSEQIMKDELLIEKSLIDTVVHYSKQAEESGLDGVVCSVHEAKAIYQAVSPSFLTVTPGIRMSEDAANDQVRVATPAIAREKGSSAIVVGRSITKAEDPVKAYKAVRLEWEGIKS

来源 Source

来源生物 organism	Bacillus subtilis
NCBI Class编号 ncbi_taxonomy_id	1423
宿主生物 host_organism	Escherichia coli

Entity 2 Entity 2 non-polymer

Description description	URIDINE-5'-MONOPHOSPHATE
Molecular weight formula_weight	324.2 kDa
Source method src_method	syn
Copy count entity_count	3

Entity 3 Entity 3 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	226

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7. Fold Classification (SCOP + CATH) 6 domains

SCOP 2.08 (3 domains)

Domain ID domain_id	d1dbta_
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	d1dbtb_
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	d1dbtc_
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 (3 domains)

Domain ID domain_id	1dbtA00
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	1dbtB00
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	1dbtC00
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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8. Citations (1)

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Unit-cell length a length_a	78.410 Å
Unit-cell length b length_b	89.760 Å
Unit-cell length c length_c	105.900 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	12

Space group space_group	P 21 21 2
Space-group number int_tables_number	18
Crystal system crystal_system	—

Resolution resolution	2.400 Å
Low-resolution limit resolution_low	20.000 Å
R factor r_factor	0.1930
R_work r_work	0.1930
R_free r_free	0.2280

fit	/app/data/saxs_computation/db/1dbt/1dbt.fit
pddf	/app/data/pr_computation/db/1dbt/1dbt.pr.out
profile	/app/data/saxs_computation/db/1dbt/1dbt.dat

CRYSTAL STRUCTURE OF OROTIDINE 5'-MONOPHOSPHATE DECARBOXYLASE FROM BACILLUS SUBTILIS COMPLEXED WITH UMP

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

SAXS scattering curve SAXS Profile

P(r) Distance Distribution P(r) Distribution

2. Structure Basics 2. Structure Basics

3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

5. Crystallography and Experiment 5. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

Diffraction experiment Diffraction