SAXSdb — 7uof

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

Dihydroorotase

Methanocaldococcus jannaschii

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 monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count	Chain A； UniProt 1–423	Non-standard monomer：Yes (specific site not provided by mmCIF)	ZN ZINC ION × 11	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 7.5；298 K；35% PEG400, 0.1 M Na Hepes pH 7.5, 0.1 M Zn acetate.	Resolution 1.90 Å R-free 0.215

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.

Other PDB	Difference from Current Entry 7UOF	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
9YD7 Complex of Dihydroorotase from M. jannaschii with Carbamoyl Aspartate Deposited 2025-09-22	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1–423（423 aa）	Non-standard monomer：Yes (specific site not provided by mmCIF)	NCD N-CARBAMOYL-L-ASPARTATE × 1 ZN ZINC ION × 11	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；298 K；Reservoirs: 35% PEG400, 0.1 M Zn acetate and 0.1 M Na Mes pH 6.5. Drops: 2 ul protein 6.7 mg/ml, 1 ul reservoir, 0.5 ul dihydroorotate stock of 65 mM	Resolution 1.87 Å R-free 0.186

1 other PDB entries and 1 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	PYRC_METJA
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–423； UniProt 1–423

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	7uof
Deposition date deposition_date	2022-04-12
Structure title title	Dihydroorotase from M. jannaschii
Keywords keywords	HYDROLASE, DE NOVO PYRIMIDINE BIOSYNTHESIS, AMIDOHYDROLASE SUPERFAMILY, METALLOENZYME, ZINC BINDING, HISTIDINATE ANION; HYDROLASE
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	22.52 Å
Radius of gyration Rg (electron density) rg_electron	21.48 Å
Forward intensity I(0) i0	37572200.00
Molecular weight molecular_weight	48856.0 kDa
Excluded volume excluded_volume	61712 Å³
Envelope volume envelope_volume	69440 Å³
Hydration-shell volume shell_volume	26353 Å³
Envelope diameter envelope_diameter	77.3 Å
Shell Rg shell_rg	28.95 Å
Envelope Rg envelope_rg	21.85 Å
Shape Rg shape_rg	21.40 Å
Total Rg total_rg	22.62 Å
Total atoms total_atoms	3400
Residues n_residues	422
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	75.2 Å
Rg (real space) rg_real	22.44 Å
Rg uncertainty (real space) rg_real_error	0.39 Å
I(0) (real space) i0_real	3.7570e+07
I(0) uncertainty (real space) i0_real_error	4.4180e+05
Rg (reciprocal space) rg_reciprocal	22.46 Å
I(0) (reciprocal space) i0_reciprocal	37570000.0000
Solution quality estimate total_estimate	0.8759
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	27.3 Å
Skewness Skewness skewness	0.291
Kurtosis Kurtosis kurtosis	-0.238
Angular range angular_range	— – 0.3550 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	9651000.0000
Real-space data points n_real_points	67
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.804; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.999; Smooth: 0.972

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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	Dihydroorotase
Molecular weight formula_weight	48226.0 kDa
EC 编号 ec_number	3.5.2.3
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A
Atom count atom_count	3619

MLLKNCRIIKDNKIIEGDILIDENGRIKKIAKDIKVDDEIIDIKNSLVIPGVIDAHVHFRWGEEKKEDFLSGSLAGINGGVCFAIDMPNNKPPITTKELFYKKLEDCKKDSKINVFLNFGVTENNYLGTVEDAKAYKIFMVKSVGDLFIEDYSKLKDILNQNKLFCIHAEHKDVINENLKKYQLNSWIDHCKIRDEKSEVEAVKEVIKNLKIIDRQSNKKPHVHFCHISTKEALYLIKKVRQELKNIKITVEVTPHHIYLNKDMAEELKGFGKFNPPLREKDDNIALIKGIVNKDVDIIASDHAPHLLEDKLKNVKNCPSGIPGIETIVPLTLNLVNKGLISLFDAIRVLSKNPAKIFNINNKIEEGNLANLTIIDLKKEGKINAELFKSKAKFSPFDGWEVKGFPIYTVINGTLYEAYGCKC

来源 Source

来源生物 organism	Methanocaldococcus jannaschii
NCBI Class编号 ncbi_taxonomy_id	2190
宿主生物 host_organism	Escherichia coli

Entity 2 Entity 2 non-polymer

Description description	ZINC ION
Molecular weight formula_weight	65.4 kDa
Source method src_method	syn
Copy count entity_count	11

Entity 3 Entity 3 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	219

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8. Citations (1)

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Unit-cell length a length_a	111.267 Å
Unit-cell length b length_b	111.267 Å
Unit-cell length c length_c	101.233 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	6

Space group space_group	P 32 2 1
Space-group number int_tables_number	154
Crystal system crystal_system	trigonal

Resolution resolution	1.900 Å
Low-resolution limit resolution_low	48.180 Å
R factor r_factor	0.1799
R_work r_work	0.1783
R_free r_free	0.2146

fit	/app/data/saxs_computation/uo/7uof/7uof.fit
pddf	/app/data/pr_computation/uo/7uof/7uof.pr.out
profile	/app/data/saxs_computation/uo/7uof/7uof.dat

Dihydroorotase from M. jannaschii

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

Dihydroorotase

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