SAXSdb — 3gri

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

Dihydroorotase

Staphylococcus aureus subsp. aureus MW2

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein monomer	Monomer	Protein 1	ZINC ION × 1 CHLORIDE ION × 2 CALCIUM ION × 2 water × 1	Consistent with protein count
2	Protein monomer	Monomer	Protein 1	ZINC ION × 1 CHLORIDE ION × 1 CALCIUM ION × 2 water × 1	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	PYRC_STAAW
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–424； UniProt 1–424 Author chain B； PDBConstruct 1–424； UniProt 1–424

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	3gri
Deposition date deposition_date	2009-03-25
Structure title title	The Crystal Structure of a Dihydroorotase from Staphylococcus aureus
Keywords keywords	;HYDROLASE, IDP00795, Metal-binding, Pyrimidine biosynthesis, Structural Genomics, Center for Structural Genomics of Infectious Diseases, CSGID ;; 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.

3gri__assembly_1__model_1

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

Download this curve (.dat)

3gri__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

3gri__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	21.87 Å
Rg (electron density)	20.89 Å
Total Rg	21.88 Å
Atom count	3220
Residues	413
Excluded volume	57501 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`3gri__assembly_1__model_1`	monomeric （1）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`3gri__assembly_2__model_1`	monomeric （1）	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 (5)

Entity 1 Entity 1 polymer

Description description	Dihydroorotase
Molecular weight formula_weight	46849.6 kDa
EC 编号 ec_number	3.5.2.3
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	6952

MKLIKNGKVLQNGELQQADILIDGKVIKQIAPAIEPSNGVDIIDAKGHFVSPGFVDVHVHLREPGGEYKETIETGTKAAARGGFTTVCPMPNTRPVPDSVEHFEALQKLIDDNAQVRVLPYASITTRQLGKELVDFPALVKEGAFAFTDDGVGVQTASMMYEGMIEAAKVNKAIVAHCEDNSLIYGGAMHEGKRSKELGIPGIPNICESVQIARDVLLAEAAGCHYHVCHVSTKESVRVIRDAKRAGIHVTAEVTPHHLLLTEDDIPGNNAIYKMNPPLRSTEDREALLEGLLDGTIDCIATDHAPHARDEKAQPMEKAPFGIVGSETAFPLLYTHFVKNGDWTLQQLVDYLTIKPCETFNLEYGTLKENGYADLTIIDLDSEQEIKGEDFLSKADNTPFIGYKVYGNPILTMVEGEVKFEGDK

Source Source

Source organism organism	Staphylococcus aureus subsp. aureus MW2
NCBI taxonomy ID ncbi_taxonomy_id	196620
Host organism 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	2

Entity 3 Entity 3 non-polymer

Description description	CHLORIDE ION
Molecular weight formula_weight	35.5 kDa
Source method src_method	syn
Copy count entity_count	3

Entity 4 Entity 4 non-polymer

Description description	CALCIUM ION
Molecular weight formula_weight	40.1 kDa
Source method src_method	syn
Copy count entity_count	4

Entity 5 Entity 5 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	478

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6. Fold Classification (SCOP + CATH) 4 domains

CATH v4.4 (4 domains)

Domain ID domain_id	3griA01
Class class	2 — Mainly Beta
Architecture architecture	30 — Roll
Topology topology	40 — Urease, subunit C; domain 1
Homologous superfamily homologous superfamily	10 — Urease, subunit C, domain 1

Domain ID domain_id	3griA02
Class class	3 — Alpha Beta
Architecture architecture	20 — Alpha-Beta Barrel
Topology topology	20 — TIM Barrel
Homologous superfamily homologous superfamily	140 — Metal-dependent hydrolases

Domain ID domain_id	3griB01
Class class	2 — Mainly Beta
Architecture architecture	30 — Roll
Topology topology	40 — Urease, subunit C; domain 1
Homologous superfamily homologous superfamily	10 — Urease, subunit C, domain 1

Domain ID domain_id	3griB02
Class class	3 — Alpha Beta
Architecture architecture	20 — Alpha-Beta Barrel
Topology topology	20 — TIM Barrel
Homologous superfamily homologous superfamily	140 — Metal-dependent hydrolases

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Unit-cell length a length_a	50.217 Å
Unit-cell length b length_b	55.229 Å
Unit-cell length c length_c	85.647 Å
Unit-cell angle α angle_alpha	88.33 °
Unit-cell angle β angle_beta	76.56 °
Unit-cell angle γ angle_gamma	76.97 °
Molecules per unit cell Z z_pdb	2

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

Resolution resolution	2.000 Å
Low-resolution limit resolution_low	30.000 Å
R factor r_factor	0.1912
R_work r_work	0.1887
R_free r_free	0.2367

The Crystal Structure of a Dihydroorotase from Staphylococcus aureus

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

2. Structure Basics 2. Structure Basics

3. Official assembly/model SAXS Official SAXS Profiles

3gri__assembly_1__model_1

3gri__assembly_1__model_1 | I(q)

3gri__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 (5)

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 non-polymer

Entity 5 Entity 5 water

6. Fold Classification (SCOP + CATH) 4 domains

CATH v4.4 (4 domains)

7. Citations (1)

The Crystal Structure of a Dihydroorotase from Staphylococcus aureus

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

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

2. Structure Basics 2. Structure Basics

3. Official assembly/model SAXS Official SAXS Profiles

3gri__assembly_1__model_1

3gri__assembly_1__model_1 | I(q)

3gri__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 (5)

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 non-polymer

Entity 5 Entity 5 water

6. Fold Classification (SCOP + CATH) 4 domains

CATH v4.4 (4 domains)

7. Citations (1)