SAXSdb — 2hvv

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

deoxycytidylate deaminase

Streptococcus mutans

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein homooligomer	Homooligomer	Protein 6	SULFATE ION × 24 ZINC ION × 12 water × 6	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	Q8DSE5_STRMU
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 35–184； UniProt 1–150 Author chain B； PDBConstruct 35–184； UniProt 1–150

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	2hvv
Deposition date deposition_date	2006-07-31
Structure title title	Crystal structure of dCMP deaminase from Streptococcus mutans
Keywords keywords	3-layer (alpha-beta)-sandwich, HYDROLASE; 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.

2hvv__assembly_1__model_1

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

Download this curve (.dat)

2hvv__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

2hvv__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	30.39 Å
Rg (electron density)	29.20 Å
Total Rg	29.95 Å
Atom count	6852
Residues	858
Excluded volume	120710 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`2hvv__assembly_1__model_1`	hexameric （6）	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 (4)

Entity 1 Entity 1 polymer

Description description	deoxycytidylate deaminase
Molecular weight formula_weight	20414.2 kDa
EC 编号 ec_number	3.5.4.12
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	2318

MGSSHHHHHHSSGLVPRGSHMASMTGGQQMGRGSMTNRLSWQDYFMANAELISKRSTCNRAYVGAVLVKNNRIIATGYNGGVADTDNCDDVGHEMEDGHCIRTVHAEMNALIQCAKEGISANNTEIYVTHFPCINCTKALLQAGVKKITYNTAYRIHPFAIELMTQKEVEYVQHDVPRVKLGEK

Source Source

Source organism organism	Streptococcus mutans
NCBI taxonomy ID ncbi_taxonomy_id	1309
Host organism host_organism	Escherichia coli BL21(DE3)

Entity 2 Entity 2 non-polymer

Description description	SULFATE ION
Molecular weight formula_weight	96.1 kDa
Source method src_method	syn
Copy count entity_count	8

Entity 3 Entity 3 non-polymer

Description description	ZINC ION
Molecular weight formula_weight	65.4 kDa
Source method src_method	syn
Copy count entity_count	4

Entity 4 Entity 4 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	34

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6. Fold Classification (SCOP + CATH) 2 domains

CATH v4.4 (2 domains)

Domain ID domain_id	2hvvA00
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	140 — Cytidine Deaminase; domain 2
Homologous superfamily homologous superfamily	10 — Cytidine Deaminase, domain 2

Domain ID domain_id	2hvvB00
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	140 — Cytidine Deaminase; domain 2
Homologous superfamily homologous superfamily	10 — Cytidine Deaminase, domain 2

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Unit-cell length a length_a	113.233 Å
Unit-cell length b length_b	113.233 Å
Unit-cell length c length_c	113.233 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	24

Space group space_group	P 21 3
Space-group number int_tables_number	198
Crystal system crystal_system	—

Resolution resolution	3.000 Å
Low-resolution limit resolution_low	20.000 Å
R factor r_factor	0.2260
R_work r_work	0.2230
R_free r_free	0.2550

Crystal structure of dCMP deaminase from Streptococcus mutans

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

deoxycytidylate deaminase

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

2hvv__assembly_1__model_1

2hvv__assembly_1__model_1 | I(q)

2hvv__assembly_1__model_1 | P(r) · Pending

4. Crystallography and Experiment 4. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

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) 2 domains

CATH v4.4 (2 domains)

7. Citations (1)

Crystal structure of dCMP deaminase from Streptococcus mutans

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

deoxycytidylate deaminase

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

2hvv__assembly_1__model_1

2hvv__assembly_1__model_1 | I(q)

2hvv__assembly_1__model_1 | P(r) · Pending

4. Crystallography and Experiment 4. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

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) 2 domains

CATH v4.4 (2 domains)

7. Citations (1)