SAXSdb — 1v34

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

DNA primase small subunit

Pyrococcus horikoshii

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 ;URIDINE 5'-TRIPHOSPHATE ; × 1 water × 1	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	PRIS_PYRHO
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 21–366； UniProt 1–346

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	1v34
Deposition date deposition_date	2003-10-25
Structure title title	Crystal structure of Pyrococcus horikoshii DNA primase-UTP complex
Keywords keywords	Nucleotidyl transferase, RIKEN Structural Genomics/Proteomics Initiative, RSGI, Structural Genomics, Transferase; TRANSFERASE
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.

1v34__assembly_1__model_1

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

Download this curve (.dat)

1v34__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

1v34__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	22.46 Å
Rg (electron density)	21.82 Å
Total Rg	22.69 Å
Atom count	2887
Residues	346
Excluded volume	51739 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`1v34__assembly_1__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 (4)

Entity 1 Entity 1 polymer

Description description	DNA primase small subunit
Molecular weight formula_weight	42643.1 kDa
EC 编号 ec_number	2.7.7.-
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	2908

MGSSHHHHHHSSGLVPRGSHMLLREVTREERKNFYTNEWKVKDIPDFIVKTLELREFGFDHSGEGPSDRKNQYTDIRDLEDYIRATAPYAVYSSVALYEKPQEMEGWLGTELVFDIDAKDLPLRRCEHEPGTVCPICLNDAKEIVRDTVIILREELGFNDIHIIYSGRGYHIRVLDEWALKLDSKSRERILSFVSASEIEDVEEFRKLLLNKRGWFVLNHGYPRAFRLRFGYFILRIKLPHLINAGIRKSIAKSILKSKEEIYEEFVRKAILAAFPQGVGIESLAKLFALSTRFSKSYFDGRVTVDLKRILRLPSTLHSKVGLIAKYVGTNERDVMRFNPFKHAVPKFRKEEVKVEYKKFLESLGT

Source Source

Source organism organism	Pyrococcus horikoshii
NCBI taxonomy ID ncbi_taxonomy_id	53953
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	1

Entity 3 Entity 3 non-polymer

Description description	;URIDINE 5'-TRIPHOSPHATE ;
Molecular weight formula_weight	484.1 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 4 Entity 4 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	21

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6. Fold Classification (SCOP + CATH) 3 domains

SCOP 2.08 (1 domains)

Domain ID domain_id	d1v34a_
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.264 — Prim-pol domain
Superfamily Superfamily superfamily	d.264.1 — Prim-pol domain
Family Family family	d.264.1.1 — PriA-like

CATH v4.4 (2 domains)

Domain ID domain_id	1v34A01
Class class	3 — Alpha Beta
Architecture architecture	90 — Alpha-Beta Complex
Topology topology	920 — DNA primase, PRIM domain
Homologous superfamily homologous superfamily	10 — DNA primase, PRIM domain

Domain ID domain_id	1v34A02
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	8 — Helicase, Ruva Protein; domain 3
Homologous superfamily homologous superfamily	160 — DNA primase S; domain 2

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Unit-cell length a length_a	76.386 Å
Unit-cell length b length_b	76.386 Å
Unit-cell length c length_c	128.830 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	—

Resolution resolution	2.700 Å
Low-resolution limit resolution_low	20.000 Å
R factor r_factor	—
R_work r_work	0.2101
R_free r_free	0.2623

Crystal structure of Pyrococcus horikoshii DNA primase-UTP complex

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

DNA primase small subunit

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

1v34__assembly_1__model_1

1v34__assembly_1__model_1 | I(q)

1v34__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 (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) 3 domains

SCOP 2.08 (1 domains)

CATH v4.4 (2 domains)

7. Citations (1)

Crystal structure of Pyrococcus horikoshii DNA primase-UTP complex

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

DNA primase small subunit

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

1v34__assembly_1__model_1

1v34__assembly_1__model_1 | I(q)

1v34__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 (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) 3 domains

SCOP 2.08 (1 domains)

CATH v4.4 (2 domains)

7. Citations (1)