SAXSdb — 4m4w

▼

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

Replicative helicase

Geobacillus stearothermophilus

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 15	DNA primase × 3 （Q9X4D0） Primosomal protein DnaI × 6 （P06567）	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	Q9X4C9_GEOSE
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–454； UniProt 1–454 Author chain B； PDBConstruct 1–454； UniProt 1–454 Author chain C； PDBConstruct 1–454； UniProt 1–454 Author chain D； PDBConstruct 1–454； UniProt 1–454 Author chain E； PDBConstruct 1–454； UniProt 1–454 Author chain F； PDBConstruct 1–454； UniProt 1–454

DNA primase

Geobacillus stearothermophilus

UniProt Q9X4D0

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 15	Replicative helicase × 6 （Q9X4C9） Primosomal protein DnaI × 6 （P06567）	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	PRIM_GEOSE
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain G； PDBConstruct 1–143； UniProt 455–597 Author chain H； PDBConstruct 1–143； UniProt 455–597 Author chain I； PDBConstruct 1–143； UniProt 455–597

Primosomal protein DnaI

Bacillus subtilis subsp. subtilis

UniProt P06567

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 15	Replicative helicase × 6 （Q9X4C9） DNA primase × 3 （Q9X4D0）	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	DNAI_BACSU
Isoform	—
PDB entities	3
Chains and sequence ranges	Author chain J； PDBConstruct 1–311； UniProt 1–311 Author chain K； PDBConstruct 1–311； UniProt 1–311 Author chain L； PDBConstruct 1–311； UniProt 1–311 Author chain M； PDBConstruct 1–311； UniProt 1–311 Author chain N； PDBConstruct 1–311； UniProt 1–311 Author chain O； PDBConstruct 1–311； UniProt 1–311

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.

▼

2. Structure Basics 2. Structure Basics

Entry ID entry_id	4m4w
Deposition date deposition_date	2013-08-07
Structure title title	Mechanistic implications for the bacterial primosome assembly of the structure of a helicase-helicase loader complex
Keywords keywords	primase, helicase loader, DnaB, DnaG, DnaI, DNA replication, REPLICATION; REPLICATION
Experimental Method method	X-RAY DIFFRACTION

▼

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.

4m4w__assembly_1__model_1

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

Download this curve (.dat)

4m4w__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

4m4w__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	59.80 Å
Rg (electron density)	58.96 Å
Total Rg	59.17 Å
Atom count	31981
Residues	4025
Excluded volume	573030 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`4m4w__assembly_1__model_1`	pentadecameric （15）	Success	4.1.3-1-20251215 (887e7ef)	View Download

▶

4. Crystallography and Experiment 4. Crystallography & Experiment

▶

5. Entities and Polymers Entities & Polymers (3)

Entity 1 Entity 1 polymer

Description description	Replicative helicase
Molecular weight formula_weight	50699.4 kDa
Source method src_method	man
Copy count entity_count	6

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B,C,D,E,F
Atom count atom_count	31981

MSELFSERIPPQSIEAEQAVLGAVFLDPAALVPASEILIPEDFYRAAHQKIFHAMLRVADRGEPVDLVTVTAELAASEQLEEIGGVSYLSELADAVPTAANVEYYARIVEEKSVLRRLIRTATSIAQDGYTREDEIDVLLDEADRKIMEVSQRKHSGAFKNIKDILVQTYDNIEMLHNRDGEITGIPTGFTELDRMTSGFQRSDLIIVAARPSVGKTAFALNIAQNVATKTNENVAIFSLEMSAQQLVMRMLCAEGNINAQNLRTGKLTPEDWGKLTMAMGSLSNAGIYIDDTPSIRVSDIRAKCRRLKQESGLGMIVIDYLQLIQGSGRSKENRQQEVSEISRSLKALARELEVPVIALSQLSRSVEQRQDKRPMMSDIRESGSIEQDADIVAFLYRDDYYNKDSENKNIIEIIIAKQRNGPVGTVQLAFIKEYNKFVNLERRFDEAQIPPGA

Source Source

Source organism organism	Geobacillus stearothermophilus
NCBI taxonomy ID ncbi_taxonomy_id	1422
Host organism host_organism	Escherichia coli

Entity 2 Entity 2 polymer

Description description	DNA primase
Molecular weight formula_weight	16796.5 kDa
Source method src_method	man
Copy count entity_count	3

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	G,H,I

KLLPAFQNAERLLLAHMMRSRDVALVVQERIGGRFNIEEHRALAAYIYAFYEEGHEADPGALISRIPGELQPLASELSLLLIADDVSEQELEDYIRHVLNRPKWLMLKVKEQEKTEAERRKDFLTAARIAKEMIEMKKMLSSS

Source Source

Source organism organism	Geobacillus stearothermophilus
NCBI taxonomy ID ncbi_taxonomy_id	1422
Host organism host_organism	Escherichia coli

Entity 3 Entity 3 polymer

Description description	Primosomal protein DnaI
Molecular weight formula_weight	36991.2 kDa
Source method src_method	man
Copy count entity_count	6

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	J,K,L,M,N,O

MEPIGRSLQGVTGRPDFQKRLEQMKEKVMKDQDVQAFLKENEEVIDQKMIEKSLNKLYEYIEQSKNCSYCSEDENCNNLLEGYHPKLVVNGRSIDIEYYECPVKRKLDQQKKQQSLMKSMYIQQDLLGATFQQVDISDPSRLAMFQHVTDFLKSYNETGKGKGLYLYGKFGVGKTFMLAAIANELAEKEYSSMIVYVPEFVRELKNSLQDQTLEEKLNMVKTTPVLMLDDIGAESMTSWVRDEVIGTVLQHRMSQQLPTFFSSNFSPDELKHHFTYSQRGEKEEVKAARLMERILYLAAPIRLDGENRRHPHHHHHH

Source Source

Source organism organism	Bacillus subtilis subsp. subtilis
NCBI taxonomy ID ncbi_taxonomy_id	224308
Host organism host_organism	Escherichia coli

▶

Unit-cell length a length_a	229.055 Å
Unit-cell length b length_b	229.055 Å
Unit-cell length c length_c	364.294 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	36

Space group space_group	P 31 2 1
Space-group number int_tables_number	152
Crystal system crystal_system	—

Resolution resolution	6.100 Å
Low-resolution limit resolution_low	20.000 Å
R factor r_factor	0.3797
R_work r_work	0.3791
R_free r_free	0.3915

Mechanistic implications for the bacterial primosome assembly of the structure of a helicase-helicase loader complex

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

Replicative helicase

State in the Current Structure

Other States of the Same Protein in the Database

DNA primase

State in the Current Structure

Other States of the Same Protein in the Database

Primosomal protein DnaI

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

4m4w__assembly_1__model_1

4m4w__assembly_1__model_1 | I(q)

4m4w__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 (3)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 polymer

Polymer Polymer

Source Source

Entity 3 Entity 3 polymer

Polymer Polymer

Source Source

7. Citations (1)

Mechanistic implications for the bacterial primosome assembly of the structure of a helicase-helicase loader complex

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

Replicative helicase

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

DNA primase

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

Primosomal protein DnaI

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

4m4w__assembly_1__model_1

4m4w__assembly_1__model_1 | I(q)

4m4w__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 (3)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 polymer

Polymer Polymer

Source Source

Entity 3 Entity 3 polymer

Polymer Polymer

Source Source

7. Citations (1)