SAXSdb — 10xk

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

Chromosomal replication initiator protein DnaA

Bifidobacterium primatium

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 homooligomer Homooligomer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count	Chain A； UniProt 1–87 Chain E； UniProt 1–87	Not recorded	No other associated polymer	X-RAY DIFFRACTION mmCIF provides none of the parsed experimental conditions	Resolution 2.40 Å R-free 0.236
2	Protein homooligomer Homooligomer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count	Chain B； UniProt 1–87 Chain D； UniProt 1–87	Not recorded	No other associated polymer	X-RAY DIFFRACTION mmCIF provides none of the parsed experimental conditions	Resolution 2.40 Å R-free 0.236
3	Protein homooligomer Homooligomer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count	Chain C； UniProt 1–87 Chain F； UniProt 1–87	Not recorded	No other associated polymer	X-RAY DIFFRACTION mmCIF provides none of the parsed experimental conditions	Resolution 2.40 Å R-free 0.236
4	Protein homooligomer Homooligomer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count	Chain G； UniProt 1–87 Chain H； UniProt 1–87	Not recorded	No other associated polymer	X-RAY DIFFRACTION mmCIF provides none of the parsed experimental conditions	Resolution 2.40 Å R-free 0.236

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.

No other PDB entry for the same UniProt protein was found.

View Construct and Data Evidence

UniProt name	A0A2M9HC27_9BIFI
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 4–90； UniProt 1–87 Author chain B； PDBConstruct 4–90； UniProt 1–87 Author chain C； PDBConstruct 4–90； UniProt 1–87 Author chain D； PDBConstruct 4–90； UniProt 1–87 Author chain E； PDBConstruct 4–90； UniProt 1–87 Author chain F； PDBConstruct 4–90； UniProt 1–87 Author chain G； PDBConstruct 4–90； UniProt 1–87 Author chain H； PDBConstruct 4–90； UniProt 1–87

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	10xk
Deposition date deposition_date	2026-02-11
最后修订 last_revision	2026-06-03
Structure title title	Bifidobacterium primatium DnaA DI
Keywords keywords	Initiator, DNA BINDING PROTEIN; DNA BINDING PROTEIN
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	31.13 Å
Radius of gyration Rg (electron density) rg_electron	30.52 Å
Forward intensity I(0) i0	91875300.00
Molecular weight molecular_weight	73914.0 kDa
Excluded volume excluded_volume	92101 Å³
Envelope volume envelope_volume	126110 Å³
Hydration-shell volume shell_volume	35525 Å³
Envelope diameter envelope_diameter	105.5 Å
Shell Rg shell_rg	36.57 Å
Envelope Rg envelope_rg	29.90 Å
Shape Rg shape_rg	30.50 Å
Total Rg total_rg	31.18 Å
Total atoms total_atoms	5175
Residues n_residues	689
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	97.3 Å
Rg (real space) rg_real	30.96 Å
Rg uncertainty (real space) rg_real_error	0.56 Å
I(0) (real space) i0_real	9.1880e+07
I(0) uncertainty (real space) i0_real_error	1.3350e+06
Rg (reciprocal space) rg_reciprocal	31.04 Å
I(0) (reciprocal space) i0_reciprocal	91880000.0000
Solution quality estimate total_estimate	0.9089
Solution quality rating solution_quality	EXCELLENT a EXCELLENT solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	42.0 Å
Skewness Skewness skewness	0.088
Kurtosis Kurtosis kurtosis	-0.560
Angular range angular_range	— – 0.2550 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	9062000.0000
Real-space data points n_real_points	52
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.944; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 1.000; Smooth: 0.979

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (2)

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8. Citations (1)

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Unit-cell length a length_a	55.927 Å
Unit-cell length b length_b	124.131 Å
Unit-cell length c length_c	63.747 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	97.70 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	16

Space group space_group	P 1 21 1
Space-group number int_tables_number	4
Crystal system crystal_system	monoclinic

Resolution resolution	2.400 Å
Low-resolution limit resolution_low	22.450 Å
R factor r_factor	0.1959
R_work r_work	0.1933
R_free r_free	0.2364

Description description	Chromosomal replication initiator protein DnaA
Molecular weight formula_weight	9770.0 kDa
Source method src_method	man
Copy count entity_count	8

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B,C,D,E,F,G,H
Atom count atom_count	5581

Bifidobacterium primatium DnaA DI

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

Chromosomal replication initiator protein DnaA

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

6. Entities and Polymers Entities & Polymers (2)

Entity 1 Entity 1 polymer

Polymer Polymer

来源 Source

Entity 2 Entity 2 water

8. Citations (1)

9. Files and Curves (10)

Files (7)

Curves (3)

来源生物 organism	Bifidobacterium primatium
NCBI Class编号 ncbi_taxonomy_id	2045438
宿主生物 host_organism	Escherichia coli

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	360

fit	/app/data/saxs_computation/0x/10xk/10xk.fit
pddf	/app/data/pr_computation/0x/10xk/10xk.pr.out
profile	/app/data/saxs_computation/0x/10xk/10xk.dat