SAXSdb — 10xo

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

Chromosomal replication initiator protein DnaA

Streptomyces lividans

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 1–90	Not recorded	CHLORIDE ION × 2 GLYCEROL × 2	X-RAY DIFFRACTION mmCIF provides none of the parsed experimental conditions	Resolution 2.00 Å R-free 0.264

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.

Other PDB	Difference from Current Entry 10XO	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
10XP Streptomyces lividans DnaA DI protein in the I222 space group. Deposited 2026-02-11	Different construct Different mutation/modification Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 1–90（90 aa） Chain B 1–90（90 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION mmCIF provides none of the parsed conditions	Resolution 2.00 Å R-free 0.261

1 other PDB entries and 1 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	A0A7U9DVX7_STRLI
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 4–93； UniProt 1–90

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	10xo
Deposition date deposition_date	2026-02-11
最后修订 last_revision	2026-06-03
Structure title title	Streptomyces lividans DnaA DI protein in the P6(1)22 space group
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	13.22 Å
Radius of gyration Rg (electron density) rg_electron	11.70 Å
Forward intensity I(0) i0	1769060.00
Molecular weight molecular_weight	9048.0 kDa
Excluded volume excluded_volume	11377 Å³
Envelope volume envelope_volume	12425 Å³
Hydration-shell volume shell_volume	9255 Å³
Envelope diameter envelope_diameter	36.6 Å
Shell Rg shell_rg	17.10 Å
Envelope Rg envelope_rg	11.86 Å
Shape Rg shape_rg	11.71 Å
Total Rg total_rg	13.04 Å
Total atoms total_atoms	635
Residues n_residues	84
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	39.3 Å
Rg (real space) rg_real	13.10 Å
Rg uncertainty (real space) rg_real_error	0.16 Å
I(0) (real space) i0_real	1.7690e+06
I(0) uncertainty (real space) i0_real_error	1.5930e+04
Rg (reciprocal space) rg_reciprocal	13.11 Å
I(0) (reciprocal space) i0_reciprocal	1769000.0000
Solution quality estimate total_estimate	0.9036
Solution quality rating solution_quality	EXCELLENT a EXCELLENT solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	17.4 Å
Skewness Skewness skewness	0.004
Kurtosis Kurtosis kurtosis	-0.424
Angular range angular_range	— – 0.5000 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	263500.0000
Real-space data points n_real_points	80
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.928; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.974; Smooth: 0.985

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (4)

Entity 1 Entity 1 polymer

Description description	Chromosomal replication initiator protein DnaA
Molecular weight formula_weight	10064.5 kDa
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	710

GSHMADVPADLAAVWPRVLEQLLGEGRGQGVESKDEHWIRRCQPLALVADTALLAVPNEFAKGVLEGRLAPIVSETLSRECGRPIRIAITVDD

来源 Source

来源生物 organism	Streptomyces lividans
NCBI Class编号 ncbi_taxonomy_id	1916
宿主生物 host_organism	Escherichia coli

Entity 2 Entity 2 non-polymer

Description description	CHLORIDE ION
Molecular weight formula_weight	35.5 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 3 Entity 3 non-polymer

Description description	GLYCEROL
Molecular weight formula_weight	92.1 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	48

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8. Citations (1)

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Unit-cell length a length_a	57.460 Å
Unit-cell length b length_b	57.460 Å
Unit-cell length c length_c	99.032 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	12

Space group space_group	P 61 2 2
Space-group number int_tables_number	178
Crystal system crystal_system	hexagonal

Resolution resolution	2.000 Å
Low-resolution limit resolution_low	22.230 Å
R factor r_factor	0.2320
R_work r_work	0.2283
R_free r_free	0.2642

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

Streptomyces lividans DnaA DI protein in the P6(1)22 space group

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