SAXSdb — 10xc

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

Chromosomal replication initiator protein DnaA

Nocardia asteroides

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 1–96	Not recorded	CHLORIDE ION × 2	X-RAY DIFFRACTION mmCIF provides none of the parsed experimental conditions	Resolution 1.20 Å R-free 0.180

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 10XC	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
10XA Nocardia asteroides DnaA DI in the P31(1)21 space group Deposited 2026-02-11	Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 1–96（96 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION mmCIF provides none of the parsed conditions	Resolution 1.25 Å R-free 0.168
10XB Nocardia asteroides DnaA DI protein in the I23 space group Deposited 2026-02-11	Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 1–96（96 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION mmCIF provides none of the parsed conditions	Resolution 2.40 Å R-free 0.244

2 other PDB entries and 2 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	U5EFM3_NOCAS
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 4–99； UniProt 1–96

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	10xc
Deposition date deposition_date	2026-02-11
最后修订 last_revision	2026-06-03
Structure title title	Nocardia asteroides DnaA DI in the P4(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	13.63 Å
Radius of gyration Rg (electron density) rg_electron	12.09 Å
Forward intensity I(0) i0	1802250.00
Molecular weight molecular_weight	9424.0 kDa
Excluded volume excluded_volume	11991 Å³
Envelope volume envelope_volume	13145 Å³
Hydration-shell volume shell_volume	9464 Å³
Envelope diameter envelope_diameter	43.7 Å
Shell Rg shell_rg	17.54 Å
Envelope Rg envelope_rg	12.45 Å
Shape Rg shape_rg	12.08 Å
Total Rg total_rg	13.50 Å
Total atoms total_atoms	1359
Residues n_residues	90
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	44.0 Å
Rg (real space) rg_real	13.54 Å
Rg uncertainty (real space) rg_real_error	0.30 Å
I(0) (real space) i0_real	1.8020e+06
I(0) uncertainty (real space) i0_real_error	2.0400e+04
Rg (reciprocal space) rg_reciprocal	13.55 Å
I(0) (reciprocal space) i0_reciprocal	1802000.0000
Solution quality estimate total_estimate	0.8004
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	3
Primary peak position r_peak_primary	18.4 Å
Skewness Skewness skewness	0.104
Kurtosis Kurtosis kurtosis	-0.303
Angular range angular_range	— – 0.5000 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	261900.0000
Real-space data points n_real_points	80
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.804; Stabil: 0.997; Sysdev: 1.000; Positv: 1.000; Valcen: 0.996; Smooth: 0.000

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (3)

Entity 1 Entity 1 polymer

Description description	Chromosomal replication initiator protein DnaA
Molecular weight formula_weight	10488.9 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	1743

GSHMDDEQNVLATVWPEVVAELTTGSADGAIPAVSRAQQAWLKLVKPLTVAQGFALLSVPSSLAQEAIERDLREPILRSLGRRLGPQVEGLGVRIAAPS

来源 Source

来源生物 organism	Nocardia asteroides
NCBI Class编号 ncbi_taxonomy_id	1824
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 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	163

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8. Citations (1)

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Unit-cell length a length_a	41.538 Å
Unit-cell length b length_b	41.538 Å
Unit-cell length c length_c	94.783 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	8

Space group space_group	P 41 2 2
Space-group number int_tables_number	91
Crystal system crystal_system	tetragonal

Resolution resolution	1.200 Å
Low-resolution limit resolution_low	21.510 Å
R factor r_factor	0.1500
R_work r_work	0.1476
R_free r_free	0.1801

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

Nocardia asteroides DnaA DI in the P4(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