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10xh

Bifidobacterium bifidum DnaA DI

Method: X-RAY DIFFRACTION Dmax: 58.3 Å Quality: GOOD
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1. Protein Identity and Related Structures Protein Identity & Related Structures

Chromosomal replication initiator protein DnaA

Bifidobacterium bifidum

UniProt A0A0M5KVR3

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 Chain B； UniProt 1–90 Not recorded No other associated polymer X-RAY DIFFRACTION mmCIF provides none of the parsed experimental conditions Resolution 1.90 Å R-free 0.221

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 A0A0M5KVR3_BIFBI
Isoform —
PDB entities 1
Chains and sequence ranges Author chain A； PDBConstruct 4–93； UniProt 1–90 Author chain B； 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.

SAXS scattering curve SAXS Profile

SAXS profile for 10xh

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 10xh
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2. Structure Basics 2. Structure Basics

Entry ID entry_id10xh
Deposition date deposition_date2026-02-11
最后修订 last_revision2026-06-03
Structure title titleBifidobacterium bifidum DnaA DI
Keywords keywordsInitiator, DNA BINDING PROTEIN; DNA BINDING PROTEIN
Experimental Method methodX-RAY DIFFRACTION
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3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

Radius of gyration Rg (Guinier) rg_guinier18.07 Å
Radius of gyration Rg (electron density) rg_electron17.15 Å
Forward intensity I(0) i06450080.00
Molecular weight molecular_weight19103.0 kDa
Excluded volume excluded_volume24198 ų
Envelope volume envelope_volume27280 ų
Hydration-shell volume shell_volume14087 ų
Envelope diameter envelope_diameter59.8 Å
Shell Rg shell_rg22.20 Å
Envelope Rg envelope_rg17.28 Å
Shape Rg shape_rg17.06 Å
Total Rg total_rg18.29 Å
Total atoms total_atoms1333
Residues n_residues174
Spherical-harmonic order n_harmonics20
q range q_range— – 0.5000 Å−1
Data points n_points101
Shell type shell_typedirectional
Solvent electron density solvent_density0.3340 e/ų
Shell contrast contrast_shell0.0300 e/ų
CRYSOL version crysol_version4.1.3
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4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

Maximum dimension Dmax dmax58.3 Å
Rg (real space) rg_real18.06 Å
Rg uncertainty (real space) rg_real_error0.36 Å
I(0) (real space) i0_real6.4500e+06
I(0) uncertainty (real space) i0_real_error7.4810e+04
Rg (reciprocal space) rg_reciprocal18.07 Å
I(0) (reciprocal space) i0_reciprocal6450000.0000
Solution quality estimate total_estimate0.8129
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks1
Primary peak position r_peak_primary57.5 Å
Skewness Skewness skewness0.330
Kurtosis Kurtosis kurtosis-0.337
Angular range angular_range— – 0.4400 Å−1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha1087000.0000
Real-space data points n_real_points75
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.857; Stabil: 0.998; Sysdev: 1.000; Positv: 1.000; Valcen: 0.998; Smooth: 0.000
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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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9. Files and Curves (10)