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2k7r

N-terminal domain of the Bacillus subtilis helicase-loading protein DnaI

Method: SOLUTION NMR Dmax: 76.8 Å Quality: REASONABLE
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1. Protein Identity and Related Structures Protein Identity & Related Structures

Primosomal protein dnaI

Bacillus subtilis

UniProt P06567

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 monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count Chain A； UniProt 1–106 Fragment：UNP residues 1-106 ZN ZINC ION × 1 SOLUTION NMR NMR measurement conditions：pH 7；298 K；Ionic strength (raw mmCIF value) 0.1；Pressure ambient NMR sample composition：0.5mM [U-95% 15N] DnaI, 0.5mM zinc ion, 10% [U-99% 2H] D2O, 90% H2O, 10mM sodium phosphate, 0.1% sodium azide, 100mM sodium chloride, 1mM DTT, 90% H2O/10% D2O | 90% H2O/10% D2O Resolution not provided

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 2K7R Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
4M4W Mechanistic implications for the bacterial primosome assembly of the structure of a helicase-helicase loader complex Deposited 2013-08-07 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 15 PDB declaration: pentadecameric
Chain J 1–311（311 aa）
Chain K 1–311（311 aa）
Chain L 1–311（311 aa）
Chain M 1–311（311 aa）
Chain N 1–311（311 aa）
Chain O 1–311（311 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION；pH 8；290 K；11-13% w/v PEG3350, 0.2 M lithium sulfate, 50 mM TRIS, pH 8.0-8.3, VAPOR DIFFUSION, temperature 290K
Resolution 6.10 Å R-free 0.392

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

View Construct and Data Evidence
UniProt name DNAI_BACSU
Isoform —
PDB entities 1
Chains and sequence ranges Author chain A； PDBConstruct 1–106； UniProt 1–106

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 2k7r

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 2k7r
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2. Structure Basics 2. Structure Basics

Entry ID entry_id2k7r
Deposition date deposition_date2008-08-19
Structure title titleN-terminal domain of the Bacillus subtilis helicase-loading protein DnaI
Keywords keywordsDnaI N-terminal domain, helicase-loading protein, ATP-binding, DNA replication, Nucleotide-binding, Primosome, REPLICATION; REPLICATION
Experimental Method methodSOLUTION NMR
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3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

Radius of gyration Rg (Guinier) rg_guinier18.05 Å
Radius of gyration Rg (electron density) rg_electron17.93 Å
Forward intensity I(0) i0956336000.00
Molecular weight molecular_weight251410.0 kDa
Excluded volume excluded_volume310510 ų
Envelope volume envelope_volume53096 ų
Hydration-shell volume shell_volume19728 ų
Envelope diameter envelope_diameter84.9 Å
Shell Rg shell_rg29.52 Å
Envelope Rg envelope_rg25.73 Å
Shape Rg shape_rg17.89 Å
Total Rg total_rg18.32 Å
Total atoms total_atoms34680
Residues n_residues2120
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 dmax76.8 Å
Rg (real space) rg_real18.35 Å
Rg uncertainty (real space) rg_real_error0.91 Å
I(0) (real space) i0_real9.5630e+08
I(0) uncertainty (real space) i0_real_error1.4130e+07
Rg (reciprocal space) rg_reciprocal18.31 Å
I(0) (reciprocal space) i0_reciprocal956300000.0000
Solution quality estimate total_estimate0.7120
Solution quality rating solution_quality REASONABLE a REASONABLE solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary16.6 Å
Skewness Skewness skewness0.640
Kurtosis Kurtosis kurtosis0.150
Angular range angular_range— – 0.4400 Å−1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha270300.0000
Real-space data points n_real_points75
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.364; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.161; Smooth: 0.999
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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)