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1z8s

DnaB binding domain of DnaG (P16) from Bacillus stearothermophilus (residues 452-597)

Method: SOLUTION NMR Dmax: 60.5 Å Quality: GOOD
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1. Protein Identity and Related Structures Protein Identity & Related Structures

DNA primase

Geobacillus stearothermophilus

UniProt Q9X4D0

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 451–597 Fragment：P16, Residues 451-597 No other associated polymer SOLUTION NMR NMR measurement conditions：pH 6.8；298 K；Ionic strength (raw mmCIF value) 20mM potassium phosphate, 200mM sodium chloride；Pressure ambient NMR measurement conditions：pH 6.8；298 K；Ionic strength (raw mmCIF value) 20mM potassium phosphate, 200mM sodium chloride；Pressure ambient NMR measurement conditions：pH 6.8；298 K；Ionic strength (raw mmCIF value) 20mM potassium phosphate, 200mM sodium chloride；Pressure ambient NMR sample composition：1mM U-15N P16 | 90% H2O/10% D2O NMR sample composition：1mM U-15N U13C P16 | 90% H2O/10% D2O NMR sample composition：0.5mM U-15N P16 | 50% H2O/50% 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 1Z8S Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
1D0Q STRUCTURE OF THE ZINC-BINDING DOMAIN OF BACILLUS STEAROTHERMOPHILUS DNA PRIMASE Deposited 1999-09-14 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain A 1–103（103 aa） Fragment：ZINC-BINDING DOMAIN
Chain B 1–103（103 aa） Fragment：ZINC-BINDING DOMAIN
Not recorded ZN ZINC ION × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.1；298 K；LITHIUM SULFATE, SODIUM CITRATE, ZINC ACETATE, pH 6.1, VAPOR DIFFUSION, HANGING DROP, temperature 298.0K
Resolution 1.71 Å R-free 0.225
2R6A Crystal Form BH1 Deposited 2007-09-05 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 × 9 PDB declaration: nonameric
Chain C 455–597（143 aa） Fragment：Helicase Binding Domain
Non-standard monomer：Yes (specific site not provided by mmCIF) SO4 SULFATE ION × 12 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION；pH 6；298 K；1.0M Lithium Sulfate, 5% MPD, pH 6.0, VAPOR DIFFUSION, temperature 298K
Resolution 2.90 Å R-free 0.297
2R6C Crystal Form BH2 Deposited 2007-09-05 Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 18 PDB declaration: octadecameric
Chain G 455–597（143 aa） Fragment：Helicase Binding Domain
Chain H 455–597（143 aa） Fragment：Helicase Binding Domain
Chain I 455–597（143 aa） Fragment：Helicase Binding Domain
Non-standard monomer：Yes (specific site not provided by mmCIF) Non-standard monomer：Yes (specific site not provided by mmCIF) Non-standard monomer：Yes (specific site not provided by mmCIF) No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION；pH 6.5；298 K；0.5M Sodium Succinate, pH 6.5, VAPOR DIFFUSION, temperature 298K
Resolution 4.00 Å R-free 0.344
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 experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 15 PDB declaration: pentadecameric
Chain G 455–597（143 aa） Fragment：Helicase Binding Domain (UNP residues 455-597)
Chain H 455–597（143 aa） Fragment：Helicase Binding Domain (UNP residues 455-597)
Chain I 455–597（143 aa） Fragment：Helicase Binding Domain (UNP residues 455-597)
Non-standard monomer：Yes (specific site not provided by mmCIF) Non-standard monomer：Yes (specific site not provided by mmCIF) Non-standard monomer：Yes (specific site not provided by mmCIF) 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

4 other PDB entries and 4 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name PRIM_BACST
Isoform —
PDB entities 1
Chains and sequence ranges Author chain A； PDBConstruct 1–146； UniProt 451–597

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 1z8s

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 1z8s
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2. Structure Basics 2. Structure Basics

Entry ID entry_id1z8s
Deposition date deposition_date2005-03-31
Structure title titleDnaB binding domain of DnaG (P16) from Bacillus stearothermophilus (residues 452-597)
Keywords keywordstwo alpha helical sub-domains, TRANSFERASE; TRANSFERASE
Experimental Method methodSOLUTION NMR
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3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

Radius of gyration Rg (Guinier) rg_guinier17.64 Å
Radius of gyration Rg (electron density) rg_electron17.29 Å
Forward intensity I(0) i0394027000.00
Molecular weight molecular_weight168170.0 kDa
Excluded volume excluded_volume211780 ų
Envelope volume envelope_volume56396 ų
Hydration-shell volume shell_volume22460 ų
Envelope diameter envelope_diameter67.6 Å
Shell Rg shell_rg27.75 Å
Envelope Rg envelope_rg21.28 Å
Shape Rg shape_rg17.26 Å
Total Rg total_rg17.78 Å
Total atoms total_atoms23969
Residues n_residues1460
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 dmax60.5 Å
Rg (real space) rg_real17.68 Å
Rg uncertainty (real space) rg_real_error0.45 Å
I(0) (real space) i0_real3.9400e+08
I(0) uncertainty (real space) i0_real_error4.6260e+06
Rg (reciprocal space) rg_reciprocal17.67 Å
I(0) (reciprocal space) i0_reciprocal394000000.0000
Solution quality estimate total_estimate0.7830
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks3
Primary peak position r_peak_primary18.6 Å
Skewness Skewness skewness0.375
Kurtosis Kurtosis kurtosis-0.440
Angular range angular_range— – 0.4500 Å−1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha2176000.0000
Real-space data points n_real_points76
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.772; Stabil: 0.999; Sysdev: 1.000; Positv: 1.000; Valcen: 0.862; Smooth: 0.000
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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (1)

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7. Fold Classification (SCOP + CATH) 2 domains

CATH v4.4 (2 domains)

Domain ID domain_id1z8sA01
Class class1 — Mainly Alpha
Architecture architecture10 — Orthogonal Bundle
Topology topology860 — DNAb Helicase; Chain A
Homologous superfamily homologous superfamily10 — DNAb Helicase; Chain A
Domain ID domain_id1z8sA02
Class class6 — Special
Architecture architecture10 — Helix non-globular
Topology topology140 — Helix Hairpins
Homologous superfamily homologous superfamily360 —
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8. Citations (1)

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9. Files and Curves (10)