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1d0q

STRUCTURE OF THE ZINC-BINDING DOMAIN OF BACILLUS STEAROTHERMOPHILUS DNA PRIMASE

Method: X-RAY DIFFRACTION Dmax: 71.0 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 homooligomer Homooligomer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count Chain A； UniProt 1–103 Chain B； UniProt 1–103 Fragment：ZINC-BINDING DOMAIN 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

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 1D0Q Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
1Z8S DnaB binding domain of DnaG (P16) from Bacillus stearothermophilus (residues 452-597) Deposited 2005-03-31 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 451–597（147 aa） Fragment：P16, Residues 451-597
Not recorded No recorded non-water small molecule 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
2R6A Crystal Form BH1 Deposited 2007-09-05 Different construct Different mutation/modification Different oligomeric state Different ligand/ion 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 ligand/ion 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 ligand/ion 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 1–103； UniProt 1–103 Author chain B； PDBConstruct 1–103； UniProt 1–103

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 1d0q

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 1d0q
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2. Structure Basics 2. Structure Basics

Entry ID entry_id1d0q
Deposition date deposition_date1999-09-14
Structure title titleSTRUCTURE OF THE ZINC-BINDING DOMAIN OF BACILLUS STEAROTHERMOPHILUS DNA PRIMASE
Keywords keywordsDNA PRIMASE, ZINC-BINDING MOTIF, PROTEIN, TRANSFERASE; TRANSFERASE
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_guinier21.36 Å
Radius of gyration Rg (electron density) rg_electron20.65 Å
Forward intensity I(0) i09178890.00
Molecular weight molecular_weight22556.0 kDa
Excluded volume excluded_volume28203 ų
Envelope volume envelope_volume34325 ų
Hydration-shell volume shell_volume15088 ų
Envelope diameter envelope_diameter71.0 Å
Shell Rg shell_rg25.41 Å
Envelope Rg envelope_rg20.97 Å
Shape Rg shape_rg20.63 Å
Total Rg total_rg21.43 Å
Total atoms total_atoms1584
Residues n_residues204
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 dmax71.0 Å
Rg (real space) rg_real21.46 Å
Rg uncertainty (real space) rg_real_error0.61 Å
I(0) (real space) i0_real9.1790e+06
I(0) uncertainty (real space) i0_real_error1.3530e+05
Rg (reciprocal space) rg_reciprocal21.45 Å
I(0) (reciprocal space) i0_reciprocal9179000.0000
Solution quality estimate total_estimate0.8679
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary19.8 Å
Skewness Skewness skewness0.386
Kurtosis Kurtosis kurtosis-0.546
Angular range angular_range— – 0.3700 Å−1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha1873000.0000
Real-space data points n_real_points69
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.834; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.829; Smooth: 0.949
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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (3)

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7. Fold Classification (SCOP + CATH) 4 domains

SCOP 2.08 (2 domains)

Domain ID domain_idd1d0qa_
Class classg — Small proteins
Fold Fold foldg.41 — Rubredoxin-like
Superfamily Superfamily superfamilyg.41.3 — Zinc beta-ribbon
Family Family familyg.41.3.2 — DNA primase zinc finger
Domain ID domain_idd1d0qb_
Class classg — Small proteins
Fold Fold foldg.41 — Rubredoxin-like
Superfamily Superfamily superfamilyg.41.3 — Zinc beta-ribbon
Family Family familyg.41.3.2 — DNA primase zinc finger

CATH v4.4 (2 domains)

Domain ID domain_id1d0qA00
Class class3 — Alpha Beta
Architecture architecture90 — Alpha-Beta Complex
Topology topology580 — DNA Primase; Chain A
Homologous superfamily homologous superfamily10 — Zinc finger, CHC2-type domain
Domain ID domain_id1d0qB00
Class class3 — Alpha Beta
Architecture architecture90 — Alpha-Beta Complex
Topology topology580 — DNA Primase; Chain A
Homologous superfamily homologous superfamily10 — Zinc finger, CHC2-type domain
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8. Citations (1)

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9. Files and Curves (10)