SAXSdb — 3b39

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

DNA primase

Escherichia coli

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–DNA Monomer Protein × 1 DNA 1 PDB declaration: dimeric（2） Consistent with all polymer counts	Chain A； UniProt 111–429	Fragment：RNA Polymerase Domain	;DNA (5'-D(DCPDAPDAPDAPDGPDCPDCPDAPDAPDAPDAPDGPDGPDAP*DC)-3') ; × 1	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 5；292 K；21% PEG 4000, 100 mM ammonium acetate, 50 mM sodium acetate (pH 5.0), VAPOR DIFFUSION, HANGING DROP, temperature 292K	Resolution 2.35 Å R-free 0.254
2	Protein–DNA Monomer Protein × 1 DNA 1 PDB declaration: dimeric（2） Consistent with all polymer counts	Chain B； UniProt 111–429	Fragment：RNA Polymerase Domain	;DNA (5'-D(DCPDAPDAPDAPDGPDCPDCPDAPDAPDAPDAPDGPDGPDAP*DC)-3') ; × 1	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 5；292 K；21% PEG 4000, 100 mM ammonium acetate, 50 mM sodium acetate (pH 5.0), VAPOR DIFFUSION, HANGING DROP, temperature 292K	Resolution 2.35 Å R-free 0.254

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 3B39	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
1DD9 STRUCTURE OF THE DNAG CATALYTIC CORE Deposited 1999-11-09	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 111–433（323 aa） Fragment：36 KDA CATALYTIC CORE DOMAIN	Not recorded	SR STRONTIUM ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5；293 K；18-21% PEG4000, 5% PEG200, 30% ETHYLENE GLYCOL, 0.2M AMMONIUM ACETATE, 0.05M SODIUM ACETATE, PH 5.0, 0.1% DIOXANE, 2-8 MM SRCL2, VAPOR DIFFUSION, HANGING DROP	Resolution 1.60 Å R-free 0.276
1DDE STRUCTURE OF THE DNAG CATALYTIC CORE Deposited 1999-11-09	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 111–433（323 aa） Fragment：36 KDA CATALYTIC CORE DOMAIN	Not recorded	Y1 YTTRIUM ION × 4	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5；293 K；18-21% PEG4000, 5% PEG200, 30% ETHYLENE GLYCOL, 0.2M AMMONIUM ACETATE, 0.05M SODIUM ACETATE, PH 5.0, 0.1% DIOXANE, 2-8 MM YCL2, VAPOR DIFFUSION, HANGING DROP	Resolution 1.70 Å R-free 0.263
1EQN E.COLI PRIMASE CATALYTIC CORE Deposited 2000-04-05	Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 109–429（321 aa） Fragment：CATALYTIC CORE	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, HANGING DROP；pH 8.3；293 K；PEG 4000, DTT, Tris/HCl, sodium acetate, pH 8.3, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 2.90 Å R-free 0.276
1EQN E.COLI PRIMASE CATALYTIC CORE Deposited 2000-04-05	Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain B 109–429（321 aa） Fragment：CATALYTIC CORE	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, HANGING DROP；pH 8.3；293 K；PEG 4000, DTT, Tris/HCl, sodium acetate, pH 8.3, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 2.90 Å R-free 0.276
1EQN E.COLI PRIMASE CATALYTIC CORE Deposited 2000-04-05	Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 3 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain C 109–429（321 aa） Fragment：CATALYTIC CORE	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, HANGING DROP；pH 8.3；293 K；PEG 4000, DTT, Tris/HCl, sodium acetate, pH 8.3, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 2.90 Å R-free 0.276
1EQN E.COLI PRIMASE CATALYTIC CORE Deposited 2000-04-05	Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 4 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain D 109–429（321 aa） Fragment：CATALYTIC CORE	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, HANGING DROP；pH 8.3；293 K；PEG 4000, DTT, Tris/HCl, sodium acetate, pH 8.3, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 2.90 Å R-free 0.276
1EQN E.COLI PRIMASE CATALYTIC CORE Deposited 2000-04-05	Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 5 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain E 109–429（321 aa） Fragment：CATALYTIC CORE	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, HANGING DROP；pH 8.3；293 K；PEG 4000, DTT, Tris/HCl, sodium acetate, pH 8.3, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 2.90 Å R-free 0.276
1T3W Crystal Structure of the E.coli DnaG C-terminal domain (residues 434 to 581) Deposited 2004-04-28	Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 434–581（148 aa）	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, HANGING DROP；pH 4.6；277 K；5% v/v PEG4000, 0.2M ammonium sulfate, 0.1M sodium acetate, pH 4.6, VAPOR DIFFUSION, HANGING DROP, temperature 277K	Resolution 2.80 Å R-free 0.308
1T3W Crystal Structure of the E.coli DnaG C-terminal domain (residues 434 to 581) Deposited 2004-04-28	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain B 434–581（148 aa）	Non-standard monomer：Yes (specific site not provided by mmCIF)	ACY ACETIC ACID × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 4.6；277 K；5% v/v PEG4000, 0.2M ammonium sulfate, 0.1M sodium acetate, pH 4.6, VAPOR DIFFUSION, HANGING DROP, temperature 277K	Resolution 2.80 Å R-free 0.308
1T3W Crystal Structure of the E.coli DnaG C-terminal domain (residues 434 to 581) Deposited 2004-04-28	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 3 Protein homooligomer Homooligomer；Protein × 4 PDB declaration: tetrameric	Chain A 434–581（148 aa） Chain B 434–581（148 aa）	Non-standard monomer：Yes (specific site not provided by mmCIF) Non-standard monomer：Yes (specific site not provided by mmCIF)	ACY ACETIC ACID × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 4.6；277 K；5% v/v PEG4000, 0.2M ammonium sulfate, 0.1M sodium acetate, pH 4.6, VAPOR DIFFUSION, HANGING DROP, temperature 277K	Resolution 2.80 Å R-free 0.308
2HAJ Solution structure of the helicase-binding domain of Escherichia coli primase Deposited 2006-06-13	Different construct Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 434–581（148 aa） Fragment：Helicase-binding domain, residues 447-581	Not recorded	No recorded non-water small molecule	SOLUTION NMR NMR measurement conditions pH 6.1；298 K；Ionic strength (raw mmCIF value) 100mM NaCl；Pressure 1 NMR sample composition 0.3mM DnaG-C U-15N, 13C; 10mM phosphate buffer(pH 6.10); 100mM NaCl; 90% H2O, 10% D2O \| 90% H2O/10% D2O NMR sample composition 0.3mM DnaG-C; 10mM phosphate buffer(pH 6.10); 100mM NaCl; 90% H2O, 10% D2O \| 90% H2O/10% D2O	Resolution not provided
6CBR DnaG Primase C-terminal domain complex with SSB C-terminal peptide Deposited 2018-02-05	Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Insufficient information Monomer；Protein × 1 PDB declaration: monomeric	Chain A 434–581（148 aa） Fragment：DnaG C-terminal domain (UNP residues 434-581), linker peptide, SSB C-terminal peptide (UNP residues 131-139)	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 4.6；294 K；10% w/v PEG3000, 5 mM zinc acetate, 5 mM 1,10-phenanthroline, 100 mM sodium acetate, pH 4.6	Resolution 1.50 Å R-free 0.179
6CBR DnaG Primase C-terminal domain complex with SSB C-terminal peptide Deposited 2018-02-05	Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 2 Insufficient information Monomer；Protein × 1 PDB declaration: monomeric	Chain B 434–581（148 aa） Fragment：DnaG C-terminal domain (UNP residues 434-581), linker peptide, SSB C-terminal peptide (UNP residues 131-139)	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 4.6；294 K；10% w/v PEG3000, 5 mM zinc acetate, 5 mM 1,10-phenanthroline, 100 mM sodium acetate, pH 4.6	Resolution 1.50 Å R-free 0.179
6CBS DnaG Primase C-terminal domain complex with SSB C-terminal peptide Deposited 2018-02-05	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Insufficient information Monomer；Protein × 1 PDB declaration: monomeric	Chain A 434–581（148 aa） Fragment：DnaG C-terminal domain (UNP residues 434-581), linker peptide, SSB C-terminal peptide (UNP residues 130-139)	Not recorded	ZN ZINC ION × 3 ACY ACETIC ACID × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 4.6；294 K；7.5% w/v PEG3000, 15 mM zinc acetate, 100 mM sodium acetate, pH 4.6	Resolution 1.85 Å R-free 0.224
6CBS DnaG Primase C-terminal domain complex with SSB C-terminal peptide Deposited 2018-02-05	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Insufficient information Monomer；Protein × 1 PDB declaration: monomeric	Chain B 434–581（148 aa） Fragment：DnaG C-terminal domain (UNP residues 434-581), linker peptide, SSB C-terminal peptide (UNP residues 130-139)	Not recorded	ZN ZINC ION × 3 ACY ACETIC ACID × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 4.6；294 K；7.5% w/v PEG3000, 15 mM zinc acetate, 100 mM sodium acetate, pH 4.6	Resolution 1.85 Å R-free 0.224
6CBT DnaG Primase C-terminal domain complex with SSB C-terminal peptide Deposited 2018-02-05	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Insufficient information Monomer；Protein × 1 PDB declaration: monomeric	Chain A 434–581（148 aa） Fragment：DnaG C-terminal domain (UNP residues 434-581), linker peptide, SSB C-terminal peptide (UNP residues 130-139)	Not recorded	ZN ZINC ION × 2 ACY ACETIC ACID × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 4.6；294 K；9.5% w/v PEG3000, 10 mM zinc acetate, 100 mM sodium acetate, pH 4.6	Resolution 2.10 Å R-free 0.229
6CBT DnaG Primase C-terminal domain complex with SSB C-terminal peptide Deposited 2018-02-05	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Insufficient information Monomer；Protein × 1 PDB declaration: monomeric	Chain B 434–581（148 aa） Fragment：DnaG C-terminal domain (UNP residues 434-581), linker peptide, SSB C-terminal peptide (UNP residues 130-139)	Not recorded	ZN ZINC ION × 1 ACY ACETIC ACID × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 4.6；294 K；9.5% w/v PEG3000, 10 mM zinc acetate, 100 mM sodium acetate, pH 4.6	Resolution 2.10 Å R-free 0.229
7T22 E. coli DnaB bound to three DnaG C-terminal domains, ssDNA, ADP and AlF4 Deposited 2021-12-02	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Heteromer；Protein × 9 PDB declaration: decameric	Chain G 434–581（148 aa） Fragment：C-terminal domain Chain H 434–581（148 aa） Fragment：C-terminal domain Chain I 434–581（148 aa） Fragment：C-terminal domain	Mutation：R568C Mutation：R568C Mutation：R568C	ADP ADENOSINE-5'-DIPHOSPHATE × 5 ALF TETRAFLUOROALUMINATE ION × 5 MG MAGNESIUM ION × 5	ELECTRON MICROSCOPY cryo-EM buffer pH 7.6；20 mM Tris-HCl, pH 7.6, 100 mM NaCl, 5 mM MgCl2, 3 mM DTT, 0.25 mM EDTA and 100 micromolar ADP. cryo-EM vitrification conditions Cryogen ETHANE；3 microL of sample was applied to glow-discharged grids. Grids were blotted at 6 degrees C for 3.5 s with no extra blot force.	Resolution 4.20 Å
9ECO E. coli DnaB bound to three DnaG C-terminal domains, ssDNA, ADP and AlF4 Deposited 2024-11-14	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: nonameric	Chain G 434–581（148 aa） Fragment：C-terminal domain Chain H 434–581（148 aa） Fragment：C-terminal domain	Mutation：R568C Mutation：R568C	ALF TETRAFLUOROALUMINATE ION × 5 ADP ADENOSINE-5'-DIPHOSPHATE × 5 MG MAGNESIUM ION × 5	ELECTRON MICROSCOPY cryo-EM buffer pH 7.6；20 mM Tris-HCl, pH 7.6, 100 mM NaCl, 5 mM MgCl2, 3 mM DTT, 0.25 mM EDTA and 100 micromolar ADP, 0.5 mM AlCl3, 5 mM NaF. cryo-EM vitrification conditions Cryogen ETHANE；3 microL of sample was applied to glow-discharged grids. Grids were blotted at 6 degrees C for 3.5 s with no extra blot force.	Resolution 2.83 Å

10 other PDB entries and 19 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	PRIM_ECOLI
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain A； PDBConstruct 4–322； UniProt 111–429 Author chain B； PDBConstruct 4–322； UniProt 111–429

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	3b39
Deposition date deposition_date	2007-10-19
Structure title title	Structure of the DnaG primase catalytic domain bound to ssDNA
Keywords keywords	;Protein-DNA complex, TOPRIM fold, DNA replication, DNA-directed RNA polymerase, Metal-binding, Nucleotidyltransferase, Primosome, Transcription, Transferase, Zinc-finger, transferase-DNA COMPLEX ;; transferase/DNA
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	28.28 Å
Radius of gyration Rg (electron density) rg_electron	27.23 Å
Forward intensity I(0) i0	100841000.00
Molecular weight molecular_weight	74239.0 kDa
Excluded volume excluded_volume	91064 Å³
Envelope volume envelope_volume	117810 Å³
Hydration-shell volume shell_volume	35703 Å³
Envelope diameter envelope_diameter	86.1 Å
Shell Rg shell_rg	34.98 Å
Envelope Rg envelope_rg	26.77 Å
Shape Rg shape_rg	27.23 Å
Total Rg total_rg	28.00 Å
Total atoms total_atoms	5208
Residues n_residues	641
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	84.8 Å
Rg (real space) rg_real	28.09 Å
Rg uncertainty (real space) rg_real_error	0.41 Å
I(0) (real space) i0_real	1.0080e+08
I(0) uncertainty (real space) i0_real_error	1.3940e+06
Rg (reciprocal space) rg_reciprocal	28.15 Å
I(0) (reciprocal space) i0_reciprocal	100800000.0000
Solution quality estimate total_estimate	0.9120
Solution quality rating solution_quality	EXCELLENT a EXCELLENT solution
P(r) peaks n_peaks	1
Primary peak position r_peak_primary	34.9 Å
Skewness Skewness skewness	0.109
Kurtosis Kurtosis kurtosis	-0.605
Angular range angular_range	— – 0.2800 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	20180000.0000
Real-space data points n_real_points	57
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.967; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.991; Smooth: 0.961

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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	;DNA (5'-D(DCPDAPDAPDAPDGPDCPDCPDAPDAPDAPDAPDGPDGPDAP*DC)-3') ;
Molecular weight formula_weight	4605.0 kDa
Source method src_method	syn
Copy count entity_count	2

Polymer Polymer

Polymer type type	polydeoxyribonucleotide
Chain IDs strand_id	C,D
Atom count atom_count	5354

CAAAGCCAAAAGGAC

Entity 2 Entity 2 polymer

Description description	DNA primase
Molecular weight formula_weight	36289.0 kDa
EC 编号 ec_number	2.7.7.-
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B

SNAHQRQTLYQLMDGLNTFYQQSLQQPVATSARQYLEKRGLSHEVIARFAIGFAPPGWDNVLKRFGGNPENRQSLIDAGMLVTNDQGRSYDRFRERVMFPIRDKRGRVIGFGGRVLGNDTPKYLNSPETDIFHKGRQLYGLYEAQQDNAEPNRLLVVEGYMDVVALAQYGINYAVASLGTSTTADHIQLLFRATNNVICCYDGDRAGRDAAWCALETALPYMTDGRQLRFMFLPDGEDPDTLVRKEGKEAFEARMEQAMPLSAFLFNSLMPQVDLSTPDGRARLSTLALPLISQVPGETLRIYLRQELGNKLGILDDSQLER

来源 Source

来源生物 organism	Escherichia coli
NCBI Class编号 ncbi_taxonomy_id	83333
宿主生物 host_organism	Escherichia coli

Entity 3 Entity 3 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	146

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7. Fold Classification (SCOP + CATH) 10 domains

SCOP 2.08 (4 domains)

Domain ID domain_id	d3b39a1
Class class	e — Multi-domain proteins (alpha and beta)
Fold Fold fold	e.13 — DNA primase core
Superfamily Superfamily superfamily	e.13.1 — DNA primase core
Family Family family	e.13.1.1 — DNA primase DnaG catalytic core

Domain ID domain_id	d3b39a2
Class class	l — Artifacts
Fold Fold fold	l.1 — Tags
Superfamily Superfamily superfamily	l.1.1 — Tags
Family Family family	l.1.1.1 — Tags

Domain ID domain_id	d3b39b1
Class class	e — Multi-domain proteins (alpha and beta)
Fold Fold fold	e.13 — DNA primase core
Superfamily Superfamily superfamily	e.13.1 — DNA primase core
Family Family family	e.13.1.1 — DNA primase DnaG catalytic core

Domain ID domain_id	d3b39b2
Class class	l — Artifacts
Fold Fold fold	l.1 — Tags
Superfamily Superfamily superfamily	l.1.1 — Tags
Family Family family	l.1.1.1 — Tags

CATH v4.4 (6 domains)

Domain ID domain_id	3b39A01
Class class	3 — Alpha Beta
Architecture architecture	90 — Alpha-Beta Complex
Topology topology	980 — DNA primase DNAg catalytic core, N-terminal domain
Homologous superfamily homologous superfamily	10 — DNA primase, catalytic core, N-terminal domain

Domain ID domain_id	3b39A02
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	1360 — Dna Topoisomerase Vi A Subunit; Chain: A, domain 2
Homologous superfamily homologous superfamily	10 —

Domain ID domain_id	3b39A03
Class class	1 — Mainly Alpha
Architecture architecture	20 — Up-down Bundle
Topology topology	50 — Pheromone ER-1
Homologous superfamily homologous superfamily	20 — DnaG, RNA polymerase domain, helical bundle

Domain ID domain_id	3b39B01
Class class	3 — Alpha Beta
Architecture architecture	90 — Alpha-Beta Complex
Topology topology	980 — DNA primase DNAg catalytic core, N-terminal domain
Homologous superfamily homologous superfamily	10 — DNA primase, catalytic core, N-terminal domain

Domain ID domain_id	3b39B02
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	1360 — Dna Topoisomerase Vi A Subunit; Chain: A, domain 2
Homologous superfamily homologous superfamily	10 —

Domain ID domain_id	3b39B03
Class class	1 — Mainly Alpha
Architecture architecture	20 — Up-down Bundle
Topology topology	50 — Pheromone ER-1
Homologous superfamily homologous superfamily	20 — DnaG, RNA polymerase domain, helical bundle

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8. Citations (1)

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Unit-cell length a length_a	136.829 Å
Unit-cell length b length_b	136.829 Å
Unit-cell length c length_c	71.071 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	90.00 °
Unit-cell angle γ angle_gamma	120.00 °
Molecules per unit cell Z z_pdb	12

Space group space_group	P 62
Space-group number int_tables_number	171
Crystal system crystal_system	—

Resolution resolution	2.350 Å
Low-resolution limit resolution_low	40.000 Å
R factor r_factor	0.2140
R_work r_work	0.2119
R_free r_free	0.2544

fit	/app/data/saxs_computation/b3/3b39/3b39.fit
pddf	/app/data/pr_computation/b3/3b39/3b39.pr.out
profile	/app/data/saxs_computation/b3/3b39/3b39.dat

Structure of the DnaG primase catalytic domain bound to ssDNA

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

DNA primase

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

6. Entities and Polymers Entities & Polymers (3)

Entity 1 Entity 1 polymer

Polymer Polymer

Entity 2 Entity 2 polymer

Polymer Polymer

来源 Source

Entity 3 Entity 3 water

7. Fold Classification (SCOP + CATH) 10 domains

SCOP 2.08 (4 domains)

CATH v4.4 (6 domains)

8. Citations (1)

9. Files and Curves (10)

Files (7)

Curves (3)