SAXSdb — 6dtz

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

DNA primase large subunit

Saccharomyces cerevisiae (strain ATCC 204508 / S288c)

UniProt P20457

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 316–512	Mutation：Y397F	SF4 IRON/SULFUR CLUSTER × 1 MPD (4S)-2-METHYL-2,4-PENTANEDIOL × 2 MRD (4R)-2-METHYLPENTANE-2,4-DIOL × 1	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 8.5；289 K；100 mM TRIS, 40% MPD	Resolution 1.36 Å R-free 0.179

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 6DTZ	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
3LGB Crystal Structure of the Fe-S Domain of the yeast DNA primase Deposited 2010-01-20	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 317–512（196 aa） Fragment：Fe-S DOMAIN	Non-standard monomer：Yes (specific site not provided by mmCIF)	SF4 IRON/SULFUR CLUSTER × 1 EPE 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；291 K；0.1M TrisHCl pH 7.5, 1mM Zn acetate, 11% ethanol, VAPOR DIFFUSION, HANGING DROP, temperature 291K	Resolution 1.54 Å R-free 0.164
3LGB Crystal Structure of the Fe-S Domain of the yeast DNA primase Deposited 2010-01-20	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain B 317–512（196 aa） Fragment：Fe-S DOMAIN	Non-standard monomer：Yes (specific site not provided by mmCIF)	SF4 IRON/SULFUR CLUSTER × 1 ZN ZINC ION × 2 GOL GLYCEROL × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；291 K；0.1M TrisHCl pH 7.5, 1mM Zn acetate, 11% ethanol, VAPOR DIFFUSION, HANGING DROP, temperature 291K	Resolution 1.54 Å R-free 0.164
6DTV Crystal structure of eukaryotic DNA primase large subunit iron-sulfur cluster domain Y395F mutant Deposited 2018-06-18	Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 316–512（197 aa）	Not recorded	SF4 IRON/SULFUR CLUSTER × 1 MPD (4S)-2-METHYL-2,4-PENTANEDIOL × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8.5；289 K；MPD, TRIS 8.5	Resolution 1.12 Å R-free 0.137
6DU0 Crystal structure of eukaryotic DNA primase large subunit iron-sulfur cluster domain Y395L mutant Deposited 2018-06-18	Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 316–512（197 aa）	Mutation：Y395L	GOL GLYCEROL × 1 SF4 IRON/SULFUR CLUSTER × 1 MPD (4S)-2-METHYL-2,4-PENTANEDIOL × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8.5；289 K；100 mM TRIS 8.5, 40-60% MPD	Resolution 1.82 Å R-free 0.324
8B9A S. cerevisiae replisome + Ctf4, bound by pol alpha primase. Complex engaged with a fork DNA substrate containing a 60 nucleotide lagging strand. Deposited 2022-10-05	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Heteromer；Protein × 21 PDB declaration: 23-meric	Chain A 1–528（528 aa）	Not recorded	ANP PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER × 4 MG MAGNESIUM ION × 4 ZN ZINC ION × 4	ELECTRON MICROSCOPY cryo-EM buffer pH 7.6 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.50 Å
8B9B S. cerevisiae replisome + Ctf4, bound by pol alpha. Complex engaged with a fork DNA substrate containing a 60 nucleotide lagging strand. Deposited 2022-10-05	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Heteromer；Protein × 21 PDB declaration: 23-meric	Chain A 1–528（528 aa）	Not recorded	ANP PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER × 4 MG MAGNESIUM ION × 4 ZN ZINC ION × 4	ELECTRON MICROSCOPY cryo-EM buffer pH 7.6 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.50 Å
8B9C S. cerevisiae pol alpha - replisome complex Deposited 2022-10-05	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Heteromer；Protein × 18 PDB declaration: eicosameric	Chain A 1–528（528 aa）	Not recorded	ANP PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER × 4 MG MAGNESIUM ION × 4 ZN ZINC ION × 4	ELECTRON MICROSCOPY cryo-EM buffer pH 7.6 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 4.60 Å

6 other PDB entries and 7 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	PRI2_YEAST
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 5–201； UniProt 316–512

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	6dtz
Deposition date deposition_date	2018-06-18
Structure title title	Crystal structure of eukaryotic DNA primase large subunit iron-sulfur cluster domain, Y397F mutant
Keywords keywords	DNA primase, p58, iron-sulfur cluster, replication, regulatory subunit; REPLICATION
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	17.60 Å
Radius of gyration Rg (electron density) rg_electron	16.55 Å
Forward intensity I(0) i0	9447540.00
Molecular weight molecular_weight	22080.0 kDa
Excluded volume excluded_volume	27345 Å³
Envelope volume envelope_volume	30792 Å³
Hydration-shell volume shell_volume	15760 Å³
Envelope diameter envelope_diameter	60.8 Å
Shell Rg shell_rg	22.40 Å
Envelope Rg envelope_rg	16.91 Å
Shape Rg shape_rg	16.57 Å
Total Rg total_rg	17.45 Å
Total atoms total_atoms	1537
Residues n_residues	183
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	61.8 Å
Rg (real space) rg_real	17.54 Å
Rg uncertainty (real space) rg_real_error	0.47 Å
I(0) (real space) i0_real	9.4480e+06
I(0) uncertainty (real space) i0_real_error	1.2500e+05
Rg (reciprocal space) rg_reciprocal	17.54 Å
I(0) (reciprocal space) i0_reciprocal	9448000.0000
Solution quality estimate total_estimate	0.8546
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	22.2 Å
Skewness Skewness skewness	0.272
Kurtosis Kurtosis kurtosis	-0.253
Angular range angular_range	— – 0.4500 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	1866000.0000
Real-space data points n_real_points	76
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.714; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.968; Smooth: 0.996

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (5)

Entity 1 Entity 1 polymer

Description description	DNA primase large subunit
Molecular weight formula_weight	23347.3 kDa
EC 编号 ec_number	2.7.7.-
Mutation mutation	Y397F
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A
Atom count atom_count	1746

GPGSDDEINAQSVWSEEISSNYPLCIKNLMEGLKKNHHLRYYGRQQLSLFLKGIGLSADEALKFWSEAFTRNGNMTMEKFNKEYRFSFRHNYGLEGNRINYKPWDCHTILSKPRPGRGDYHGCPFRDWSHERLSAELRSMKLTQAQIISVLDSCQKGEYTIACTKVFEMTHNSASADLEIGEQTHIAHPNLYFERSRQLQK

来源 Source

来源生物 organism	Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
通用名 common_name	;Baker's yeast ;
NCBI Class编号 ncbi_taxonomy_id	559292
宿主生物 host_organism	Escherichia coli

Entity 2 Entity 2 non-polymer

Description description	IRON/SULFUR CLUSTER
Molecular weight formula_weight	351.6 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 3 Entity 3 non-polymer

Description description	(4S)-2-METHYL-2,4-PENTANEDIOL
Molecular weight formula_weight	118.2 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 4 Entity 4 non-polymer

Description description	(4R)-2-METHYLPENTANE-2,4-DIOL
Molecular weight formula_weight	118.2 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 5 Entity 5 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	157

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8. Citations (1)

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Unit-cell length a length_a	40.806 Å
Unit-cell length b length_b	50.810 Å
Unit-cell length c length_c	90.035 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	90.00 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	4

Space group space_group	P 21 21 21
Space-group number int_tables_number	19
Crystal system crystal_system	—

Resolution resolution	1.360 Å
Low-resolution limit resolution_low	22.120 Å
R factor r_factor	0.1570
R_work r_work	0.1550
R_free r_free	0.1790

fit	/app/data/saxs_computation/dt/6dtz/6dtz.fit
pddf	/app/data/pr_computation/dt/6dtz/6dtz.pr.out
profile	/app/data/saxs_computation/dt/6dtz/6dtz.dat

Crystal structure of eukaryotic DNA primase large subunit iron-sulfur cluster domain, Y397F mutant

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

DNA primase large subunit

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