SAXSdb — 3wi3

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

DNA replication regulator SLD3

Saccharomyces cerevisiae

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 148–430	Fragment：UNP RESIDUES 148-430	SO4 SULFATE ION × 1 EDO 1,2-ETHANEDIOL × 16	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 8.4；293 K；PEG 4000, LiSO4, pH 8.4, vapor diffusion, hanging drop, temperature 293K	Resolution 2.40 Å R-free 0.262
2	Protein monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count	Chain B； UniProt 148–430	Fragment：UNP RESIDUES 148-430	SO4 SULFATE ION × 1 EDO 1,2-ETHANEDIOL × 8	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 8.4；293 K；PEG 4000, LiSO4, pH 8.4, vapor diffusion, hanging drop, temperature 293K	Resolution 2.40 Å R-free 0.262
3	Protein monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count	Chain C； UniProt 148–430	Fragment：UNP RESIDUES 148-430	SO4 SULFATE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 8.4；293 K；PEG 4000, LiSO4, pH 8.4, vapor diffusion, hanging drop, temperature 293K	Resolution 2.40 Å R-free 0.262

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 3WI3	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
8J09 Crystal structure of the Sld3 Cdc45-binding-domain, in complex with Cdc45 Deposited 2023-04-10	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 154–420（267 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293.15 K；0.2M sodium acetate, 0.1M Bis-Tris propane (pH6.5: pH8.5 = 3:7), 20%(w/v) PEG33500	Resolution 2.61 Å R-free 0.262
9RHI pre-Initiation Complex on ARS1 DNA (monomer) Deposited 2025-06-09	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 × 17 PDB declaration: 19-meric	Chain Q 1–668（668 aa） Chain T 1–668（668 aa）	Not recorded	ZN ZINC ION × 5 ADP ADENOSINE-5'-DIPHOSPHATE × 1 MG MAGNESIUM ION × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.20 Å
9RHJ Pre-Initiation Complex on ARS1 DNA (dimer) Deposited 2025-06-09	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 × 30 PDB declaration: 32-meric	Chain Q 1–668（668 aa） Chain T 1–668（668 aa）	Not recorded	ZN ZINC ION × 10 ADP ADENOSINE-5'-DIPHOSPHATE × 2 MG MAGNESIUM ION × 2	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.40 Å
9RHL Phospho-DH bound by Sld3-MBD on ARS1 DNA Deposited 2025-06-09	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 × 14 PDB declaration: 16-meric	Chain H 1–668（668 aa） Chain I 1–668（668 aa）	Not recorded	ZN ZINC ION × 10 ADP ADENOSINE-5'-DIPHOSPHATE × 4 MG MAGNESIUM ION × 4	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.10 Å
9RHM Phospho-MCM double hexamer bound to Sld3-Sld7-Cdc45 on ARS1 DNA Deposited 2025-06-09	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 × 17 PDB declaration: 19-meric	Chain H 1–668（668 aa） Chain I 1–668（668 aa）	Not recorded	ZN ZINC ION × 10 ADP ADENOSINE-5'-DIPHOSPHATE × 4 MG MAGNESIUM ION × 4	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.70 Å

5 other PDB entries and 5 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	SLD3_YEAST
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 2–284； UniProt 148–430 Author chain B； PDBConstruct 2–284； UniProt 148–430 Author chain C； PDBConstruct 2–284； UniProt 148–430

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	3wi3
Deposition date deposition_date	2013-09-05
Structure title title	Crystal Structure of the Sld3/Treslin domain from yeast Sld3
Keywords keywords	REPLICATION REGULATOR, CDC45-BINDING, ALPHA HELICAL; REPLICATION REGULATOR
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	32.54 Å
Radius of gyration Rg (electron density) rg_electron	32.00 Å
Forward intensity I(0) i0	80614400.00
Molecular weight molecular_weight	75405.0 kDa
Excluded volume excluded_volume	96226 Å³
Envelope volume envelope_volume	118880 Å³
Hydration-shell volume shell_volume	32132 Å³
Envelope diameter envelope_diameter	112.3 Å
Shell Rg shell_rg	37.44 Å
Envelope Rg envelope_rg	31.89 Å
Shape Rg shape_rg	32.00 Å
Total Rg total_rg	32.44 Å
Total atoms total_atoms	5304
Residues n_residues	632
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	106.5 Å
Rg (real space) rg_real	32.62 Å
Rg uncertainty (real space) rg_real_error	0.88 Å
I(0) (real space) i0_real	8.0610e+07
I(0) uncertainty (real space) i0_real_error	1.2740e+06
Rg (reciprocal space) rg_reciprocal	32.59 Å
I(0) (reciprocal space) i0_reciprocal	80610000.0000
Solution quality estimate total_estimate	0.8785
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	28.3 Å
Skewness Skewness skewness	0.299
Kurtosis Kurtosis kurtosis	-0.637
Angular range angular_range	— – 0.2450 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	30330000.0000
Real-space data points n_real_points	50
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.877; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.918; Smooth: 0.867

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (4)

Entity 1 Entity 1 polymer

Description description	DNA replication regulator SLD3
Molecular weight formula_weight	34243.9 kDa
Source method src_method	man
Copy count entity_count	3

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B,C
Atom count atom_count	5473

MSKINDYYSDPKEYIESKYYDALFSIHTPLAYFVKSNLVRLKNTCRTKYGSDSYKIAYQAMLQKFLLSIVQFKDRHDNRLLLEPFSSPIADEKRKNCLTKFVIQDENKNSSTIADLCVVLKSREIKLQILLLLEIIGLNDLDWNFRDFEKKYKLKLKKRSLNLTKKGLVRRRSKKKTSEKDKGIERITTSLDYCEQLDLYLDRACILDILLSSETPNPDAIEASNGTIQEHKKNILDKSKEASLVGFINYVLIPYFNKKVPHAVEFIIQKLKGPSMRPKRALKKLEHHHHHH

来源 Source

来源生物 organism	Saccharomyces cerevisiae
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	SULFATE ION
Molecular weight formula_weight	96.1 kDa
Source method src_method	syn
Copy count entity_count	3

Entity 3 Entity 3 non-polymer

Description description	1,2-ETHANEDIOL
Molecular weight formula_weight	62.1 kDa
Source method src_method	syn
Copy count entity_count	24

Entity 4 Entity 4 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	169

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7. Fold Classification (SCOP + CATH) 3 domains

CATH v4.4 (3 domains)

Domain ID domain_id	3wi3A00
Class class	1 — Mainly Alpha
Architecture architecture	20 — Up-down Bundle
Topology topology	58 — Methane Monooxygenase Hydroxylase; Chain G, domain 1
Homologous superfamily homologous superfamily	2130 —

Domain ID domain_id	3wi3B00
Class class	1 — Mainly Alpha
Architecture architecture	20 — Up-down Bundle
Topology topology	58 — Methane Monooxygenase Hydroxylase; Chain G, domain 1
Homologous superfamily homologous superfamily	2130 —

Domain ID domain_id	3wi3C00
Class class	1 — Mainly Alpha
Architecture architecture	20 — Up-down Bundle
Topology topology	58 — Methane Monooxygenase Hydroxylase; Chain G, domain 1
Homologous superfamily homologous superfamily	2130 —

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8. Citations (1)

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Unit-cell length a length_a	65.264 Å
Unit-cell length b length_b	92.820 Å
Unit-cell length c length_c	160.870 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	12

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

Resolution resolution	2.400 Å
Low-resolution limit resolution_low	19.640 Å
R factor r_factor	0.2190
R_work r_work	0.2168
R_free r_free	0.2624

fit	/app/data/saxs_computation/wi/3wi3/3wi3.fit
pddf	/app/data/pr_computation/wi/3wi3/3wi3.pr.out
profile	/app/data/saxs_computation/wi/3wi3/3wi3.dat

Crystal Structure of the Sld3/Treslin domain from yeast Sld3

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

DNA replication regulator SLD3

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