5hog

Crystal structure of the carboxy-terminal domain of yeast Ctf4 bound to Dna2.

Method: X-RAY DIFFRACTION Dmax: 107.2 Å Quality: GOOD

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

DNA polymerase alpha-binding protein

Saccharomyces cerevisiae

UniProt Q01454

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 heterocomplex Heteromer Protein × 5 PDB declaration: pentameric(5) Consistent with protein copy count Chain A; UniProt 450–927 Chain B; UniProt 450–927 Chain C; UniProt 450–927 Fragment:UNP residues 450-927 Dna2p × 2 (A0A0D4IHI3) X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, HANGING DROP;292 K;0.2 M tri-sodium citrate pH 6.2, 7-9% PEG 8000 and 0.45-0.9 M NaCl. Resolution 3.09 Å R-free 0.226

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.

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

View Construct and Data Evidence
UniProt name CTF4_YEAST
Isoform
PDB entities 1
Chains and sequence ranges Author chain A; PDBConstruct 1–478; UniProt 450–927 Author chain B; PDBConstruct 1–478; UniProt 450–927 Author chain C; PDBConstruct 1–478; UniProt 450–927

Dna2p

OrganismNot specified

UniProt A0A0D4IHI3

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 heterocomplex Heteromer Protein × 5 PDB declaration: pentameric(5) Consistent with protein copy count Chain D; UniProt 207–223 Chain E; UniProt 207–223 Fragment:UNP residues 207-223 DNA polymerase alpha-binding protein × 3 (Q01454) X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, HANGING DROP;292 K;0.2 M tri-sodium citrate pH 6.2, 7-9% PEG 8000 and 0.45-0.9 M NaCl. Resolution 3.09 Å R-free 0.226

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.

No other PDB entry for the same UniProt protein was found.

View Construct and Data Evidence
UniProt name A0A0D4IHI3_YEASX
Isoform
PDB entities 2
Chains and sequence ranges Author chain D; PDBConstruct 1–17; UniProt 207–223 Author chain E; PDBConstruct 1–17; UniProt 207–223

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 5hog

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 5hog
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2. Structure Basics 2. Structure Basics

Entry ID entry_id5hog
Deposition date deposition_date2016-01-19
Structure title titleCrystal structure of the carboxy-terminal domain of yeast Ctf4 bound to Dna2.
Keywords keywordsDNA replication, adaptor protein, beta-propeller domain, replication; REPLICATION
Experimental Method methodX-RAY DIFFRACTION

3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

Radius of gyration Rg (Guinier) rg_guinier34.72
Radius of gyration Rg (electron density) rg_electron33.73
Forward intensity I(0) i0265995000.00
Molecular weight molecular_weight134620.0 kDa
Excluded volume excluded_volume169660 ų
Envelope volume envelope_volume220060 ų
Hydration-shell volume shell_volume52299 ų
Envelope diameter envelope_diameter112.2
Shell Rg shell_rg41.98
Envelope Rg envelope_rg33.91
Shape Rg shape_rg33.72
Total Rg total_rg34.36
Total atoms total_atoms9503
Residues n_residues1180
Spherical-harmonic order n_harmonics20
q range q_range— – 0.5000 −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

4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

Maximum dimension Dmax dmax107.2
Rg (real space) rg_real34.59
Rg uncertainty (real space) rg_real_error0.69
I(0) (real space) i0_real2.6600e+08
I(0) uncertainty (real space) i0_real_error3.8130e+06
Rg (reciprocal space) rg_reciprocal34.67
I(0) (reciprocal space) i0_reciprocal266000000.0000
Solution quality estimate total_estimate0.8961
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks1
Primary peak position r_peak_primary42.0
Skewness Skewness skewness0.190
Kurtosis Kurtosis kurtosis-0.550
Angular range angular_range— – 0.2300 −1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha90240000.0000
Real-space data points n_real_points47
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.956; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.994; Smooth: 0.784

5. Crystallography and Experiment 5. Crystallography & Experiment

6. Entities and Polymers Entities & Polymers (3)

8. Citations (2)

9. Files and Curves (10)