+Open data
-Basic information
Entry | Database: PDB / ID: 5da7 | ||||||
---|---|---|---|---|---|---|---|
Title | monomeric PCNA bound to a small protein inhibitor | ||||||
Components |
| ||||||
Keywords | DNA binding protein/inhibitor / complex / inhibitor / DNA binding protein-inhibitor complex | ||||||
Function / homology | Function and homology information DNA polymerase processivity factor activity / leading strand elongation / regulation of DNA replication / DNA binding / identical protein binding Similarity search - Function | ||||||
Biological species | Thermococcus kodakarensis (archaea) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.802 Å | ||||||
Authors | Ladner, J.E. / Altieri, A.S. / Kelman, Z. | ||||||
Citation | Journal: Nucleic Acids Res. / Year: 2016 Title: A small protein inhibits proliferating cell nuclear antigen by breaking the DNA clamp. Authors: Altieri, A.S. / Ladner, J.E. / Li, Z. / Robinson, H. / Sallman, Z.F. / Marino, J.P. / Kelman, Z. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 5da7.cif.gz | 126.8 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb5da7.ent.gz | 99.4 KB | Display | PDB format |
PDBx/mmJSON format | 5da7.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5da7_validation.pdf.gz | 470.5 KB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 5da7_full_validation.pdf.gz | 481.1 KB | Display | |
Data in XML | 5da7_validation.xml.gz | 22.2 KB | Display | |
Data in CIF | 5da7_validation.cif.gz | 29.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/da/5da7 ftp://data.pdbj.org/pub/pdb/validation_reports/da/5da7 | HTTPS FTP |
-Related structure data
Related structure data | 5daiC 3lx1S S: Starting model for refinement C: citing same article (ref.) |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
2 |
| ||||||||
Unit cell |
|
-Components
#1: Protein | Mass: 29099.311 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Thermococcus kodakarensis (strain ATCC BAA-918 / JCM 12380 / KOD1) (archaea) Strain: ATCC BAA-918 / JCM 12380 / KOD1 / Gene: pcn1, TK0535 / Production host: Escherichia coli (E. coli) / References: UniProt: Q5JF32 #2: Protein | Mass: 7629.947 Da / Num. of mol.: 2 / Source method: obtained synthetically Source: (synth.) Thermococcus kodakarensis (strain ATCC BAA-918 / JCM 12380 / KOD1) (archaea) References: UniProt: Q5JH72 #3: Chemical | ChemComp-SO4 / |
---|
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
---|
-Sample preparation
Crystal | Density Matthews: 4.37 Å3/Da / Density % sol: 71.85 % |
---|---|
Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 4 Details: Well solution: 1.2 M ammonium sulfate, 50 mM sodium citrate buffer, and 10% glycerol |
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: NSLS / Beamline: X29A / Wavelength: 1.075 Å |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Sep 15, 2014 |
Radiation | Monochromator: coated mirror / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.075 Å / Relative weight: 1 |
Reflection | Resolution: 2.8→30 Å / Num. obs: 30707 / % possible obs: 98.9 % / Redundancy: 19.8 % / Rmerge(I) obs: 0.116 / Net I/σ(I): 36.6 |
Reflection shell | Resolution: 2.8→2.9 Å / Rmerge(I) obs: 0.892 |
-Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3LX1 Resolution: 2.802→29.962 Å / SU ML: 0.35 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 30.15 / Stereochemistry target values: ML
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.802→29.962 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell |
|