+Open data
-Basic information
Entry | Database: PDB / ID: 8dkd | ||||||
---|---|---|---|---|---|---|---|
Title | Sliding clamp from M. thermoresistibile | ||||||
Components | Beta sliding clamp | ||||||
Keywords | DNA BINDING PROTEIN | ||||||
Function / homology | Function and homology information DNA polymerase III complex / DNA strand elongation involved in DNA replication / 3'-5' exonuclease activity / DNA-directed DNA polymerase activity / DNA binding / cytoplasm Similarity search - Function | ||||||
Biological species | Mycolicibacterium thermoresistibile ATCC 19527 (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.2 Å | ||||||
Authors | Kapur, M.K. / Gray, O.J. / Honzatko, R.H. / Nelson, S.N. | ||||||
Funding support | United States, 1items
| ||||||
Citation | Journal: To Be Published Title: Interaction of sliding clamp with mycobacterial polymerases Authors: Kapur, M.K. / Gray, O.J. / Honzatko, R.H. / Nelson, S.N. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 8dkd.cif.gz | 184.5 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb8dkd.ent.gz | 119.5 KB | Display | PDB format |
PDBx/mmJSON format | 8dkd.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 8dkd_validation.pdf.gz | 423.3 KB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 8dkd_full_validation.pdf.gz | 427.2 KB | Display | |
Data in XML | 8dkd_validation.xml.gz | 15.9 KB | Display | |
Data in CIF | 8dkd_validation.cif.gz | 21.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/dk/8dkd ftp://data.pdbj.org/pub/pdb/validation_reports/dk/8dkd | HTTPS FTP |
-Related structure data
Related structure data | 8dj6C 8dk9C 3p16S S: Starting model for refinement C: citing same article (ref.) |
---|---|
Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
| ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||||||
Unit cell |
|
-Components
#1: Protein | Mass: 41677.191 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mycolicibacterium thermoresistibile ATCC 19527 (bacteria) Strain: ATCC 19527 / DSM 44167 / CIP 105390 / JCM 6362 / NCTC 10409 / 316 Gene: KEK_10778 / Production host: Escherichia coli (E. coli) / References: UniProt: G7CIP4 |
---|---|
#2: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 4.87 Å3/Da / Density % sol: 74.76 % |
---|---|
Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop Details: 4 M ammonium acetate , 0.1 M bis-tris propane, 8% glycerol |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: ALS / Beamline: 4.2.2 / Wavelength: 1 Å |
Detector | Type: RDI CMOS_8M / Detector: CMOS / Date: Mar 6, 2019 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 3.2→44.79 Å / Num. obs: 12983 / % possible obs: 93 % / Redundancy: 8.2 % / Biso Wilson estimate: 116.7 Å2 / CC1/2: 0.99 / Rmerge(I) obs: 0.084 / Rpim(I) all: 0.03 / Net I/σ(I): 24.8 |
Reflection shell | Resolution: 3.2→3.2 Å / Rmerge(I) obs: 0.91 / Num. unique obs: 243 / CC1/2: 0.595 |
-Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3P16 Resolution: 3.2→19.97 Å / SU ML: 0.5149 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 34.1119 Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 121.4 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 3.2→19.97 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell |
|