[English] 日本語
Yorodumi- PDB-5a4n: Crystal structure of BPSL1147, a PC4 homolog from Burkholderia ps... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5a4n | ||||||
---|---|---|---|---|---|---|---|
Title | Crystal structure of BPSL1147, a PC4 homolog from Burkholderia pseudomallei K96243 (tetragonal crystal form) | ||||||
Components | BPSL1147 | ||||||
Keywords | DNA BINDING PROTEIN / DNA-BINDING PROTEIN / TRANSCRIPTION / DNA REPLICATION / RECOMBINATION AND REPAIR | ||||||
Function / homology | Transcriptional coactivator p15 (PC4), C-terminal / Transcriptional Coactivator p15 (PC4) / ssDNA-binding transcriptional regulator / regulation of DNA-templated transcription / DNA binding / Transcriptional coactivator p15 (PC4) C-terminal domain-containing protein Function and homology information | ||||||
Biological species | BURKHOLDERIA PSEUDOMALLEI (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.96 Å | ||||||
Authors | Werten, S. / Bayer, N. / Hinrichs, W. | ||||||
Citation | Journal: Gene / Year: 2016 Title: Structural Analysis and Knock-Out of a Burkholderia Pseudomallei Homolog of the Eukaryotic Transcription Coactivator Pc4. Authors: Werten, S. / Kohler, C. / Bayer, N. / Steinmetz, I. / Hinrichs, W. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 5a4n.cif.gz | 70.2 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb5a4n.ent.gz | 54 KB | Display | PDB format |
PDBx/mmJSON format | 5a4n.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5a4n_validation.pdf.gz | 434.5 KB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 5a4n_full_validation.pdf.gz | 435.6 KB | Display | |
Data in XML | 5a4n_validation.xml.gz | 8 KB | Display | |
Data in CIF | 5a4n_validation.cif.gz | 10.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/a4/5a4n ftp://data.pdbj.org/pub/pdb/validation_reports/a4/5a4n | HTTPS FTP |
-Related structure data
Related structure data | 5a4oC 1pcfS C: citing same article (ref.) S: Starting model for refinement |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||||||
Unit cell |
| ||||||||||||
Components on special symmetry positions |
|
-Components
#1: Protein | Mass: 8555.798 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) BURKHOLDERIA PSEUDOMALLEI (bacteria) / Strain: K96243 / Plasmid: PET-11A / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q63VU8 #2: Chemical | ChemComp-CL / #3: Water | ChemComp-HOH / | |
---|
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 3.4 Å3/Da / Density % sol: 64 % / Description: NONE |
---|---|
Crystal grow | Temperature: 295 K / pH: 8.5 Details: 20 MM TRIS/HCL PH 8.5, 2.1 M KCL, TEMPERATURE 295 K |
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 0.91841 |
Detector | Type: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Nov 28, 2012 / Details: MIRRORS |
Radiation | Monochromator: SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.91841 Å / Relative weight: 1 |
Reflection | Resolution: 1.96→47.5 Å / Num. obs: 17393 / % possible obs: 99.6 % / Observed criterion σ(I): -3 / Redundancy: 10.4 % / Biso Wilson estimate: 39.7 Å2 / Rmerge(I) obs: 0.08 / Net I/σ(I): 21.4 |
Reflection shell | Resolution: 1.96→2.08 Å / Redundancy: 9.8 % / Rmerge(I) obs: 1.18 / Mean I/σ(I) obs: 2.1 / % possible all: 97.8 |
-Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1PCF, CHAINS A AND B WITH HELICAL REGIONS DELETED Resolution: 1.96→56.53 Å / Cor.coef. Fo:Fc: 0.954 / Cor.coef. Fo:Fc free: 0.931 / SU B: 9.029 / SU ML: 0.111 / Cross valid method: THROUGHOUT / ESU R: 0.138 / ESU R Free: 0.139 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES WITH TLS ADDED
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 43.062 Å2
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.96→56.53 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
|