+Open data
-Basic information
Entry | Database: PDB / ID: 1zd0 | ||||||
---|---|---|---|---|---|---|---|
Title | Crystal structure of Pfu-542154 conserved hypothetical protein | ||||||
Components | hypothetical protein PF0523 | ||||||
Keywords | STRUCTURAL GENOMICS / UNKNOWN FUNCTION / PSI / Protein Structure Initiative / Southeast Collaboratory for Structural Genomics / SECSG | ||||||
Function / homology | Function and homology information PF0523-like / CGI121/TPRKB / CGI121/TPRKB / CGI121/TPRKB superfamily / Kinase binding protein CGI-121 / 2-Layer Sandwich / Alpha Beta Similarity search - Domain/homology | ||||||
Biological species | Pyrococcus furiosus (archaea) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAS / SAD / Resolution: 1.7 Å | ||||||
Authors | Habel, J.E. / Liu, Z.J. / Horanyi, P.S. / Florence, Q.J.T. / Tempel, W. / Zhou, W. / Chen, L. / Lee, D. / Nguyen, J. / Chang, S.H. ...Habel, J.E. / Liu, Z.J. / Horanyi, P.S. / Florence, Q.J.T. / Tempel, W. / Zhou, W. / Chen, L. / Lee, D. / Nguyen, J. / Chang, S.H. / Bereton, P. / Izumi, M. / Jenny Jr., F.E. / Poole II, F.L. / Shah, C. / Sugar, F.J. / Adams, M.W.W. / Rose, J.P. / Wang, B.C. / Southeast Collaboratory for Structural Genomics (SECSG) | ||||||
Citation | Journal: To be Published Title: Crystal structure of Pfu-542154 conserved hypothetical protein Authors: Habel, J.E. / Liu, Z.J. / Horanyi, P.S. / Florence, Q.J.T. / Tempel, W. / Zhou, W. / Chen, L. / Lee, D. / Nguyen, J. / Chang, S.H. / Bereton, P. / Izumi, M. / Jenny Jr., F.E. / Poole II, F.L. ...Authors: Habel, J.E. / Liu, Z.J. / Horanyi, P.S. / Florence, Q.J.T. / Tempel, W. / Zhou, W. / Chen, L. / Lee, D. / Nguyen, J. / Chang, S.H. / Bereton, P. / Izumi, M. / Jenny Jr., F.E. / Poole II, F.L. / Shah, C. / Sugar, F.J. / Adams, M.W.W. / Rose, J.P. / Wang, B.C. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 1zd0.cif.gz | 42.9 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb1zd0.ent.gz | 31.7 KB | Display | PDB format |
PDBx/mmJSON format | 1zd0.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1zd0_validation.pdf.gz | 411.5 KB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 1zd0_full_validation.pdf.gz | 412.2 KB | Display | |
Data in XML | 1zd0_validation.xml.gz | 5.4 KB | Display | |
Data in CIF | 1zd0_validation.cif.gz | 7.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/zd/1zd0 ftp://data.pdbj.org/pub/pdb/validation_reports/zd/1zd0 | HTTPS FTP |
-Related structure data
Similar structure data | |
---|---|
Other databases |
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
| ||||||||
Components on special symmetry positions |
|
-Components
#1: Protein | Mass: 16851.504 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Pyrococcus furiosus (archaea) / Gene: PF0523 / Plasmid: pET24 DBAM / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: GenBank: 18976895, UniProt: Q8U3E5*PLUS | ||||
---|---|---|---|---|---|
#2: Chemical | ChemComp-MG / | ||||
#3: Chemical | ChemComp-UNX / #4: Chemical | #5: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 3 |
---|
-Sample preparation
Crystal |
| ||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Crystal grow |
|
-Data collection
Diffraction |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Diffraction source |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 1.7→50 Å / Num. obs: 15870 / % possible obs: 98.1 % / Redundancy: 9.5 % / Rmerge(I) obs: 0.045 / Χ2: 1.235 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell |
|
-Phasing
Phasing | Method: SAD | |||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Phasing MAD | D res high: 2.5 Å / D res low: 20 Å / FOM : 0.3 / Reflection: 5262 | |||||||||||||||||||||||||||||||||||||||||||||||||
Phasing MAD shell |
| |||||||||||||||||||||||||||||||||||||||||||||||||
Phasing dm | FOM : 0.54 / FOM acentric: 0.56 / FOM centric: 0.46 / Reflection: 5906 / Reflection acentric: 4908 / Reflection centric: 998 | |||||||||||||||||||||||||||||||||||||||||||||||||
Phasing dm shell |
|
-Processing
Software |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: SAS / Resolution: 1.7→46.27 Å / Cor.coef. Fo:Fc: 0.955 / Cor.coef. Fo:Fc free: 0.924 / SU B: 4.79 / SU ML: 0.086 / SU R Cruickshank DPI: 0.124 / Cross valid method: THROUGHOUT / ESU R Free: 0.127 / Stereochemistry target values: Engh & Huber Details: ARP/WARP and MOLPROBITY were also used in the refinement
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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: 30.738 Å2
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.7→46.27 Å
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 1.7→1.744 Å / Total num. of bins used: 20
|