+Open data
-Basic information
Entry | Database: PDB / ID: 2p17 | ||||||
---|---|---|---|---|---|---|---|
Title | Crystal structure of GK1651 from Geobacillus kaustophilus | ||||||
Components | Pirin-like protein | ||||||
Keywords | STRUCTURAL GENOMICS / UNKNOWN FUNCTION / GK1651 / Geobacillus Kaustophilus / SOUTHEAST COLLABORATORY FOR STRUCTURAL GENOMICS / Protein Structure Initiative / SECSG / RIKEN Structural Genomics/Proteomics Initiative / RSGI / PSI | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Geobacillus kaustophilus (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.52 Å | ||||||
Authors | Zhu, J. / Swindell II, J.T. / Chen, L. / Ebihara, A. / Shinkai, A. / Kuramitsu, S. / Yokoyama, S. / Fu, Z.-Q. / Rose, J.P. / Wang, B.C. ...Zhu, J. / Swindell II, J.T. / Chen, L. / Ebihara, A. / Shinkai, A. / Kuramitsu, S. / Yokoyama, S. / Fu, Z.-Q. / Rose, J.P. / Wang, B.C. / Southeast Collaboratory for Structural Genomics (SECSG) / RIKEN Structural Genomics/Proteomics Initiative (RSGI) | ||||||
Citation | Journal: To be Published Title: Crystal structure of GK1651 from Geobacillus kaustophilus Authors: Zhu, J. / Swindell II, J.T. / Chen, L. / Ebihara, A. / Shinkai, A. / Kuramitsu, S. / Yokoyama, S. / Fu, Z.-Q. / Rose, J.P. / Wang, B.C. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 2p17.cif.gz | 64 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb2p17.ent.gz | 50.5 KB | Display | PDB format |
PDBx/mmJSON format | 2p17.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2p17_validation.pdf.gz | 422.5 KB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 2p17_full_validation.pdf.gz | 423.8 KB | Display | |
Data in XML | 2p17_validation.xml.gz | 13.3 KB | Display | |
Data in CIF | 2p17_validation.cif.gz | 19.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/p1/2p17 ftp://data.pdbj.org/pub/pdb/validation_reports/p1/2p17 | HTTPS FTP |
-Related structure data
Related structure data | |
---|---|
Similar structure data | |
Other databases |
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
|
-Components
#1: Protein | Mass: 31459.168 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Geobacillus kaustophilus (bacteria) / Strain: HTA426 / Gene: GK1651 / Plasmid: pET-15b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21-CodonPlus(DE3)-RIL-X / References: UniProt: Q5KZF0 |
---|---|
#2: Chemical | ChemComp-FE / |
#3: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 1.79 Å3/Da / Density % sol: 31.4 % |
---|---|
Crystal grow | Temperature: 291 K / Method: microbatch / pH: 4.6 Details: MICROBATCH USING 1.0 MICROLITER DROPS CONTAINING EQUAL VOLUMES OF PROTEIN CONCENTRATE (5.09 mg/ml) AND SOLUTION CONTAING 30% w/v PEG 4000, 0.1 M SODIUM ACETATE, 0.2 M AMMONIUM ACETATE PH 4.6, TEMPERATURE 291K |
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 0.9724 Å |
Detector | Type: MARRESEARCH / Detector: CCD / Date: Jan 31, 2007 / Details: ROSENBAUM |
Radiation | Monochromator: SI CHANNEL 220 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9724 Å / Relative weight: 1 |
Reflection | Resolution: 1.52→50 Å / Num. all: 35234 / Num. obs: 35234 / % possible obs: 100 % / Observed criterion σ(I): 0 / Redundancy: 14.1 % / Rsym value: 0.061 |
Reflection shell | Resolution: 1.52→1.57 Å / Redundancy: 13.1 % / Mean I/σ(I) obs: 22.5 / Num. unique all: 3479 / Rsym value: 0.17 / % possible all: 100 |
-Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: SAD / Resolution: 1.52→19.18 Å / Cor.coef. Fo:Fc: 0.954 / Cor.coef. Fo:Fc free: 0.943 / SU B: 1.19 / SU ML: 0.046 / Cross valid method: THROUGHOUT / ESU R: 0.086 / ESU R Free: 0.084 Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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: 14.19 Å2
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.52→19.18 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 1.52→1.558 Å / Total num. of bins used: 20
|