[English] 日本語
Yorodumi- PDB-3gpk: Crystal Structure of PpiC-type peptidyl-prolyl cis-trans isomeras... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3gpk | ||||||
---|---|---|---|---|---|---|---|
Title | Crystal Structure of PpiC-type peptidyl-prolyl cis-trans isomerase domain at 1.55A resolution. | ||||||
Components | PpiC-type peptidyl-prolyl cis-trans isomerase | ||||||
Keywords | ISOMERASE / PEPTIDYL-PROLYL CIS-TRANS ISOMERASE / ROTAMASE / PPIase domain / NYSGXRC / 11189O3 / PSI2. / Structural Genomics / Protein Structure Initiative / New York SGX Research Center for Structural Genomics / Chaperone | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Novosphingobium aromaticivorans (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.55 Å | ||||||
Authors | Satyanarayana, L. / Eswaramoorthy, S. / Burley, S.K. / Swaminathan, S. / New York SGX Research Center for Structural Genomics (NYSGXRC) | ||||||
Citation | Journal: To be Published Title: Crystal Structure of PpiC-type peptidyl-prolyl cis-trans isomerase domain at 1.55A resolution. Authors: Satyanarayana, L. / Eswaramoorthy, S. / Burley, S.K. / Swaminathan, S. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 3gpk.cif.gz | 55.6 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb3gpk.ent.gz | 42.6 KB | Display | PDB format |
PDBx/mmJSON format | 3gpk.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/gp/3gpk ftp://data.pdbj.org/pub/pdb/validation_reports/gp/3gpk | HTTPS FTP |
---|
-Related structure data
Similar structure data | |
---|---|
Other databases |
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
2 |
| ||||||||
Unit cell |
|
-Components
#1: Protein | Mass: 12254.417 Da / Num. of mol.: 2 Fragment: PpiC-type peptidyl-prolyl cis-trans isomerase domain Source method: isolated from a genetically manipulated source Details: TOP10-INVITROGEN Source: (gene. exp.) Novosphingobium aromaticivorans (bacteria) Strain: DSM 12444 / Gene: Saro_0888 / Plasmid: pSGX3 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3) Codon+RIL / References: UniProt: Q2G9Z0, peptidylprolyl isomerase #2: Chemical | #3: Water | ChemComp-HOH / | |
---|
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 2.06 Å3/Da / Density % sol: 40.27 % |
---|---|
Crystal grow | Temperature: 294 K / Method: vapor diffusion, sitting drop / pH: 7.5 Details: pH 7.5 HEPES BUFFER AND 2M AMMONIUM SULPHATE, VAPOR DIFFUSION, SITTING DROP, temperature 294K |
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: NSLS / Beamline: X29A / Wavelength: 0.979 Å |
Detector | Type: ADSC QUANTUM Q315r / Detector: CCD / Date: Mar 11, 2009 / Details: mirrors |
Radiation | Monochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.979 Å / Relative weight: 1 |
Reflection | Resolution: 1.55→50 Å / Num. obs: 28915 / % possible obs: 96.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 6.8 % / Biso Wilson estimate: 17.4 Å2 / Rmerge(I) obs: 0.046 / Rsym value: 0.046 / Net I/σ(I): 17.3 |
Reflection shell | Resolution: 1.55→1.65 Å / Redundancy: 3.8 % / Rmerge(I) obs: 0.298 / Mean I/σ(I) obs: 17.6 / Num. unique all: 1063 / Rsym value: 0.298 / % possible all: 74.9 |
-Processing
Software |
| |||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: SAD / Resolution: 1.55→40 Å / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
| |||||||||||||||||||||||||
Displacement parameters | Biso mean: 17.4 Å2
| |||||||||||||||||||||||||
Refine analyze |
| |||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.55→40 Å
| |||||||||||||||||||||||||
Refine LS restraints |
| |||||||||||||||||||||||||
LS refinement shell | Resolution: 1.55→1.65 Å / Rfactor Rfree error: 0.034
|