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Open data
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Basic information
Entry | Database: PDB / ID: 1j2a | ||||||
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Title | Structure of E. coli cyclophilin B K163T mutant | ||||||
![]() | cyclophilin B | ||||||
![]() | ISOMERASE / BETA BARREL | ||||||
Function / homology | ![]() protein peptidyl-prolyl isomerization / peptidylprolyl isomerase / peptidyl-prolyl cis-trans isomerase activity / protein folding / outer membrane-bounded periplasmic space / periplasmic space Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Konno, M. / Sano, Y. / Okudaira, K. / Kawaguchi, Y. / Yamagishi-Ohmori, Y. / Fushinobu, S. / Matsuzawa, H. | ||||||
![]() | ![]() Title: Escherichia coli cyclophilin B binds a highly distorted form of trans-prolyl peptide isomer Authors: Konno, M. / Sano, Y. / Okudaira, K. / Kawaguchi, Y. / Yamagishi-Ohmori, Y. / Fushinobu, S. / Matsuzawa, H. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 44.8 KB | Display | ![]() |
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PDB format | ![]() | 31.4 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 424.6 KB | Display | ![]() |
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Full document | ![]() | 427.7 KB | Display | |
Data in XML | ![]() | 9.2 KB | Display | |
Data in CIF | ![]() | 11.8 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 1v9tC ![]() 1vaiC ![]() 1j28 ![]() 1j29 S: Starting model for refinement C: citing same article ( |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 18070.326 Da / Num. of mol.: 1 / Mutation: K163T Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() References: UniProt: P20752, UniProt: P0AFL3*PLUS, peptidylprolyl isomerase |
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#2: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.72 Å3/Da / Density % sol: 54.36 % | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8 Details: ammonium sulfate, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 293.0K | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 20 ℃ / Method: vapor diffusion, hanging drop | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 293 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: WEISSENBERG / Detector: DIFFRACTOMETER / Date: Oct 6, 2000 |
Radiation | Monochromator: SI / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.8→80 Å / Num. obs: 19219 / % possible obs: 99 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Rmerge(I) obs: 0.069 / Net I/σ(I): 14.8 |
Reflection shell | Resolution: 1.8→1.86 Å / Rmerge(I) obs: 0.402 / % possible all: 96.5 |
Reflection | *PLUS Num. measured all: 133992 |
Reflection shell | *PLUS % possible obs: 96.5 % |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 1J28 ![]() 1j28 Resolution: 1.8→8 Å / σ(F): 2
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Refinement step | Cycle: LAST / Resolution: 1.8→8 Å
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Refinement | *PLUS Lowest resolution: 8 Å | ||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||
Refine LS restraints | *PLUS
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LS refinement shell | *PLUS Highest resolution: 1.8 Å / Lowest resolution: 1.82 Å / Rfactor Rfree: 0.311 / Rfactor Rwork: 0.287 |