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- PDB-3b09: Crystal structure of the N-domain of FKBP22 from Shewanella sp. SIB1 -
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Open data
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Basic information
Entry | Database: PDB / ID: 3b09 | ||||||
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Title | Crystal structure of the N-domain of FKBP22 from Shewanella sp. SIB1 | ||||||
![]() | Peptidyl-prolyl cis-trans isomerase | ||||||
![]() | CHAPERONE / Val-Leu zipper / helices | ||||||
Function / homology | ![]() peptidylprolyl isomerase / peptidyl-prolyl cis-trans isomerase activity / protein folding Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Budiman, C. / Angkawidjaja, C. / Motoike, H. / Koga, Y. / Takano, K. / Kanaya, S. | ||||||
![]() | ![]() Title: Crystal structure of N-domain of FKBP22 from Shewanella sp. SIB1: dimer dissociation by disruption of Val-Leu knot Authors: Budiman, C. / Angkawidjaja, C. / Motoike, H. / Koga, Y. / Takano, K. / Kanaya, S. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 21.3 KB | Display | ![]() |
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PDB format | ![]() | 16.2 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 427.9 KB | Display | ![]() |
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Full document | ![]() | 428.6 KB | Display | |
Data in XML | ![]() | 4.7 KB | Display | |
Data in CIF | ![]() | 5.9 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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1 | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 9706.961 Da / Num. of mol.: 1 / Fragment: N-terminal domain, residues 1-68 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() |
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#2: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.38 Å3/Da / Density % sol: 48.35 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, sitting drop / pH: 6.2 Details: 0.1M Na/K Phosphate, 20% PEG 1000, 0.2 M NaCl, pH 6.2, VAPOR DIFFUSION, SITTING DROP, temperature 277K |
-Data collection
Diffraction | Mean temperature: 100 K | ||||||||||||
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Diffraction source | Source: ![]() ![]() ![]() | ||||||||||||
Detector | Type: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Jul 15, 2010 / Details: mirrors | ||||||||||||
Radiation | Monochromator: mirrors / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||
Radiation wavelength |
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Reflection | Resolution: 1.9→50 Å / Num. obs: 7712 / % possible obs: 98.3 % / Observed criterion σ(F): 5 / Observed criterion σ(I): 5 / Redundancy: 5.4 % / Rmerge(I) obs: 0.114 / Rsym value: 0.119 / Net I/σ(I): 18.2 | ||||||||||||
Reflection shell | Resolution: 1.9→1.93 Å / Redundancy: 5.3 % / Rmerge(I) obs: 0.423 / Mean I/σ(I) obs: 2.6 / Num. unique all: 364 / Rsym value: 0.398 / % possible all: 100 |
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Processing
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Refinement | Method to determine structure: ![]()
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 30.92 Å2
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Refinement step | Cycle: LAST / Resolution: 1.9→34.38 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.899→1.948 Å / Total num. of bins used: 20
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