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- PDB-2bkl: Structural and Mechanistic Analysis of Two Prolyl Endopeptidases:... -
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Open data
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Basic information
Entry | Database: PDB / ID: 2bkl | ||||||
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Title | Structural and Mechanistic Analysis of Two Prolyl Endopeptidases: Role of Inter-Domain Dynamics in Catalysis and Specificity | ||||||
![]() | PROLYL ENDOPEPTIDASE | ||||||
![]() | HYDROLASE / PROLYL ENDOPEPTIDASE / MECHANISTIC STUDY / CELIAC SPRUE / PROTEASE | ||||||
Function / homology | ![]() | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Khosla, C. / Shan, L. / Mathews, I.I. | ||||||
![]() | ![]() Title: Structural and Mechanistic Analysis of Two Prolyl Endopeptidases: Role of Interdomain Dynamics in Catalysis and Specificity Authors: Shan, L. / Mathews, I.I. / Khosla, C. #1: Journal: Biochem.J. / Year: 2004 Title: Comparative Biochemical Analysis of Three Bacterial Prolyl Endopeptidases: Implications for Celiac Sprue Authors: Shan, L. / Marti, T. / Sollid, L.M. / Gray, G.M. / Khosla, C. #2: Journal: Science / Year: 2002 Title: Structural Basis for Gluten Intolerance in Celiac Sprue Authors: Shan, L. / Molberg, O. / Parrot, I. / Hausch, F. / Filiz, F. / Gray, G.M. / Sollid, L.M. / Khosla, C. #3: Journal: Cell.Mol.Life.Sci. / Year: 2002 Title: The Prolyl Oligopeptidase Family Authors: Polgar, L. | ||||||
History |
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Remark 700 | SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN ... SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN THE SHEET RECORDS BELOW, TWO SHEETS ARE DEFINED. |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 304.5 KB | Display | ![]() |
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PDB format | ![]() | 244.8 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1.4 MB | Display | ![]() |
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Full document | ![]() | 1.4 MB | Display | |
Data in XML | ![]() | 59.7 KB | Display | |
Data in CIF | ![]() | 91.3 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 1yr2C ![]() 1qfsS 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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1 | ![]()
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2 | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 77777.359 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Details: Z-ALA PROLINAL / Source: (gene. exp.) ![]() ![]() ![]() #2: Chemical | #3: Chemical | #4: Chemical | ChemComp-SO4 / | #5: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.3 Å3/Da / Density % sol: 45 % |
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Crystal grow | pH: 6 / Details: 26% METHOXY PEG 5K AND 0.1MES (PH 6.01). |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC CCD / Detector: CCD / Date: Dec 19, 2003 |
Radiation | Monochromator: DOUBLE CRYSTAL, SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.5→50 Å / Num. obs: 225366 / % possible obs: 98.9 % / Observed criterion σ(I): 0 / Redundancy: 4.1 % / Biso Wilson estimate: 15.3 Å2 / Rmerge(I) obs: 0.07 / Net I/σ(I): 12.8 |
Reflection shell | Resolution: 1.5→1.55 Å / Redundancy: 4 % / Rmerge(I) obs: 0.47 / Mean I/σ(I) obs: 2.8 / % possible all: 97.7 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 1QFS Resolution: 1.5→30 Å / Cor.coef. Fo:Fc: 0.966 / Cor.coef. Fo:Fc free: 0.958 / SU B: 1.062 / SU ML: 0.04 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.066 / ESU R Free: 0.067 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. SOME OF THE RESIDUES ARE MODELED WITH ALTERNATE CONFORMATIONS.
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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: BABINET MODEL WITH MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 10.34 Å2
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Refinement step | Cycle: LAST / Resolution: 1.5→30 Å
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Refine LS restraints |
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