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- PDB-8b57: Structure of prolyl endoprotease from Aspergillus niger CBS 109712 -
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Open data
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Basic information
Entry | Database: PDB / ID: 8b57 | ||||||
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Title | Structure of prolyl endoprotease from Aspergillus niger CBS 109712 | ||||||
![]() | Prolyl Endoprotease from Aspergillus niger CBS 109712 | ||||||
![]() | HYDROLASE / Endoprotease / proline-specific / S28 peptidase | ||||||
Function / homology | DI(HYDROXYETHYL)ETHER![]() | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Pijning, T. / Vujicic-Zagar, A. / Van der Laan, J.M. / De Jong, R.M. / Dijkstra, B.W. | ||||||
Funding support | 1items
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![]() | ![]() Title: Structural and time-resolved mechanistic investigations of protein hydrolysis by the acidic proline-specific endoprotease from Aspergillus niger. Authors: Pijning, T. / Vujicic-Zagar, A. / van der Laan, J.M. / de Jong, R.M. / Ramirez-Palacios, C. / Vente, A. / Edens, L. / Dijkstra, B.W. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 216.6 KB | Display | ![]() |
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PDB format | ![]() | 173.1 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1.8 MB | Display | ![]() |
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Full document | ![]() | 1.8 MB | Display | |
Data in XML | ![]() | 20.7 KB | Display | |
Data in CIF | ![]() | 29.2 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 8bbxC C: citing same article ( |
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Similar structure data | Similarity search - Function & homology ![]() |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Components
-Protein , 1 types, 1 molecules A
#1: Protein | Mass: 54254.133 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Details: Patent WO2015177152A1 / Source: (gene. exp.) ![]() ![]() ![]() ![]() |
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-Sugars , 4 types, 7 molecules ![](data/chem/img/NAG.gif)
#2: Polysaccharide | #3: Polysaccharide | alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-[alpha-D- ...alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose | Source method: isolated from a genetically manipulated source #4: Polysaccharide | beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta- ...beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose | #5: Sugar | |
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-Non-polymers , 5 types, 109 molecules ![](data/chem/img/GOL.gif)
![](data/chem/img/PEG.gif)
![](data/chem/img/PG4.gif)
![](data/chem/img/1PE.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/PEG.gif)
![](data/chem/img/PG4.gif)
![](data/chem/img/1PE.gif)
![](data/chem/img/HOH.gif)
#6: Chemical | #7: Chemical | ChemComp-PEG / | #8: Chemical | ChemComp-PG4 / | #9: Chemical | ChemComp-1PE / | #10: Water | ChemComp-HOH / | |
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-Details
Has ligand of interest | N |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 3.27 Å3/Da / Density % sol: 62.35 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5 Details: 26-29% (w/v) PEG 3350, 0.1 M sodium citrate pH 5.0, 0.1 M ammonium tartrate pH 7.2, 20 mM HAc/NaAc pH 5.0, 50 mM NaCl |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Feb 1, 2009 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9195 Å / Relative weight: 1 |
Reflection | Resolution: 2.42→66.24 Å / Num. obs: 27027 / % possible obs: 100 % / Redundancy: 9.2 % / Rmerge(I) obs: 0.108 / Net I/σ(I): 14.5 |
Reflection shell | Resolution: 2.42→2.55 Å / Redundancy: 9.1 % / Rmerge(I) obs: 0.636 / Mean I/σ(I) obs: 3.7 / Num. unique obs: 3897 / % possible all: 99.9 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: composite model Resolution: 2.42→66.24 Å / Cor.coef. Fo:Fc: 0.957 / Cor.coef. Fo:Fc free: 0.933 / SU B: 13.7 / SU ML: 0.159 / Cross valid method: THROUGHOUT / ESU R: 0.292 / ESU R Free: 0.209 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: U VALUES : WITH TLS ADDED HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : RESIDUAL ONLY
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.1 Å / Solvent model: MASK | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 42.924 Å2
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Refinement step | Cycle: LAST / Resolution: 2.42→66.24 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.42→2.483 Å / Total num. of bins used: 20
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Refinement TLS params. | Method: refined / Origin x: 28.257 Å / Origin y: 60.631 Å / Origin z: -6.031 Å
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