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Open data
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Basic information
Entry | Database: PDB / ID: 6zep | ||||||
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Title | Flavourzyme Leucine Aminopeptidase A proenzyme | ||||||
![]() | Leucine aminopeptidase A | ||||||
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Function / homology | ![]() ![]() ![]() ![]() ![]() ![]() Similarity search - Function | ||||||
Biological species | ![]() ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Watson, K.A. / Baltulionis, G. | ||||||
Funding support | ![]()
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![]() | ![]() Title: The role of propeptide-mediated autoinhibition and intermolecular chaperone in the maturation of cognate catalytic domain in leucine aminopeptidase. Authors: Baltulionis, G. / Blight, M. / Robin, A. / Charalampopoulos, D. / Watson, K.A. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 175.1 KB | Display | ![]() |
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PDB format | ![]() | 137.4 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 6zeqC ![]() 7oezC ![]() 1rtqS 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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Unit cell |
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Components
-Protein / Sugars , 2 types, 2 molecules A
#1: Protein | Mass: 41151.719 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() Gene: lapA, AO090011000052 / Production host: ![]() ![]() References: UniProt: Q2U1F3, ![]() |
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#2: Polysaccharide | alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-3)-[alpha-D- ...alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-[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 |
-Non-polymers , 4 types, 486 molecules ![](data/chem/img/ZN.gif)
![](data/chem/img/CL.gif)
![](data/chem/img/EDO.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/CL.gif)
![](data/chem/img/EDO.gif)
![](data/chem/img/HOH.gif)
#3: Chemical | #4: Chemical | ChemComp-CL / | ![]() #5: Chemical | ChemComp-EDO / | ![]() #6: Water | ChemComp-HOH / | ![]() |
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-Details
Has ligand of interest | Y |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.47 Å3/Da / Density % sol: 50.17 % |
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Crystal grow![]() | Temperature: 293 K / Method: vapor diffusion, hanging drop Details: 0.1 M Bis-Tris, pH = 5.5, 0.2 M NaCl, 25% PEG 3,350 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Dec 3, 2015 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength![]() |
Reflection | Resolution: 1.61→42.611 Å / Num. obs: 53338 / % possible obs: 99.48 % / Redundancy: 4.3 % / Rmerge(I) obs: 0.07303 / Net I/σ(I): 11.36 |
Reflection shell | Resolution: 1.61→1.668 Å / Rmerge(I) obs: 0.8915 / Mean I/σ(I) obs: 1.59 / Num. unique obs: 5269 / CC1/2: 0.55 / CC star: 0.842 / Rrim(I) all: 0.08292 |
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Processing
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Refinement | Method to determine structure![]() ![]() Starting model: 1RTQ Resolution: 1.61→42.611 Å / SU ML: 0.2 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 17.16
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.61→42.611 Å
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Refine LS restraints |
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LS refinement shell |
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Refinement TLS params. | Method: refined / Origin x: 6.4382 Å / Origin y: -2.2698 Å / Origin z: 9.909 Å
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Refinement TLS group | Selection details: all |