+Open data
-Basic information
Entry | Database: PDB / ID: 6zeq | ||||||
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Title | Aspergillus oryzae Leucine Aminopeptidase A mature enzyme | ||||||
Components | Leucine aminopeptidase A | ||||||
Keywords | HYDROLASE / M28 peptidase / prodomain / intramolecular chaperone / bimetallic aminopeptidase | ||||||
Function / homology | Function and homology information Hydrolases; Acting on peptide bonds (peptidases); Aminopeptidases / metalloexopeptidase activity / aminopeptidase activity / proteolysis / extracellular region / metal ion binding Similarity search - Function | ||||||
Biological species | Aspergillus oryzae (mold) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.97 Å | ||||||
Authors | Watson, K.A. / Baltulionis, G. | ||||||
Funding support | United Kingdom, 1items
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Citation | Journal: J.Struct.Biol. / Year: 2021 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: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6zeq.cif.gz | 90.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6zeq.ent.gz | 65.6 KB | Display | PDB format |
PDBx/mmJSON format | 6zeq.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ze/6zeq ftp://data.pdbj.org/pub/pdb/validation_reports/ze/6zeq | HTTPS FTP |
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-Related structure data
Related structure data | 6zepC 7oezC 1rtqS C: citing same article (ref.) S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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Components on special symmetry positions |
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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.) Aspergillus oryzae (strain ATCC 42149 / RIB 40) (mold) Strain: ATCC 42149 / RIB 40 / Gene: lapA, AO090011000052 / Production host: Komagataella pastoris (fungus) / Variant (production host): X33 References: UniProt: Q2U1F3, Hydrolases; Acting on peptide bonds (peptidases); Aminopeptidases |
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#2: Polysaccharide | 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 , 5 types, 476 molecules
#3: Chemical | #4: Chemical | ChemComp-CL / | #5: Chemical | ChemComp-SO4 / #6: Chemical | ChemComp-EDO / #7: Water | ChemComp-HOH / | |
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-Details
Has ligand of interest | Y |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 3.68 Å3/Da / Density % sol: 66.6 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / Details: 0.1M Citrate, pH = 5.0, 3.2 M Ammonium sulphate |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I02 / Wavelength: 0.97949 Å |
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: 0.97949 Å / Relative weight: 1 |
Reflection | Resolution: 1.97→73.81 Å / Num. obs: 43994 / % possible obs: 100 % / Redundancy: 13.1 % / Rmerge(I) obs: 0.2203 / Net I/σ(I): 10.35 |
Reflection shell | Resolution: 1.97→2.041 Å / Rmerge(I) obs: 2.178 / Mean I/σ(I) obs: 1.18 / Num. unique obs: 4297 / CC1/2: 0.653 / CC star: 0.889 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1RTQ Resolution: 1.97→73.81 Å / SU ML: 0.27 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 22.77 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 104.36 Å2 / Biso mean: 37.8875 Å2 / Biso min: 19.83 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 1.97→73.81 Å
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 15
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