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Yorodumi- PDB-6ypa: The C146A variant of an amidase from Pyrococcus horikoshii with b... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6ypa | ||||||
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Title | The C146A variant of an amidase from Pyrococcus horikoshii with bound glutaramide | ||||||
Components | CN hydrolase domain-containing protein | ||||||
Keywords | HYDROLASE / amidase of the nitrilase superfamily | ||||||
Function / homology | Function and homology information beta-alanine biosynthetic process via 3-ureidopropionate / N-carbamoylputrescine amidase activity / beta-ureidopropionase activity / putrescine biosynthetic process from arginine Similarity search - Function | ||||||
Biological species | Pyrococcus horikoshii (archaea) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.58 Å | ||||||
Authors | Sewell, B.T. / Su, S. / Venter, P. / Makumire, S. | ||||||
Funding support | United Kingdom, 1items
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Citation | Journal: To Be Published Title: The structure of the C146A variant of the amidase from Pyrococcus horikoshii bound to glutaramide suggests the basis of amide recognition. Authors: Sewell, B.T. / Su, S. / Venter, P. / Makumire, S. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6ypa.cif.gz | 232.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6ypa.ent.gz | 184.8 KB | Display | PDB format |
PDBx/mmJSON format | 6ypa.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6ypa_validation.pdf.gz | 1.3 MB | Display | wwPDB validaton report |
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Full document | 6ypa_full_validation.pdf.gz | 1.4 MB | Display | |
Data in XML | 6ypa_validation.xml.gz | 42.9 KB | Display | |
Data in CIF | 6ypa_validation.cif.gz | 61.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/yp/6ypa ftp://data.pdbj.org/pub/pdb/validation_reports/yp/6ypa | HTTPS FTP |
-Related structure data
Related structure data | 1j31S S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 31983.697 Da / Num. of mol.: 4 / Mutation: C146A Source method: isolated from a genetically manipulated source Source: (gene. exp.) Pyrococcus horikoshii (archaea) / Gene: PH0642 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: O58376 #2: Chemical | ChemComp-P6W / #3: Chemical | ChemComp-GOL / | #4: Water | ChemComp-HOH / | 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: 2.05 Å3/Da / Density % sol: 39.96 % |
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Crystal grow | Temperature: 300 K / Method: vapor diffusion, hanging drop Details: 2.5-4.0 mg/ml protein, 0.1 M Imidazole, MES monohydrate (acid) buffer at pH 6.5, 20% v/v Glycerol, 10% w/v PEG 4000, 0.2M Glutaramide |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N | ||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I04-1 / Wavelength: 1 Å | ||||||||||||||||||||||||
Detector | Type: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Feb 14, 2010 | ||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 | ||||||||||||||||||||||||
Reflection | Resolution: 1.58→100.64 Å / Num. obs: 144086 / % possible obs: 100 % / Redundancy: 8.8 % / Biso Wilson estimate: 18.89 Å2 / Rpim(I) all: 0.042 / Rrim(I) all: 0.125 / Net I/σ(I): 8.8 / Num. measured all: 1264338 | ||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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-Phasing
Phasing | Method: molecular replacement | |||||||||
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Phasing MR |
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1j31 Resolution: 1.58→80.492 Å / SU ML: 0.21 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 33.41 Details: Alternating cycles of Phenix refine and manual adjustment with coot. One cycle oof PDB-REDO
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 97 Å2 / Biso mean: 31.1176 Å2 / Biso min: 15.31 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 1.58→80.492 Å
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0
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