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Yorodumi- PDB-7mfq: crystal structure of the L136 aminotransferase from acanthamoeba ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 7mfq | ||||||
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Title | crystal structure of the L136 aminotransferase from acanthamoeba polyphaga mimivirus in complex with the TDP-viosamine external aldimine | ||||||
Components | L136 aminotransferase | ||||||
Keywords | TRANSFERASE / mimivirus / aminotransferase / viosamine | ||||||
Function / homology | DegT/DnrJ/EryC1/StrS aminotransferase / DegT/DnrJ/EryC1/StrS aminotransferase family / Pyridoxal phosphate-dependent transferase, major domain / Pyridoxal phosphate-dependent transferase / Chem-T4K / Uncharacterized protein L136 Function and homology information | ||||||
Biological species | Acanthamoeba polyphaga mimivirus | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.95 Å | ||||||
Authors | Seltzner, C.A. / Thoden, J.B. / Holden, H.M. | ||||||
Funding support | United States, 1items
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Citation | Journal: Protein Sci. / Year: 2021 Title: Characterization of an aminotransferase from Acanthamoeba polyphaga Mimivirus. Authors: Seltzner, C.A. / Ferek, J.D. / Thoden, J.B. / Holden, H.M. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7mfq.cif.gz | 326.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7mfq.ent.gz | 254.3 KB | Display | PDB format |
PDBx/mmJSON format | 7mfq.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/mf/7mfq ftp://data.pdbj.org/pub/pdb/validation_reports/mf/7mfq | HTTPS FTP |
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-Related structure data
Related structure data | 7mfoC 7mfpSC 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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2 |
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Unit cell |
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-Components
-Protein , 1 types, 4 molecules ABCD
#1: Protein | Mass: 40230.652 Da / Num. of mol.: 4 / Mutation: K185A Source method: isolated from a genetically manipulated source Source: (gene. exp.) Acanthamoeba polyphaga mimivirus / Gene: MIMI_L136 / Production host: Escherichia coli (E. coli) / References: UniProt: Q5UPL1 |
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-Non-polymers , 5 types, 1254 molecules
#2: Chemical | ChemComp-T4K / ( #3: Chemical | ChemComp-CL / #4: Chemical | ChemComp-EDO / #5: Chemical | #6: 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: 2.25 Å3/Da / Density % sol: 45.23 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6 Details: protein incubated with 1 mM PLP and 5 MM TDP-viosamine 18-22% PEG-3350, 2% MPD, 100 mM MES |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SEALED TUBE / Type: BRUKER D8 QUEST / Wavelength: 1.54178 Å |
Detector | Type: Bruker PHOTON II / Detector: PIXEL / Date: Oct 22, 2019 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.54178 Å / Relative weight: 1 |
Reflection | Resolution: 1.95→50 Å / Num. obs: 105900 / % possible obs: 99.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 10.7 % / Rsym value: 0.09 / Net I/σ(I): 16.2 |
Reflection shell | Resolution: 1.95→2.05 Å / Redundancy: 5.1 % / Mean I/σ(I) obs: 3.5 / Num. unique obs: 14581 / Rsym value: 0.411 / % possible all: 99.7 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 7mfp Resolution: 1.95→29.052 Å / Cor.coef. Fo:Fc: 0.948 / Cor.coef. Fo:Fc free: 0.916 / SU B: 4.335 / SU ML: 0.117 / Cross valid method: FREE R-VALUE / ESU R: 0.173 / ESU R Free: 0.156 Details: Hydrogens have been added in their riding positions
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 14.791 Å2
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Refinement step | Cycle: LAST / Resolution: 1.95→29.052 Å
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Refine LS restraints |
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LS refinement shell |
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