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Yorodumi- PDB-4plt: Crystal structure of ancestral apicomplexan malate dehydrogenase ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4plt | ||||||||||||
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Title | Crystal structure of ancestral apicomplexan malate dehydrogenase with oxamate. | ||||||||||||
Components | malate dehydrogenase | ||||||||||||
Keywords | OXIDOREDUCTASE / Ancestral Sequence Reconstruction / Dehydrogenase / Apicomplexa / Specificity | ||||||||||||
Function / homology | Function and homology information lactate metabolic process / L-lactate dehydrogenase activity / pyruvate metabolic process / nucleotide binding Similarity search - Function | ||||||||||||
Biological species | Apicomplexa (apicomplexans) | ||||||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.6 Å | ||||||||||||
Authors | Boucher, J.I. / Jacobowitz, J.R. / Beckett, B.C. / Classen, S. / Theobald, D.L. | ||||||||||||
Funding support | United States, 3items
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Citation | Journal: Elife / Year: 2014 Title: An atomic-resolution view of neofunctionalization in the evolution of apicomplexan lactate dehydrogenases. Authors: Boucher, J.I. / Jacobowitz, J.R. / Beckett, B.C. / Classen, S. / Theobald, D.L. | ||||||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4plt.cif.gz | 272.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4plt.ent.gz | 217.7 KB | Display | PDB format |
PDBx/mmJSON format | 4plt.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4plt_validation.pdf.gz | 1.5 MB | Display | wwPDB validaton report |
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Full document | 4plt_full_validation.pdf.gz | 1.5 MB | Display | |
Data in XML | 4plt_validation.xml.gz | 55.5 KB | Display | |
Data in CIF | 4plt_validation.cif.gz | 79 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/pl/4plt ftp://data.pdbj.org/pub/pdb/validation_reports/pl/4plt | HTTPS FTP |
-Related structure data
Related structure data | 4plcC 4plfC 4plgC 4plhC 4plvC 4plwC 4plyC 4plzC 2hjrS 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
#1: Protein | Mass: 36458.961 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Apicomplexa (apicomplexans) / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 DE3 (pLysS) / References: UniProt: A0A075B5H0*PLUS #2: Chemical | ChemComp-NAI / #3: Chemical | ChemComp-OXM / #4: Water | ChemComp-HOH / | |
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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: 2.48 Å3/Da / Density % sol: 50.38 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: 20mg/mL protein with 2mM NADH/L-oxamate; well solution: 20% (w/v) PEG-1500, 0.1M HEPES, pH7.5 |
-Data collection
Diffraction | Mean temperature: 90 K |
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Diffraction source | Source: SYNCHROTRON / Site: ALS / Beamline: 12.3.1 / Wavelength: 1.115866 Å |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Sep 12, 2012 |
Radiation | Monochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.115866 Å / Relative weight: 1 |
Reflection | Resolution: 1.6→50 Å / Num. obs: 350147 / % possible obs: 98.5 % / Redundancy: 2.5 % / Biso Wilson estimate: 26.91 Å2 / Rmerge(I) obs: 0.08 / Net I/σ(I): 6.66 |
Reflection shell | Resolution: 1.6→1.7 Å / Redundancy: 2.4 % / Rmerge(I) obs: 2.36 / Mean I/σ(I) obs: 0.41 / % possible all: 97.9 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 2HJR Resolution: 1.6→43.432 Å / FOM work R set: 0.7516 / SU ML: 0.36 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 31.47 / 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: 86.73 Å2 / Biso mean: 33.41 Å2 / Biso min: 14.08 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 1.6→43.432 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 30
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