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Yorodumi- PDB-4plw: Crystal structure of ancestral apicomplexan malate dehydrogenase ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4plw | ||||||||||||
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Title | Crystal structure of ancestral apicomplexan malate dehydrogenase with lactate. | ||||||||||||
Components | malate dehydrogenase | ||||||||||||
Keywords | OXIDOREDUCTASE / Ancestral Sequence Reconstruction / Dehydrogenase / Apicomplexa / Specificity | ||||||||||||
Function / homology | Function and homology information carboxylic acid metabolic process / oxidoreductase activity, acting on the CH-OH group of donors, NAD or NADP as acceptor / nucleotide binding Similarity search - Function | ||||||||||||
Biological species | Apicomplexa (apicomplexans) | ||||||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.85 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 | 4plw.cif.gz | 276.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4plw.ent.gz | 221.9 KB | Display | PDB format |
PDBx/mmJSON format | 4plw.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4plw_validation.pdf.gz | 1.5 MB | Display | wwPDB validaton report |
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Full document | 4plw_full_validation.pdf.gz | 1.5 MB | Display | |
Data in XML | 4plw_validation.xml.gz | 56.2 KB | Display | |
Data in CIF | 4plw_validation.cif.gz | 81.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/pl/4plw ftp://data.pdbj.org/pub/pdb/validation_reports/pl/4plw | HTTPS FTP |
-Related structure data
Related structure data | 4plcC 4plfC 4plgC 4plhC 4pltC 4plvC 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: 35814.312 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: A0A075B5H2*PLUS #2: Chemical | ChemComp-NAI / #3: Chemical | ChemComp-PO4 / #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: 2.43 Å3/Da / Density % sol: 49.43 % |
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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-lactate; 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: 1.85→50 Å / Num. obs: 115626 / % possible obs: 99.9 % / Redundancy: 8.1 % / Biso Wilson estimate: 32.59 Å2 / Rmerge(I) obs: 0.148 / Net I/σ(I): 12.47 |
Reflection shell | Resolution: 1.85→1.96 Å / Redundancy: 8 % / Rmerge(I) obs: 3.35 / Mean I/σ(I) obs: 0.66 / % possible all: 99.5 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 2HJR Resolution: 1.85→48.789 Å / SU ML: 0.27 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 24.66 / 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: 98.1 Å2 / Biso mean: 36.9145 Å2 / Biso min: 18.22 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 1.85→48.789 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: 23
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