+Open data
-Basic information
Entry | Database: PDB / ID: 4uul | |||||||||
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Title | Apo trichomonas vaginalis lactate dehydrogenase L91R | |||||||||
Components | L-LACTATE DEHYDROGENASELactate dehydrogenase | |||||||||
Keywords | OXIDOREDUCTASE | |||||||||
Function / homology | Function and homology information L-malate dehydrogenase activity / malate metabolic process / L-lactate dehydrogenase / L-lactate dehydrogenase activity / oxaloacetate metabolic process / NADH metabolic process / tricarboxylic acid cycle / nucleotide binding Similarity search - Function | |||||||||
Biological species | TRICHOMONAS VAGINALIS (eukaryote) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.28 Å | |||||||||
Authors | Steindel, P.A. / Chen, E.H. / L Theobald, D. | |||||||||
Citation | Journal: Protein Sci. / Year: 2016 Title: Gradual Neofunctionalization in the Convergent Evolution of Trichomonad Lactate and Malate Dehydrogenases. Authors: Steindel, P.A. / Chen, E.H. / Wirth, J.D. / 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 | 4uul.cif.gz | 411.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4uul.ent.gz | 345.7 KB | Display | PDB format |
PDBx/mmJSON format | 4uul.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/uu/4uul ftp://data.pdbj.org/pub/pdb/validation_reports/uu/4uul | HTTPS FTP |
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-Related structure data
Related structure data | 4uumC 4uunC 4uuoC 4uupC 5a1tC 5mdhS 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: 37998.348 Da / Num. of mol.: 2 / Mutation: YES Source method: isolated from a genetically manipulated source Source: (gene. exp.) TRICHOMONAS VAGINALIS (eukaryote) / Plasmid: PET-21B / Production host: ESCHERICHIA COLI (E. coli) / References: UniProt: O96445, L-lactate dehydrogenase #2: 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: 2.49 Å3/Da / Density % sol: 51 % / Description: NONE |
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Crystal grow | pH: 7 Details: 21 MG/ML PROTEIN, 100 MM HEPES PH 7.0, 10% PEG-6000, 5% MPD |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: NSLS / Beamline: X29A / Wavelength: 1.08 |
Detector | Type: ADSC CCD / Detector: CCD / Date: Aug 17, 2011 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.08 Å / Relative weight: 1 |
Reflection | Resolution: 1.3→44.7 Å / Num. obs: 175089 / % possible obs: 90.3 % / Observed criterion σ(I): 2.61 / Redundancy: 13.1 % / Biso Wilson estimate: 15.9 Å2 / Rmerge(I) obs: 0.05 / Net I/σ(I): 28.2 |
Reflection shell | Resolution: 1.28→1.31 Å / Rmerge(I) obs: 0.82 / Mean I/σ(I) obs: 2.61 / % possible all: 47.5 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: HOMOLOGY MODEL BASED ON PDB ENTRY 5MDH Resolution: 1.28→30.712 Å / SU ML: 0.1 / σ(F): 1.99 / Phase error: 16.37 / 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 mean: 25.4 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.28→30.712 Å
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Refine LS restraints |
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LS refinement shell |
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