[English] 日本語
Yorodumi- PDB-4uup: Reconstructed ancestral trichomonad malate dehydrogenase in compl... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4uup | |||||||||
---|---|---|---|---|---|---|---|---|---|---|
Title | Reconstructed ancestral trichomonad malate dehydrogenase in complex with NADH, SO4, and PO4 | |||||||||
Components | MALATE DEHYDROGENASE | |||||||||
Keywords | OXIDOREDUCTASE | |||||||||
Function / homology | L-2-Hydroxyisocaproate Dehydrogenase; Chain A, domain 2 / Lactate dehydrogenase/glycoside hydrolase, family 4, C-terminal / NAD(P)-binding Rossmann-like Domain / Alpha-Beta Complex / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta / 1,4-DIHYDRONICOTINAMIDE ADENINE DINUCLEOTIDE / PHOSPHATE ION Function and homology information | |||||||||
Biological species | SYNTHETIC CONSTRUCT (others) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.543 Å | |||||||||
Authors | Steindel, P.A. / Chen, E.H. / Theobald, D.L. | |||||||||
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 |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 4uup.cif.gz | 396.1 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb4uup.ent.gz | 333.3 KB | Display | PDB format |
PDBx/mmJSON format | 4uup.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/uu/4uup ftp://data.pdbj.org/pub/pdb/validation_reports/uu/4uup | HTTPS FTP |
---|
-Related structure data
Related structure data | 4uulC 4uumC 4uunC 4uuoC 5a1tC 5mdhS C: citing same article (ref.) S: Starting model for refinement |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
|
-Components
#1: Protein | Mass: 36941.242 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) SYNTHETIC CONSTRUCT (others) / Plasmid: PET-21B / Production host: ESCHERICHIA COLI (E. coli) / References: malate dehydrogenase #2: Chemical | #3: Chemical | ChemComp-PO4 / | #4: Chemical | ChemComp-SO4 / | #5: Water | ChemComp-HOH / | Sequence details | DESIGNED SEQUENCE | |
---|
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 2.2 Å3/Da / Density % sol: 44.1 % / Description: NONE |
---|---|
Crystal grow | pH: 8 Details: 5 MG/ML PROTEIN, 100 MM TRIS, PH 8.0, 25% PEG 4000, AND 0.2M LI2SO4 |
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: ALS / Beamline: 12.3.1 / Wavelength: 1.12 |
Detector | Type: ADSC CCD / Detector: CCD / Date: Dec 12, 2012 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.12 Å / Relative weight: 1 |
Reflection | Resolution: 1.54→46.5 Å / Num. obs: 91959 / % possible obs: 93.6 % / Observed criterion σ(I): 0.65 / Redundancy: 8.3 % / Biso Wilson estimate: 22.3 Å2 / Rmerge(I) obs: 0.083 / Net I/σ(I): 14.59 |
Reflection shell | Resolution: 1.54→1.58 Å / Rmerge(I) obs: 1.331 / Mean I/σ(I) obs: 0.65 / Rsym value: 1.11 / % possible all: 58.6 |
-Processing
Software |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: HOMOLOGY MODEL BASED ON PDB ENTRY 5MDH Resolution: 1.543→46.539 Å / SU ML: 0.2 / σ(F): 1.33 / Phase error: 27.02 / Stereochemistry target values: ML
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 34.1 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.543→46.539 Å
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell |
|