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Yorodumi- PDB-5dru: Structure of His387Ala mutant of the propionaldehyde dehydrogenas... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5dru | ||||||
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Title | Structure of His387Ala mutant of the propionaldehyde dehydrogenase from the Clostridium phytofermentans fucose utilisation bacterial microcompartment | ||||||
Components | Aldehyde Dehydrogenase | ||||||
Keywords | OXIDOREDUCTASE / Acylating aldehyde dehydrogenase / bacterial microcompartment | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Clostridium phytofermentans (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.083 Å | ||||||
Authors | Tuck, L.R. / Altenbach, K. / Fu, A.T. / Crawshaw, A.D. / Campopiano, D.J. / Clarke, D.J. / Marles-Wright, J. | ||||||
Citation | Journal: Sci Rep / Year: 2016 Title: Insight into Coenzyme A cofactor binding and the mechanism of acyl-transfer in an acylating aldehyde dehydrogenase from Clostridium phytofermentans. Authors: Tuck, L.R. / Altenbach, K. / Ang, T.F. / Crawshaw, A.D. / Campopiano, D.J. / Clarke, D.J. / Marles-Wright, J. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5dru.cif.gz | 252.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5dru.ent.gz | 206.8 KB | Display | PDB format |
PDBx/mmJSON format | 5dru.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5dru_validation.pdf.gz | 438.3 KB | Display | wwPDB validaton report |
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Full document | 5dru_full_validation.pdf.gz | 440.8 KB | Display | |
Data in XML | 5dru_validation.xml.gz | 18 KB | Display | |
Data in CIF | 5dru_validation.cif.gz | 25.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/dr/5dru ftp://data.pdbj.org/pub/pdb/validation_reports/dr/5dru | HTTPS FTP |
-Related structure data
Related structure data | 4c3sSC 5dbvC S: Starting model for refinement C: citing same article (ref.) |
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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: 47629.781 Da / Num. of mol.: 1 / Fragment: UNP residues 20-462 / Mutation: H387A Source method: isolated from a genetically manipulated source Source: (gene. exp.) Clostridium phytofermentans (bacteria) / Gene: Cphy_1178 / Plasmid: pET28a / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A9KN57 |
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#2: Chemical | ChemComp-SO4 / |
#3: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 2.13 Å3/Da / Density % sol: 42.42 % / Description: bipyramidal |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 4.7 Details: PROTEIN IN 50 MM TRIS.HCL, PH 8.0, 150 MM NACL. 1:2 HANGING DROPS OVER: 0.1 M SODIUM ACETATE, PH 4.7, 1.7 - 1.8 M AMMONIUM SULPHATE PH range: 4.5 - 5 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.97 Å |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Apr 20, 2015 |
Radiation | Monochromator: Double crystal monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97 Å / Relative weight: 1 |
Reflection | Resolution: 2.083→40.53 Å / Num. all: 24570 / Num. obs: 24570 / % possible obs: 98.85 % / Redundancy: 10 % / Rmerge(I) obs: 0.081 / Rsym value: 0.085 / Net I/σ(I): 18.94 |
Reflection shell | Resolution: 2.083→2.158 Å / Redundancy: 9.7 % / Rmerge(I) obs: 1.227 / Mean I/σ(I) obs: 1.63 / % possible all: 99.25 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4c3s Resolution: 2.083→40.53 Å / SU ML: 0.27 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 28.26 / 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 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.083→40.53 Å
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Refine LS restraints |
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LS refinement shell |
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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