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Yorodumi- PDB-1t90: Crystal structure of methylmalonate semialdehyde dehydrogenase fr... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1t90 | ||||||
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Title | Crystal structure of methylmalonate semialdehyde dehydrogenase from Bacillus subtilis | ||||||
Components | Probable methylmalonate-semialdehyde dehydrogenase | ||||||
Keywords | OXIDOREDUCTASE / NAD | ||||||
Function / homology | Function and homology information valine metabolic process / malonate-semialdehyde dehydrogenase (acetylating) activity / methylmalonate-semialdehyde dehydrogenase (CoA-acylating) / methylmalonate-semialdehyde dehydrogenase (acylating, NAD) activity / inositol catabolic process / thymine catabolic process / valine catabolic process / Oxidoreductases; Acting on the aldehyde or oxo group of donors; With NAD+ or NADP+ as acceptor Similarity search - Function | ||||||
Biological species | Bacillus subtilis (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å | ||||||
Authors | Dubourg, H. / Didierjean, C. / Stines-Chaumeil, C. / Talfournier, F. / Branlant, G. / Aubry, A. / Corbier, C. | ||||||
Citation | Journal: To be published Title: Crystal structure analysis of Methylmalonate-Semialdehyde Dehydrogenase from Bacillus subtilis. Authors: Dubourg, H. / Didierjean, C. / Stines-Chaumeil, C. / Talfournier, F. / Branlant, G. / Aubry, A. / Corbier, C. #1: Journal: To be published Title: Expression, purification, crystallization and preliminary X-ray diffraction data of Methylmalonate-Semialdehyde Dehydrogenase from Bacillus subtilis Authors: Dubourg, G. / Stines-Chaumeil, C. / Didierjean, C. / Talfournier, F. / Branlant, G. / Aubry, A. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1t90.cif.gz | 391.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1t90.ent.gz | 319.6 KB | Display | PDB format |
PDBx/mmJSON format | 1t90.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1t90_validation.pdf.gz | 1.6 MB | Display | wwPDB validaton report |
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Full document | 1t90_full_validation.pdf.gz | 1.6 MB | Display | |
Data in XML | 1t90_validation.xml.gz | 83.4 KB | Display | |
Data in CIF | 1t90_validation.cif.gz | 113.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/t9/1t90 ftp://data.pdbj.org/pub/pdb/validation_reports/t9/1t90 | HTTPS FTP |
-Related structure data
Similar structure data |
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-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 53379.727 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Bacillus subtilis (bacteria) / Gene: MMSA, IOLA, E83A, BSU39760 / Plasmid: pSKmsdbsub / Production host: Escherichia coli (E. coli) / Strain (production host): DH5a References: UniProt: P42412, methylmalonate-semialdehyde dehydrogenase (CoA-acylating) #2: Chemical | ChemComp-NAD / #3: 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: 3.6 Å3/Da / Density % sol: 65 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.8 Details: Ammonium sulfate, pH 7.8, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: X11 / Wavelength: 0.8126 Å |
Detector | Type: MARRESEARCH / Detector: CCD / Date: Dec 3, 2002 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.8126 Å / Relative weight: 1 |
Reflection | Resolution: 2.5→20 Å / Num. all: 108345 / Num. obs: 108345 / % possible obs: 99.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Rmerge(I) obs: 0.138 |
Reflection shell | Resolution: 2.5→2.59 Å / % possible all: 91.9 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.5→20 Å / σ(F): 0 / Stereochemistry target values: Engh & Huber
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Refinement step | Cycle: LAST / Resolution: 2.5→20 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.5→2.59 Å / Rfactor Rfree error: 0.016
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