[English] 日本語
Yorodumi- PDB-3ad9: Heterotetrameric Sarcosine Oxidase from Corynebacterium sp. U-96 ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3ad9 | ||||||
---|---|---|---|---|---|---|---|
Title | Heterotetrameric Sarcosine Oxidase from Corynebacterium sp. U-96 sarcosine-reduced form | ||||||
Components | (SARCOSINE OXIDASE ...) x 4 | ||||||
Keywords | OXIDOREDUCTASE / Sarcosine Oxidase | ||||||
Function / homology | Function and homology information sarcosine oxidase (5,10-methylenetetrahydrofolate-forming) / sarcosine catabolic process / sarcosine oxidase activity / tetrahydrofolate metabolic process / mitochondrial respiratory chain complex I assembly / nucleotide binding / metal ion binding / cytoplasm / cytosol Similarity search - Function | ||||||
Biological species | Corynebacterium sp. U-96 (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å | ||||||
Authors | Suzuki, H. / Moriguchi, T. / Ida, K. | ||||||
Citation | Journal: J.Biochem. / Year: 2010 Title: Channeling and conformational changes in the heterotetrameric sarcosine oxidase from Corynebacterium sp. U-96. Authors: Moriguchi, T. / Ida, K. / Hikima, T. / Ueno, G. / Yamamoto, M. / Suzuki, H. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 3ad9.cif.gz | 352.9 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb3ad9.ent.gz | 277.4 KB | Display | PDB format |
PDBx/mmJSON format | 3ad9.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3ad9_validation.pdf.gz | 1.3 MB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 3ad9_full_validation.pdf.gz | 1.3 MB | Display | |
Data in XML | 3ad9_validation.xml.gz | 69.3 KB | Display | |
Data in CIF | 3ad9_validation.cif.gz | 99.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ad/3ad9 ftp://data.pdbj.org/pub/pdb/validation_reports/ad/3ad9 | HTTPS FTP |
-Related structure data
Related structure data | 3ad7C 3ad8C 3adaC 1x31S S: Starting model for refinement C: citing same article (ref.) |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| |||||||||
---|---|---|---|---|---|---|---|---|---|---|
1 |
| |||||||||
Unit cell |
| |||||||||
Components on special symmetry positions |
|
-Components
-SARCOSINE OXIDASE ... , 4 types, 4 molecules ABCD
#1: Protein | Mass: 102850.258 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Corynebacterium sp. U-96 (bacteria) / Gene: soxA / Plasmid: PET31B / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q50LF0 |
---|---|
#2: Protein | Mass: 44048.691 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Corynebacterium sp. U-96 (bacteria) / Gene: soxB / Plasmid: PET31B / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) References: UniProt: Q50LF2, sarcosine oxidase (formaldehyde-forming) |
#3: Protein | Mass: 21427.186 Da / Num. of mol.: 1 / Fragment: UNP residues 11-205 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Corynebacterium sp. U-96 (bacteria) / Gene: soxG / Plasmid: PET31B / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q50LE9 |
#4: Protein | Mass: 11445.771 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Corynebacterium sp. U-96 (bacteria) / Gene: soxD / Plasmid: PET31B / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q50LF1 |
-Non-polymers , 6 types, 918 molecules
#5: Chemical | ChemComp-NAD / | ||||||||
---|---|---|---|---|---|---|---|---|---|
#6: Chemical | ChemComp-SO4 / #7: Chemical | ChemComp-FAD / | #8: Chemical | ChemComp-FMN / | #9: Chemical | ChemComp-ZN / | #10: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 3.13 Å3/Da / Density % sol: 60.72 % |
---|---|
Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8.5 Details: 0.1M TRIS-HCL, 1.9M AMMONIUM SULFATE, 10MM CUSO4, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: SPring-8 / Beamline: BL44B2 / Wavelength: 1 Å |
Detector | Type: ADSC QUANTUM 210 / Detector: CCD / Date: Dec 14, 2005 |
Radiation | Monochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.3→65.51 Å / Num. obs: 101117 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 6.1 % / Biso Wilson estimate: 31.6 Å2 / Rmerge(I) obs: 0.079 / Rsym value: 0.079 / Net I/σ(I): 16.3 |
Reflection shell | Resolution: 2.3→2.42 Å / Redundancy: 6 % / Rmerge(I) obs: 0.309 / % possible all: 100 |
-Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1X31 Resolution: 2.3→61.25 Å / Cor.coef. Fo:Fc: 0.95 / Cor.coef. Fo:Fc free: 0.929 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.226 / ESU R Free: 0.186 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 27.836 Å2
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.3→61.25 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 2.3→2.36 Å / Total num. of bins used: 20
|