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Yorodumi- PDB-4x9m: Oxidized L-alpha-Glycerophosphate Oxidase from Mycoplasma pneumon... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4x9m | ||||||
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Title | Oxidized L-alpha-Glycerophosphate Oxidase from Mycoplasma pneumoniae with FAD bound | ||||||
Components | L-alpha-glycerophosphate oxidase | ||||||
Keywords | OXIDOREDUCTASE / flavoenzyme / oxidase / glycerol-3-phosphate oxidase / glycerol-3-phosphate dehydrogenase | ||||||
Function / homology | Function and homology information glycerol-3-phosphate oxidase / glycerol catabolic process / oxidoreductase activity / plasma membrane / cytoplasm Similarity search - Function | ||||||
Biological species | Mycoplasma pneumoniae (Filterable agent of primary atypical pneumonia) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 Å | ||||||
Authors | Elkhal, C.K. / Kean, K.M. / Parsonage, D. / Claiborne, A. / Karplus, P.A. | ||||||
Citation | Journal: Febs J. / Year: 2015 Title: Structure and proposed mechanism of l-alpha-glycerophosphate oxidase from Mycoplasma pneumoniae. Authors: Elkhal, C.K. / Kean, K.M. / Parsonage, D. / Maenpuen, S. / Chaiyen, P. / Claiborne, A. / Karplus, P.A. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4x9m.cif.gz | 101 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4x9m.ent.gz | 73.5 KB | Display | PDB format |
PDBx/mmJSON format | 4x9m.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4x9m_validation.pdf.gz | 537.1 KB | Display | wwPDB validaton report |
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Full document | 4x9m_full_validation.pdf.gz | 539.6 KB | Display | |
Data in XML | 4x9m_validation.xml.gz | 18.2 KB | Display | |
Data in CIF | 4x9m_validation.cif.gz | 26.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/x9/4x9m ftp://data.pdbj.org/pub/pdb/validation_reports/x9/4x9m | HTTPS FTP |
-Related structure data
Related structure data | 4x9nC 3dmeS 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 on special symmetry positions |
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-Components
#1: Protein | Mass: 46332.305 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mycoplasma pneumoniae (strain ATCC 29342 / M129) (bacteria) Strain: ATCC 29342 / M129 / Gene: MPN_051, D09_orf384, MP103 / Plasmid: pET28a / Production host: Escherichia coli (E. coli) / Strain (production host): B834 / Variant (production host): DE3 / References: UniProt: P75063 |
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#2: Chemical | ChemComp-FAD / |
#3: Chemical | ChemComp-NI / |
#4: Chemical | ChemComp-G3P / |
#5: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 2.71 Å3/Da / Density % sol: 54.56 % |
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Crystal grow | Temperature: 277.15 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: 2.68 M NaCl, 2% v/v isopropanol, 0.1 M HEPES pH 7.5 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ALS / Beamline: 5.0.3 / Wavelength: 0.9765 Å |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Sep 23, 2010 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9765 Å / Relative weight: 1 |
Reflection | Resolution: 2.4→50 Å / Num. obs: 18401 / % possible obs: 100 % / Redundancy: 23.4 % / Net I/σ(I): 22.7 |
Reflection shell | Resolution: 2.4→2.53 Å / Redundancy: 23.6 % / Mean I/σ(I) obs: 4.4 / % possible all: 99 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3DME Resolution: 2.4→49.9 Å / Cor.coef. Fo:Fc: 0.97 / Cor.coef. Fo:Fc free: 0.949 / SU B: 12.32 / SU ML: 0.15 / Cross valid method: THROUGHOUT / ESU R: 0.318 / ESU R Free: 0.217 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 37.397 Å2
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Refinement step | Cycle: LAST / Resolution: 2.4→49.9 Å
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Refine LS restraints |
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