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Yorodumi- PDB-4cnj: L-Aminoacetone oxidase from Streptococcus oligofermentans belongs... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4cnj | ||||||
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Title | L-Aminoacetone oxidase from Streptococcus oligofermentans belongs to a new 3-domain family of bacterial flavoproteins | ||||||
Components | L-AMINO ACID OXIDASE | ||||||
Keywords | OXIDOREDUCTASE / FLAVOPROTEINS | ||||||
Function / homology | Function and homology information | ||||||
Biological species | STREPTOCOCCUS OLIGOFERMENTANS (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.7 Å | ||||||
Authors | Molla, G. / Nardini, M. / Motta, P. / D'Arrigo, P. / Bolognesi, M. / Pollegioni, L. | ||||||
Citation | Journal: Biochem.J. / Year: 2014 Title: Aminoacetone Oxidase from Streptococcus Oligofermentas Belongs to a New Three-Domain Family of Bacterial Flavoproteins. Authors: Molla, G. / Nardini, M. / Motta, P. / D'Arrigo, P. / Panzeri, W. / Pollegioni, L. | ||||||
History |
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Remark 700 | SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "AE" IN EACH CHAIN ON SHEET RECORDS BELOW ... SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "AE" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 6-STRANDED BARREL THIS IS REPRESENTED BY A 7-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL. THE SHEETS PRESENTED AS "BE" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 6-STRANDED BARREL THIS IS REPRESENTED BY A 7-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL. THE SHEETS PRESENTED AS "CF" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 6-STRANDED BARREL THIS IS REPRESENTED BY A 7-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL. THE SHEETS PRESENTED AS "DF" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 6-STRANDED BARREL THIS IS REPRESENTED BY A 7-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL. |
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4cnj.cif.gz | 307.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4cnj.ent.gz | 250.6 KB | Display | PDB format |
PDBx/mmJSON format | 4cnj.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/cn/4cnj ftp://data.pdbj.org/pub/pdb/validation_reports/cn/4cnj | HTTPS FTP |
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-Related structure data
Related structure data | 4cnkC 2gqfS 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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Unit cell |
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-Components
#1: Protein | Mass: 42734.812 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) STREPTOCOCCUS OLIGOFERMENTANS (bacteria) Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): PLYSS / References: UniProt: B1PUC6, EC: 1.1.3.2 #2: Chemical | ChemComp-FAD / |
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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: 3.36 Å3/Da / Density % sol: 63.44 % / Description: NONE |
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Crystal grow | pH: 6.5 Details: 2.0 M (NH4)2SO4, 0.1 M NA-CACODYLATE OR MES (PH 6.5), AND 0.2 M NACL |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 1 |
Detector | Type: ADSC CCD / Detector: CCD |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.7→64.68 Å / Num. obs: 68683 / % possible obs: 98.7 % / Observed criterion σ(I): 2 / Redundancy: 3.7 % / Rmerge(I) obs: 0.1 / Net I/σ(I): 10.6 |
Reflection shell | Resolution: 2.7→2.85 Å / Redundancy: 3.7 % / Rmerge(I) obs: 0.53 / Mean I/σ(I) obs: 2.4 / % possible all: 99.8 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 2GQF Resolution: 2.7→49.14 Å / Cor.coef. Fo:Fc: 0.955 / Cor.coef. Fo:Fc free: 0.928 / SU B: 11.878 / SU ML: 0.235 / Cross valid method: THROUGHOUT / ESU R: 0.553 / ESU R Free: 0.297 / 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: 59.081 Å2
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Refinement step | Cycle: LAST / Resolution: 2.7→49.14 Å
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Refine LS restraints |
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