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Yorodumi- PDB-1o9p: Crystal structure of the S131A mutant of Malonamidase E2 complexe... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1o9p | ||||||
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Title | Crystal structure of the S131A mutant of Malonamidase E2 complexed with malonate from Bradyrhizobium japonicum | ||||||
Components | MALONAMIDASE E2 | ||||||
Keywords | HYDROLASE / AMIDASE / MALONATE / MALONAMIDASE | ||||||
Function / homology | Function and homology information | ||||||
Biological species | BRADYRHIZOBIUM JAPONICUM (bacteria) | ||||||
Method | X-RAY DIFFRACTION / DIRECT METHODS / Resolution: 1.8 Å | ||||||
Authors | Shin, S. / Oh, B.-H. | ||||||
Citation | Journal: J.Biol.Chem. / Year: 2003 Title: Characterization of a Novel Ser-Cisser-Lys Catalytic Triad in Comparison with the Classical Ser-His-Asp Triad Authors: Shin, S. / Yun, Y.S. / Koo, H.M. / Kim, Y.S. / Choi, K.Y. / Oh, B.-H. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1o9p.cif.gz | 171.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1o9p.ent.gz | 135.9 KB | Display | PDB format |
PDBx/mmJSON format | 1o9p.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/o9/1o9p ftp://data.pdbj.org/pub/pdb/validation_reports/o9/1o9p | HTTPS FTP |
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-Related structure data
Related structure data | 1o9nC 1o9oC 1o9qC 1obiC 1objC 1obkC 1oblC 1ochC 1ockC 1oclC 1ocmC 1gr9 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
#1: Protein | Mass: 43719.750 Da / Num. of mol.: 2 / Mutation: YES Source method: isolated from a genetically manipulated source Details: MALONATE / Source: (gene. exp.) BRADYRHIZOBIUM JAPONICUM (bacteria) / Plasmid: PUC18 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q9ZIV5 #2: Chemical | #3: Water | ChemComp-HOH / | Compound details | CIS PEPTIDE BOND BETWEEN GLYCINE 130 AND ALANINE 131 ENGINEERED | |
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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: 2 Å3/Da / Density % sol: 39.9 % | ||||||||||||||||||||||||
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Crystal grow | pH: 7 Details: 20% POLYETHYLENE GLYCOL 1000, 100 MM TRIS, PH 7.0, 15 MM MALONATE | ||||||||||||||||||||||||
Crystal grow | *PLUS pH: 7 / Method: vapor diffusion | ||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU RU300 / Wavelength: 1.5418 |
Detector | Type: RIGAKU IMAGE PLATE / Detector: IMAGE PLATE / Details: MIRRORS |
Radiation | Monochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 1.78→20 Å / Num. obs: 71433 / % possible obs: 94.3 % / Observed criterion σ(I): 1 / Redundancy: 4 % / Rsym value: 0.053 / Net I/σ(I): 22.23 |
Reflection shell | Resolution: 1.78→1.84 Å / Redundancy: 2.8 % / Mean I/σ(I) obs: 4 / Rsym value: 0.198 / % possible all: 84.7 |
Reflection | *PLUS Highest resolution: 1.8 Å / Lowest resolution: 20 Å / Num. measured all: 514152 / Rmerge(I) obs: 0.053 |
Reflection shell | *PLUS % possible obs: 84.7 % / Rmerge(I) obs: 0.198 |
-Processing
Software |
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Refinement | Method to determine structure: DIRECT METHODS Starting model: PDB ENTRY 1GR9 1gr9 Resolution: 1.8→20 Å / Cross valid method: THROUGHOUT / σ(F): 1
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Refinement step | Cycle: LAST / Resolution: 1.8→20 Å
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Refine LS restraints |
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Xplor file |
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Refinement | *PLUS % reflection Rfree: 5 % | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS |