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Yorodumi- PDB-1obk: crystal structure of the R158Q mutant of Malonamidase E2 from Bra... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1obk | ||||||
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Title | crystal structure of the R158Q mutant of Malonamidase E2 from Bradyrhizobium japonicum | ||||||
Components | MALONAMIDASE E2 | ||||||
Keywords | AMIDASE | ||||||
Function / homology | Function and homology information | ||||||
Biological species | BRADYRHIZOBIUM JAPONICUM (bacteria) | ||||||
Method | X-RAY DIFFRACTION / DIRECT METHODS / Resolution: 2.2 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 | 1obk.cif.gz | 179.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1obk.ent.gz | 142.5 KB | Display | PDB format |
PDBx/mmJSON format | 1obk.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1obk_validation.pdf.gz | 374.3 KB | Display | wwPDB validaton report |
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Full document | 1obk_full_validation.pdf.gz | 390 KB | Display | |
Data in XML | 1obk_validation.xml.gz | 18.5 KB | Display | |
Data in CIF | 1obk_validation.cif.gz | 32.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ob/1obk ftp://data.pdbj.org/pub/pdb/validation_reports/ob/1obk | HTTPS FTP |
-Related structure data
Related structure data | 1o9nC 1o9oC 1o9pC 1o9qC 1obiC 1objC 1oblC 1ochC 1ockC 1oclC 1ocmC 1gr8 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: 43706.688 Da / Num. of mol.: 2 / Mutation: YES Source method: isolated from a genetically manipulated source Details: CIS PEPTIDE BOND BETWEEN GLYCINE 130 AND SERINE 131 Source: (gene. exp.) BRADYRHIZOBIUM JAPONICUM (bacteria) / Plasmid: PUC18 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q9ZIV5 #2: Water | ChemComp-HOH / | Compound details | 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, 0.1 M TRIS-HCL, PH 7.0 |
-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: 2.2→20 Å / Num. obs: 38625 / % possible obs: 93.2 % / Observed criterion σ(I): 1 / Redundancy: 5 % / Rsym value: 0.082 / Net I/σ(I): 11.24 |
Reflection shell | Resolution: 2.2→2.28 Å / Redundancy: 3 % / Mean I/σ(I) obs: 3 / Rsym value: 0.26 / % possible all: 85.5 |
-Processing
Software |
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Refinement | Method to determine structure: DIRECT METHODS Starting model: PDB ENTRY 1GR8 1gr8 Resolution: 2.2→20 Å / Cross valid method: THROUGHOUT / σ(F): 1 Details: CIS PEPTIDE BOND BETWEEN GLYCINE 130 AND SERINE 131
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Refinement step | Cycle: LAST / Resolution: 2.2→20 Å
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Refine LS restraints |
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Xplor file |
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