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- PDB-1ocl: THE CRYSTAL STRUCTURE OF MALONAMIDASE E2 COMPLEXED WITH MALONATE ... -
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Open data
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Basic information
Entry | Database: PDB / ID: 1ocl | ||||||||||||
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Title | THE CRYSTAL STRUCTURE OF MALONAMIDASE E2 COMPLEXED WITH MALONATE FROM BRADYRHIZOBIUM JAPONICUM | ||||||||||||
![]() | MALONAMIDASE E2 | ||||||||||||
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Function / homology | ![]() | ||||||||||||
Biological species | ![]() ![]() | ||||||||||||
Method | ![]() ![]() | ||||||||||||
![]() | Shin, S. / Ha, N.-C. / Lee, T.-H. / Oh, B.-H. | ||||||||||||
![]() | ![]() 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: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 171.4 KB | Display | ![]() |
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PDB format | ![]() | 135.9 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 1o9nC ![]() 1o9oC ![]() 1o9pC ![]() 1o9qC ![]() 1obiC ![]() 1objC ![]() 1obkC ![]() 1oblC ![]() 1ochC ![]() 1ockC ![]() 1ocmC ![]() 1gr8 C: citing same article ( S: Starting model for refinement |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Components on special symmetry positions |
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Components
#1: Protein | Mass: 43591.621 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Details: CIS PEPTIDE BOND BETWEEN GLY 130 AND SER 131 / Source: (gene. exp.) ![]() ![]() ![]() ![]() ![]() #2: Chemical | ![]() #3: Water | ChemComp-HOH / | ![]() |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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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% PEG1000, 0.1M TRIS-HCL PH7.0, 15MM MALONATE, pH 7.00 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() |
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![]() |
Reflection | Resolution: 2→20 Å / Num. obs: 48851 / % possible obs: 96.4 % / Observed criterion σ(I): 1 / Redundancy: 4.5 % / Rsym value: 0.061 / Net I/σ(I): 28.4 |
Reflection shell | Resolution: 2→2.07 Å / Redundancy: 3 % / Mean I/σ(I) obs: 6.1 / Rsym value: 0.152 / % possible all: 91.3 |
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Processing
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Refinement | Method to determine structure![]() ![]() Starting model: PDB ENTRY 1GR8 ![]() 1gr8 Resolution: 2→20 Å / Cross valid method: THROUGHOUT / σ(F): 1
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Refinement step | Cycle: LAST / Resolution: 2→20 Å
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Refine LS restraints |
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Xplor file |
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